Changeset 274f9ef in flex_extract.git


Ignore:
Timestamp:
Oct 22, 2018, 11:44:47 AM (13 months ago)
Author:
Anne Philipp <anne.philipp@…>
Branches:
dev
Children:
db27c09
Parents:
708c667
Message:

Converted docstrings to numpy style and build first structure for sphinxdocumentation (incl API)

Files:
75 added
1 deleted
48 edited

Legend:

Unmodified
Added
Removed
  • documentation/Sphinx/build/html/_modules/index.html

    r708c667 r274f9ef  
    150150           
    151151  <h1>All modules for which code is available</h1>
    152 <ul><li><a href="disaggregation.html">disaggregation</a></li>
     152<ul><li><a href="ControlFile.html">ControlFile</a></li>
     153<li><a href="EcFlexpart.html">EcFlexpart</a></li>
     154<li><a href="GribTools.html">GribTools</a></li>
     155<li><a href="MarsRetrieval.html">MarsRetrieval</a></li>
     156<li><a href="UioFiles.html">UioFiles</a></li>
     157<li><a href="disaggregation.html">disaggregation</a></li>
     158<li><a href="get_mars_data.html">get_mars_data</a></li>
     159<li><a href="install.html">install</a></li>
     160<li><a href="prepare_flexpart.html">prepare_flexpart</a></li>
     161<li><a href="submit.html">submit</a></li>
    153162<li><a href="tools.html">tools</a></li>
    154163</ul>
  • documentation/Sphinx/build/html/_modules/tools.html

    r708c667 r274f9ef  
    213213<span class="c1"># ------------------------------------------------------------------------------</span>
    214214
    215 <div class="viewcode-block" id="none_or_str"><a class="viewcode-back" href="../code.html#tools.none_or_str">[docs]</a><span class="k">def</span> <span class="nf">none_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
    216     <span class="sd">&#39;&#39;&#39;</span>
    217 <span class="sd">    @Description:</span>
    218 <span class="sd">        Converts the input string into pythons None-type if the string</span>
    219 <span class="sd">        contains &quot;None&quot;.</span>
    220 
    221 <span class="sd">    @Input:</span>
    222 <span class="sd">        value: string</span>
    223 <span class="sd">            String to be checked for the &quot;None&quot; word.</span>
    224 
    225 <span class="sd">    @Return:</span>
    226 <span class="sd">        None or value:</span>
    227 <span class="sd">            Return depends on the content of the input value. If it was &quot;None&quot;,</span>
    228 <span class="sd">            then the python type None is returned. Otherwise the string itself.</span>
     215<div class="viewcode-block" id="none_or_str"><a class="viewcode-back" href="../api.html#tools.none_or_str">[docs]</a><span class="k">def</span> <span class="nf">none_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
     216    <span class="sd">&#39;&#39;&#39;Converts the input string into pythons None-type if the string</span>
     217<span class="sd">    contains string &quot;None&quot;.</span>
     218
     219<span class="sd">    Parameters</span>
     220<span class="sd">    ----------</span>
     221<span class="sd">    value : :obj:`string`</span>
     222<span class="sd">        String to be checked for the &quot;None&quot; word.</span>
     223
     224<span class="sd">    Return</span>
     225<span class="sd">    ------</span>
     226<span class="sd">    None or value:</span>
     227<span class="sd">        Return depends on the content of the input value. If it was &quot;None&quot;,</span>
     228<span class="sd">        then the python type None is returned. Otherwise the string itself.</span>
    229229<span class="sd">    &#39;&#39;&#39;</span>
    230230    <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;None&#39;</span><span class="p">:</span>
     
    232232    <span class="k">return</span> <span class="n">value</span></div>
    233233
    234 <div class="viewcode-block" id="none_or_int"><a class="viewcode-back" href="../code.html#tools.none_or_int">[docs]</a><span class="k">def</span> <span class="nf">none_or_int</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
    235     <span class="sd">&#39;&#39;&#39;</span>
    236 <span class="sd">    @Description:</span>
    237 <span class="sd">        Converts the input string into pythons None-type if the string</span>
    238 <span class="sd">        contains &quot;None&quot;. Otherwise it is converted to an integer value.</span>
    239 
    240 <span class="sd">    @Input:</span>
    241 <span class="sd">        value: string</span>
    242 <span class="sd">            String to be checked for the &quot;None&quot; word.</span>
    243 
    244 <span class="sd">    @Return:</span>
    245 <span class="sd">        None or int(value):</span>
    246 <span class="sd">            Return depends on the content of the input value. If it was &quot;None&quot;,</span>
    247 <span class="sd">            then the python type None is returned. Otherwise the string is</span>
    248 <span class="sd">            converted into an integer value.</span>
     234<div class="viewcode-block" id="none_or_int"><a class="viewcode-back" href="../api.html#tools.none_or_int">[docs]</a><span class="k">def</span> <span class="nf">none_or_int</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
     235    <span class="sd">&#39;&#39;&#39;Converts the input string into pythons None-type if the string</span>
     236<span class="sd">    contains string &quot;None&quot;. Otherwise it is converted to an integer value.</span>
     237
     238<span class="sd">    Parameters</span>
     239<span class="sd">    ----------</span>
     240<span class="sd">    value : :obj:`string`</span>
     241<span class="sd">        String to be checked for the &quot;None&quot; word.</span>
     242
     243<span class="sd">    Return</span>
     244<span class="sd">    ------</span>
     245<span class="sd">    None or int(value):</span>
     246<span class="sd">        Return depends on the content of the input value. If it was &quot;None&quot;,</span>
     247<span class="sd">        then the python type None is returned. Otherwise the string is</span>
     248<span class="sd">        converted into an integer value.</span>
    249249<span class="sd">    &#39;&#39;&#39;</span>
    250250    <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;None&#39;</span><span class="p">:</span>
     
    252252    <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">value</span><span class="p">)</span></div>
    253253
    254 <div class="viewcode-block" id="get_cmdline_arguments"><a class="viewcode-back" href="../code.html#tools.get_cmdline_arguments">[docs]</a><span class="k">def</span> <span class="nf">get_cmdline_arguments</span><span class="p">():</span>
    255     <span class="sd">&#39;&#39;&#39;</span>
    256 <span class="sd">    @Description:</span>
    257 <span class="sd">        Decomposes the command line arguments and assigns them to variables.</span>
    258 <span class="sd">        Apply default values for non mentioned arguments.</span>
    259 
    260 <span class="sd">    @Input:</span>
    261 <span class="sd">        &lt;nothing&gt;</span>
    262 
    263 <span class="sd">    @Return:</span>
    264 <span class="sd">        args: instance of ArgumentParser</span>
    265 <span class="sd">            Contains the commandline arguments from script/program call.</span>
     254<div class="viewcode-block" id="get_cmdline_arguments"><a class="viewcode-back" href="../api.html#tools.get_cmdline_arguments">[docs]</a><span class="k">def</span> <span class="nf">get_cmdline_arguments</span><span class="p">():</span>
     255    <span class="sd">&#39;&#39;&#39;Decomposes the command line arguments and assigns them to variables.</span>
     256<span class="sd">    Apply default values for non mentioned arguments.</span>
     257
     258<span class="sd">    Parameters</span>
     259<span class="sd">    ----------</span>
     260
     261<span class="sd">    Return</span>
     262<span class="sd">    ------</span>
     263<span class="sd">    args : :obj:`Namespace`</span>
     264<span class="sd">        Contains the commandline arguments from script/program call.</span>
    266265<span class="sd">    &#39;&#39;&#39;</span>
    267266
     
    342341    <span class="k">return</span> <span class="n">args</span></div>
    343342
    344 <div class="viewcode-block" id="read_ecenv"><a class="viewcode-back" href="../code.html#tools.read_ecenv">[docs]</a><span class="k">def</span> <span class="nf">read_ecenv</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
    345     <span class="sd">&#39;&#39;&#39;</span>
    346 <span class="sd">    @Description:</span>
    347 <span class="sd">        Reads the file into a dictionary where the key values are the parameter</span>
    348 <span class="sd">        names.</span>
    349 
    350 <span class="sd">    @Input:</span>
    351 <span class="sd">        filename: string</span>
    352 <span class="sd">            Path to file where the ECMWV environment parameters are stored.</span>
    353 
    354 <span class="sd">    @Return:</span>
    355 <span class="sd">        envs: dict</span>
    356 <span class="sd">            Contains the environment parameter ecuid, ecgid, gateway</span>
    357 <span class="sd">            and destination for ECMWF server environments.</span>
     343<div class="viewcode-block" id="read_ecenv"><a class="viewcode-back" href="../api.html#tools.read_ecenv">[docs]</a><span class="k">def</span> <span class="nf">read_ecenv</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
     344    <span class="sd">&#39;&#39;&#39;Reads the file into a dictionary where the key values are the parameter</span>
     345<span class="sd">    names.</span>
     346
     347<span class="sd">    Parameters</span>
     348<span class="sd">    ----------</span>
     349<span class="sd">    filename : :obj:`string`</span>
     350<span class="sd">        Path to file where the ECMWF environment parameters are stored.</span>
     351
     352<span class="sd">    Return</span>
     353<span class="sd">    ------</span>
     354<span class="sd">    envs : :obj:`dictionary`</span>
     355<span class="sd">        Contains the environment parameter ecuid, ecgid, gateway</span>
     356<span class="sd">        and destination for ECMWF server environments.</span>
    358357<span class="sd">    &#39;&#39;&#39;</span>
    359358    <span class="n">envs</span><span class="o">=</span> <span class="p">{}</span>
     
    366365    <span class="k">return</span> <span class="n">envs</span></div>
    367366
    368 <div class="viewcode-block" id="clean_up"><a class="viewcode-back" href="../code.html#tools.clean_up">[docs]</a><span class="k">def</span> <span class="nf">clean_up</span><span class="p">(</span><span class="n">c</span><span class="p">):</span>
    369     <span class="sd">&#39;&#39;&#39;</span>
    370 <span class="sd">    @Description:</span>
    371 <span class="sd">        Remove all files from intermediate directory</span>
    372 <span class="sd">        (inputdir from CONTROL file).</span>
    373 
    374 <span class="sd">    @Input:</span>
    375 <span class="sd">        c: instance of class ControlFile</span>
    376 <span class="sd">            Contains all the parameters of CONTROL file and</span>
    377 <span class="sd">            command line.</span>
    378 <span class="sd">            For more information about format and content of the parameter</span>
    379 <span class="sd">            see documentation.</span>
    380 
    381 <span class="sd">    @Return:</span>
    382 <span class="sd">        &lt;nothing&gt;</span>
     367<div class="viewcode-block" id="clean_up"><a class="viewcode-back" href="../api.html#tools.clean_up">[docs]</a><span class="k">def</span> <span class="nf">clean_up</span><span class="p">(</span><span class="n">c</span><span class="p">):</span>
     368    <span class="sd">&#39;&#39;&#39;Remove all files from intermediate directory (inputdir).</span>
     369
     370<span class="sd">    Parameters</span>
     371<span class="sd">    ----------</span>
     372<span class="sd">    c : :obj:`ControlFile`</span>
     373<span class="sd">        Contains all the parameters of CONTROL file and</span>
     374<span class="sd">        command line.</span>
     375
     376<span class="sd">    Return</span>
     377<span class="sd">    ------</span>
     378
    383379<span class="sd">    &#39;&#39;&#39;</span>
    384380
     
    397393
    398394
    399 <div class="viewcode-block" id="my_error"><a class="viewcode-back" href="../code.html#tools.my_error">[docs]</a><span class="k">def</span> <span class="nf">my_error</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;ERROR&#39;</span><span class="p">):</span>
    400     <span class="sd">&#39;&#39;&#39;</span>
    401 <span class="sd">    @Description:</span>
    402 <span class="sd">        Prints a specified error message which can be passed to the function</span>
    403 <span class="sd">        before exiting the program.</span>
    404 
    405 <span class="sd">    @Input:</span>
    406 <span class="sd">        user: list of strings</span>
    407 <span class="sd">            Contains all email addresses which should be notified.</span>
    408 <span class="sd">            It might also contain just the ecmwf user name which wil trigger</span>
    409 <span class="sd">            mailing to the associated email address for this user.</span>
    410 
    411 <span class="sd">        message: string, optional</span>
    412 <span class="sd">            Error message. Default value is &quot;ERROR&quot;.</span>
    413 
    414 <span class="sd">    @Return:</span>
    415 <span class="sd">        &lt;nothing&gt;</span>
     395<div class="viewcode-block" id="my_error"><a class="viewcode-back" href="../api.html#tools.my_error">[docs]</a><span class="k">def</span> <span class="nf">my_error</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;ERROR&#39;</span><span class="p">):</span>
     396    <span class="sd">&#39;&#39;&#39;Prints a specified error message which can be passed to the function</span>
     397<span class="sd">    before exiting the program.</span>
     398
     399<span class="sd">    Parameters</span>
     400<span class="sd">    ----------</span>
     401<span class="sd">    user : :obj:`list` of :obj:`string`</span>
     402<span class="sd">        Contains all email addresses which should be notified.</span>
     403<span class="sd">        It might also contain just the ecmwf user name which wil trigger</span>
     404<span class="sd">        mailing to the associated email address for this user.</span>
     405
     406<span class="sd">    message : :obj:`string`, optional</span>
     407<span class="sd">        Error message. Default value is &quot;ERROR&quot;.</span>
     408
     409<span class="sd">    Return</span>
     410<span class="sd">    ------</span>
     411
    416412<span class="sd">    &#39;&#39;&#39;</span>
    417413
     
    443439
    444440
    445 <div class="viewcode-block" id="normal_exit"><a class="viewcode-back" href="../code.html#tools.normal_exit">[docs]</a><span class="k">def</span> <span class="nf">normal_exit</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;Done!&#39;</span><span class="p">):</span>
    446     <span class="sd">&#39;&#39;&#39;</span>
    447 <span class="sd">    @Description:</span>
    448 <span class="sd">        Prints a specific exit message which can be passed to the function.</span>
    449 
    450 <span class="sd">    @Input:</span>
    451 <span class="sd">        user: list of strings</span>
    452 <span class="sd">            Contains all email addresses which should be notified.</span>
    453 <span class="sd">            It might also contain just the ecmwf user name which wil trigger</span>
    454 <span class="sd">            mailing to the associated email address for this user.</span>
    455 
    456 <span class="sd">        message: string, optional</span>
    457 <span class="sd">            Message for exiting program. Default value is &quot;Done!&quot;.</span>
    458 
    459 <span class="sd">    @Return:</span>
    460 <span class="sd">        &lt;nothing&gt;</span>
     441<div class="viewcode-block" id="normal_exit"><a class="viewcode-back" href="../api.html#tools.normal_exit">[docs]</a><span class="k">def</span> <span class="nf">normal_exit</span><span class="p">(</span><span class="n">users</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="s1">&#39;Done!&#39;</span><span class="p">):</span>
     442    <span class="sd">&#39;&#39;&#39;Prints a specific exit message which can be passed to the function.</span>
     443
     444<span class="sd">    Parameters</span>
     445<span class="sd">    ----------</span>
     446<span class="sd">    user : :obj:`list` of :obj:`string`</span>
     447<span class="sd">        Contains all email addresses which should be notified.</span>
     448<span class="sd">        It might also contain just the ecmwf user name which wil trigger</span>
     449<span class="sd">        mailing to the associated email address for this user.</span>
     450
     451<span class="sd">    message : :obj:`string`, optional</span>
     452<span class="sd">        Message for exiting program. Default value is &quot;Done!&quot;.</span>
     453
     454<span class="sd">    Return</span>
     455<span class="sd">    ------</span>
    461456
    462457<span class="sd">    &#39;&#39;&#39;</span>
     
    485480
    486481
    487 <div class="viewcode-block" id="product"><a class="viewcode-back" href="../code.html#tools.product">[docs]</a><span class="k">def</span> <span class="nf">product</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
    488     <span class="sd">&#39;&#39;&#39;</span>
    489 <span class="sd">    @Description:</span>
    490 <span class="sd">        This method is taken from an example at the ECMWF wiki website.</span>
    491 <span class="sd">        https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16</span>
    492 
    493 <span class="sd">        This method combines the single characters of the passed arguments</span>
    494 <span class="sd">        with each other. So that each character of each argument value</span>
    495 <span class="sd">        will be combined with each character of the other arguments as a tuple.</span>
    496 
    497 <span class="sd">        Example:</span>
    498 <span class="sd">        product(&#39;ABCD&#39;, &#39;xy&#39;) --&gt; Ax Ay Bx By Cx Cy Dx Dy</span>
    499 <span class="sd">        product(range(2), repeat = 3) --&gt; 000 001 010 011 100 101 110 111</span>
    500 
    501 <span class="sd">    @Input:</span>
    502 <span class="sd">        *args: tuple</span>
    503 <span class="sd">            Positional arguments (arbitrary number).</span>
    504 
    505 <span class="sd">        **kwds: dictionary</span>
    506 <span class="sd">            Contains all the keyword arguments from *args.</span>
    507 
    508 <span class="sd">    @Return:</span>
    509 <span class="sd">        prod: tuple</span>
    510 <span class="sd">            Return will be done with &quot;yield&quot;. A tuple of combined arguments.</span>
    511 <span class="sd">            See example in description above.</span>
     482<div class="viewcode-block" id="product"><a class="viewcode-back" href="../api.html#tools.product">[docs]</a><span class="k">def</span> <span class="nf">product</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
     483    <span class="sd">&#39;&#39;&#39;This method combines the single characters of the passed arguments</span>
     484<span class="sd">    with each other. So that each character of each argument value</span>
     485<span class="sd">    will be combined with each character of the other arguments as a tuple.</span>
     486
     487<span class="sd">    Note</span>
     488<span class="sd">    ----</span>
     489<span class="sd">    This method is taken from an example at the ECMWF wiki website.</span>
     490<span class="sd">    https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16</span>
     491
     492<span class="sd">    Example</span>
     493<span class="sd">    -------</span>
     494<span class="sd">    product(&#39;ABCD&#39;, &#39;xy&#39;) --&gt; Ax Ay Bx By Cx Cy Dx Dy</span>
     495
     496<span class="sd">    product(range(2), repeat = 3) --&gt; 000 001 010 011 100 101 110 111</span>
     497
     498<span class="sd">    Parameters</span>
     499<span class="sd">    ----------</span>
     500<span class="sd">    \*args : :obj:`tuple`</span>
     501<span class="sd">        Positional arguments (arbitrary number).</span>
     502
     503<span class="sd">    \*\*kwds : :obj:`dictionary`</span>
     504<span class="sd">        Contains all the keyword arguments from \*args.</span>
     505
     506<span class="sd">    Return</span>
     507<span class="sd">    ------</span>
     508<span class="sd">    prod : :obj:`tuple`</span>
     509<span class="sd">        Return will be done with &quot;yield&quot;. A tuple of combined arguments.</span>
     510<span class="sd">        See example in description above.</span>
    512511<span class="sd">    &#39;&#39;&#39;</span>
    513512    <span class="n">pools</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">tuple</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">*</span> <span class="n">kwds</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;repeat&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
     
    521520
    522521
    523 <div class="viewcode-block" id="silent_remove"><a class="viewcode-back" href="../code.html#tools.silent_remove">[docs]</a><span class="k">def</span> <span class="nf">silent_remove</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
    524     <span class="sd">&#39;&#39;&#39;</span>
    525 <span class="sd">    @Description:</span>
    526 <span class="sd">        Remove file if it exists.</span>
    527 <span class="sd">        The function does not fail if the file does not exist.</span>
    528 
    529 <span class="sd">    @Input:</span>
    530 <span class="sd">        filename: string</span>
    531 <span class="sd">            The name of the file to be removed without notification.</span>
    532 
    533 <span class="sd">    @Return:</span>
    534 <span class="sd">        &lt;nothing&gt;</span>
     522<div class="viewcode-block" id="silent_remove"><a class="viewcode-back" href="../api.html#tools.silent_remove">[docs]</a><span class="k">def</span> <span class="nf">silent_remove</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
     523    <span class="sd">&#39;&#39;&#39;Remove file if it exists.</span>
     524<span class="sd">    The function does not fail if the file does not exist.</span>
     525
     526<span class="sd">    Parameters</span>
     527<span class="sd">    ----------</span>
     528<span class="sd">    filename : :obj:`string`</span>
     529<span class="sd">        The name of the file to be removed without notification.</span>
     530
     531<span class="sd">    Return</span>
     532<span class="sd">    ------</span>
     533
    535534<span class="sd">    &#39;&#39;&#39;</span>
    536535    <span class="k">try</span><span class="p">:</span>
     
    544543
    545544
    546 <div class="viewcode-block" id="init128"><a class="viewcode-back" href="../code.html#tools.init128">[docs]</a><span class="k">def</span> <span class="nf">init128</span><span class="p">(</span><span class="n">filepath</span><span class="p">):</span>
    547     <span class="sd">&#39;&#39;&#39;</span>
    548 <span class="sd">    @Description:</span>
    549 <span class="sd">        Opens and reads the grib file with table 128 information.</span>
    550 
    551 <span class="sd">    @Input:</span>
    552 <span class="sd">        filepath: string</span>
    553 <span class="sd">            Path to file of ECMWF grib table number 128.</span>
    554 
    555 <span class="sd">    @Return:</span>
    556 <span class="sd">        table128: dictionary</span>
    557 <span class="sd">            Contains the ECMWF grib table 128 information.</span>
    558 <span class="sd">            The key is the parameter number and the value is the</span>
    559 <span class="sd">            short name of the parameter.</span>
     545<div class="viewcode-block" id="init128"><a class="viewcode-back" href="../api.html#tools.init128">[docs]</a><span class="k">def</span> <span class="nf">init128</span><span class="p">(</span><span class="n">filepath</span><span class="p">):</span>
     546    <span class="sd">&#39;&#39;&#39;Opens and reads the grib file with table 128 information.</span>
     547
     548<span class="sd">    Parameters</span>
     549<span class="sd">    ----------</span>
     550<span class="sd">    filepath : :obj:`string`</span>
     551<span class="sd">        Path to file of ECMWF grib table number 128.</span>
     552
     553<span class="sd">    Return</span>
     554<span class="sd">    ------</span>
     555<span class="sd">    table128 : :obj:`dictionary`</span>
     556<span class="sd">        Contains the ECMWF grib table 128 information.</span>
     557<span class="sd">        The key is the parameter number and the value is the</span>
     558<span class="sd">        short name of the parameter.</span>
    560559<span class="sd">    &#39;&#39;&#39;</span>
    561560    <span class="n">table128</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
     
    569568
    570569
    571 <div class="viewcode-block" id="to_param_id"><a class="viewcode-back" href="../code.html#tools.to_param_id">[docs]</a><span class="k">def</span> <span class="nf">to_param_id</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span> <span class="n">table</span><span class="p">):</span>
    572     <span class="sd">&#39;&#39;&#39;</span>
    573 <span class="sd">    @Description:</span>
    574 <span class="sd">        Transform parameter names to parameter ids</span>
    575 <span class="sd">        with ECMWF grib table 128.</span>
    576 
    577 <span class="sd">    @Input:</span>
    578 <span class="sd">        pars: string</span>
    579 <span class="sd">            Addpar argument from CONTROL file in the format of</span>
    580 <span class="sd">            parameter names instead of ids. The parameter short</span>
    581 <span class="sd">            names are sepearted with &quot;/&quot; and they are passed as</span>
    582 <span class="sd">            one single string.</span>
    583 
    584 <span class="sd">        table: dictionary</span>
    585 <span class="sd">            Contains the ECMWF grib table 128 information.</span>
    586 <span class="sd">            The key is the parameter number and the value is the</span>
    587 <span class="sd">            short name of the parameter.</span>
    588 
    589 <span class="sd">    @Return:</span>
    590 <span class="sd">        ipar: list of integer</span>
    591 <span class="sd">            List of addpar parameters from CONTROL file transformed to</span>
    592 <span class="sd">            parameter ids in the format of integer.</span>
     570<div class="viewcode-block" id="to_param_id"><a class="viewcode-back" href="../api.html#tools.to_param_id">[docs]</a><span class="k">def</span> <span class="nf">to_param_id</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span> <span class="n">table</span><span class="p">):</span>
     571    <span class="sd">&#39;&#39;&#39;Transform parameter names to parameter ids with ECMWF grib table 128.</span>
     572
     573<span class="sd">    Parameters</span>
     574<span class="sd">    ----------</span>
     575<span class="sd">    pars : :obj:`string`</span>
     576<span class="sd">        Addpar argument from CONTROL file in the format of</span>
     577<span class="sd">        parameter names instead of ids. The parameter short</span>
     578<span class="sd">        names are sepearted with &quot;/&quot; and they are passed as</span>
     579<span class="sd">        one single string.</span>
     580
     581<span class="sd">    table : :obj:`dictionary`</span>
     582<span class="sd">        Contains the ECMWF grib table 128 information.</span>
     583<span class="sd">        The key is the parameter number and the value is the</span>
     584<span class="sd">        short name of the parameter.</span>
     585
     586<span class="sd">    Return</span>
     587<span class="sd">    ------</span>
     588<span class="sd">    ipar : :obj:`list` of :obj:`integer`</span>
     589<span class="sd">        List of addpar parameters from CONTROL file transformed to</span>
     590<span class="sd">        parameter ids in the format of integer.</span>
    593591<span class="sd">    &#39;&#39;&#39;</span>
    594592    <span class="n">cpar</span> <span class="o">=</span> <span class="n">pars</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span>
     
    604602    <span class="k">return</span> <span class="n">ipar</span></div>
    605603
    606 <div class="viewcode-block" id="get_list_as_string"><a class="viewcode-back" href="../code.html#tools.get_list_as_string">[docs]</a><span class="k">def</span> <span class="nf">get_list_as_string</span><span class="p">(</span><span class="n">list_obj</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">&#39;, &#39;</span><span class="p">):</span>
    607     <span class="sd">&#39;&#39;&#39;</span>
    608 <span class="sd">    @Description:</span>
    609 <span class="sd">        Converts a list of arbitrary content into a single string.</span>
    610 
    611 <span class="sd">    @Input:</span>
    612 <span class="sd">        list_obj: list</span>
    613 <span class="sd">            A list with arbitrary content.</span>
    614 
    615 <span class="sd">        concatenate_sign: string, optional</span>
    616 <span class="sd">            A string which is used to concatenate the single</span>
    617 <span class="sd">            list elements. Default value is &quot;, &quot;.</span>
    618 
    619 <span class="sd">    @Return:</span>
    620 <span class="sd">        str_of_list: string</span>
    621 <span class="sd">            The content of the list as a single string.</span>
     604<div class="viewcode-block" id="get_list_as_string"><a class="viewcode-back" href="../api.html#tools.get_list_as_string">[docs]</a><span class="k">def</span> <span class="nf">get_list_as_string</span><span class="p">(</span><span class="n">list_obj</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">&#39;, &#39;</span><span class="p">):</span>
     605    <span class="sd">&#39;&#39;&#39;Converts a list of arbitrary content into a single string.</span>
     606
     607<span class="sd">    Parameters</span>
     608<span class="sd">    ----------</span>
     609<span class="sd">    list_obj : :obj:`list`</span>
     610<span class="sd">        A list with arbitrary content.</span>
     611
     612<span class="sd">    concatenate_sign : :obj:`string`, optional</span>
     613<span class="sd">        A string which is used to concatenate the single</span>
     614<span class="sd">        list elements. Default value is &quot;, &quot;.</span>
     615
     616<span class="sd">    Return</span>
     617<span class="sd">    ------</span>
     618<span class="sd">    str_of_list : :obj:`string`</span>
     619<span class="sd">        The content of the list as a single string.</span>
    622620<span class="sd">    &#39;&#39;&#39;</span>
    623621
     
    626624    <span class="k">return</span> <span class="n">str_of_list</span></div>
    627625
    628 <div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../code.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
    629     <span class="sd">&#39;&#39;&#39;</span>
    630 <span class="sd">    @Description:</span>
    631 <span class="sd">        Creates a directory and gives a warning if the directory</span>
    632 <span class="sd">        already exists. The program stops only if there is another problem.</span>
    633 
    634 <span class="sd">    @Input:</span>
    635 <span class="sd">        directory: string</span>
    636 <span class="sd">            The directory name including the path which should be created.</span>
    637 
    638 <span class="sd">    @Return:</span>
    639 <span class="sd">        &lt;nothing&gt;</span>
     626<div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../api.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
     627    <span class="sd">&#39;&#39;&#39;Creates a directory and gives a warning if the directory</span>
     628<span class="sd">    already exists. The program stops only if there is another problem.</span>
     629
     630<span class="sd">    Parameters</span>
     631<span class="sd">    ----------</span>
     632<span class="sd">    directory : :obj:`string`</span>
     633<span class="sd">        The directory name including the path which should be created.</span>
     634
     635<span class="sd">    Return</span>
     636<span class="sd">    ------</span>
     637
    640638<span class="sd">    &#39;&#39;&#39;</span>
    641639    <span class="k">try</span><span class="p">:</span>
     
    650648    <span class="k">return</span></div>
    651649
    652 <div class="viewcode-block" id="put_file_to_ecserver"><a class="viewcode-back" href="../code.html#tools.put_file_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">put_file_to_ecserver</span><span class="p">(</span><span class="n">ecd</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">ecuid</span><span class="p">,</span> <span class="n">ecgid</span><span class="p">):</span>
    653     <span class="sd">&#39;&#39;&#39;</span>
    654 <span class="sd">    @Description:</span>
    655 <span class="sd">        Uses the ecaccess-file-put command to send a file to the ECMWF servers.</span>
    656 
    657 <span class="sd">        NOTE:</span>
    658 <span class="sd">        The return value is just for testing reasons. It does not have</span>
    659 <span class="sd">        to be used from the calling function since the whole error handling</span>
    660 <span class="sd">        is done in here.</span>
    661 
    662 <span class="sd">    @Input:</span>
    663 <span class="sd">        ecd: string</span>
    664 <span class="sd">            The path were the file is stored.</span>
    665 
    666 <span class="sd">        filename: string</span>
    667 <span class="sd">            The name of the file to send to the ECMWF server.</span>
    668 
    669 <span class="sd">        target: string</span>
    670 <span class="sd">            The target queue where the file should be sent to.</span>
    671 
    672 <span class="sd">        ecuid: string</span>
    673 <span class="sd">            The user id on ECMWF server.</span>
    674 
    675 <span class="sd">        ecgid: string</span>
    676 <span class="sd">            The group id on ECMWF server.</span>
    677 
    678 <span class="sd">    @Return:</span>
    679 <span class="sd">        rcode: string</span>
    680 <span class="sd">            Resulting code of command execution. If successful the string</span>
    681 <span class="sd">            will be empty.</span>
     650<div class="viewcode-block" id="put_file_to_ecserver"><a class="viewcode-back" href="../api.html#tools.put_file_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">put_file_to_ecserver</span><span class="p">(</span><span class="n">ecd</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">ecuid</span><span class="p">,</span> <span class="n">ecgid</span><span class="p">):</span>
     651    <span class="sd">&#39;&#39;&#39;Uses the ecaccess-file-put command to send a file to the ECMWF servers.</span>
     652
     653<span class="sd">    Note</span>
     654<span class="sd">    ----</span>
     655<span class="sd">    The return value is just for testing reasons. It does not have</span>
     656<span class="sd">    to be used from the calling function since the whole error handling</span>
     657<span class="sd">    is done in here.</span>
     658
     659<span class="sd">    Parameters</span>
     660<span class="sd">    ----------</span>
     661<span class="sd">    ecd : :obj:`string`</span>
     662<span class="sd">        The path were the file is stored.</span>
     663
     664<span class="sd">    filename : :obj:`string`</span>
     665<span class="sd">        The name of the file to send to the ECMWF server.</span>
     666
     667<span class="sd">    target : :obj:`string`</span>
     668<span class="sd">        The target queue where the file should be sent to.</span>
     669
     670<span class="sd">    ecuid : :obj:`string`</span>
     671<span class="sd">        The user id on ECMWF server.</span>
     672
     673<span class="sd">    ecgid : :obj:`string`</span>
     674<span class="sd">        The group id on ECMWF server.</span>
     675
     676<span class="sd">    Return</span>
     677<span class="sd">    ------</span>
     678<span class="sd">    rcode : :obj:`string`</span>
     679<span class="sd">        Resulting code of command execution. If successful the string</span>
     680<span class="sd">        will be empty.</span>
    682681<span class="sd">    &#39;&#39;&#39;</span>
    683682
     
    698697    <span class="k">return</span> <span class="n">rcode</span></div>
    699698
    700 <div class="viewcode-block" id="submit_job_to_ecserver"><a class="viewcode-back" href="../code.html#tools.submit_job_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">submit_job_to_ecserver</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">jobname</span><span class="p">):</span>
    701     <span class="sd">&#39;&#39;&#39;</span>
    702 <span class="sd">    @Description:</span>
    703 <span class="sd">        Uses ecaccess-job-submit command to submit a job to the ECMWF server.</span>
    704 
    705 <span class="sd">        NOTE:</span>
    706 <span class="sd">        The return value is just for testing reasons. It does not have</span>
    707 <span class="sd">        to be used from the calling function since the whole error handling</span>
    708 <span class="sd">        is done in here.</span>
    709 
    710 <span class="sd">    @Input:</span>
    711 <span class="sd">        target: string</span>
    712 <span class="sd">            The target where the file should be sent to, e.g. the queue.</span>
    713 
    714 <span class="sd">        jobname: string</span>
    715 <span class="sd">            The name of the jobfile to be submitted to the ECMWF server.</span>
    716 
    717 <span class="sd">    @Return:</span>
    718 <span class="sd">        rcode: string</span>
    719 <span class="sd">            Resulting code of command execution. If successful the string</span>
    720 <span class="sd">            will contain an integer number, representing the id of the job</span>
    721 <span class="sd">            at the ecmwf server.</span>
     699<div class="viewcode-block" id="submit_job_to_ecserver"><a class="viewcode-back" href="../api.html#tools.submit_job_to_ecserver">[docs]</a><span class="k">def</span> <span class="nf">submit_job_to_ecserver</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">jobname</span><span class="p">):</span>
     700    <span class="sd">&#39;&#39;&#39;Uses ecaccess-job-submit command to submit a job to the ECMWF server.</span>
     701
     702<span class="sd">    Note</span>
     703<span class="sd">    ----</span>
     704<span class="sd">    The return value is just for testing reasons. It does not have</span>
     705<span class="sd">    to be used from the calling function since the whole error handling</span>
     706<span class="sd">    is done in here.</span>
     707
     708<span class="sd">    Parameters</span>
     709<span class="sd">    ----------</span>
     710<span class="sd">    target : :obj:`string`</span>
     711<span class="sd">        The target where the file should be sent to, e.g. the queue.</span>
     712
     713<span class="sd">    jobname : :obj:`string`</span>
     714<span class="sd">        The name of the jobfile to be submitted to the ECMWF server.</span>
     715
     716<span class="sd">    Return</span>
     717<span class="sd">    ------</span>
     718<span class="sd">    rcode : :obj:`string`</span>
     719<span class="sd">        Resulting code of command execution. If successful the string</span>
     720<span class="sd">        will contain an integer number, representing the id of the job</span>
     721<span class="sd">        at the ecmwf server.</span>
    722722<span class="sd">    &#39;&#39;&#39;</span>
    723723
  • documentation/Sphinx/build/html/_sources/api.rst.txt

    r708c667 r274f9ef  
    22============================
    33
     4.. contents::
     5    :local:
     6   
     7Porgrams
     8--------
     9
     10install
     11*******
     12
     13.. automodule:: install
     14    :members:
     15   
     16submit
     17******
     18
     19.. automodule:: submit
     20    :members:
     21   
     22Classes
     23-------
     24
     25ControlFile
     26***********
     27
     28.. automodule:: ControlFile
     29    :members:
     30   
     31EcFlexpart
     32**********
     33
     34.. automodule:: EcFlexpart
     35    :members:
     36   
     37GribTools
     38*********
     39
     40.. automodule:: GribTools
     41    :members:
     42
     43MarsRetrieval
     44*************
     45
     46.. automodule:: MarsRetrieval
     47    :members:
     48
     49UioFiles
     50********
     51
     52.. automodule:: UioFiles
     53    :members:
     54
     55
     56
     57Modules
     58-------
     59
     60get_mars_data
     61*************
     62
     63.. automodule:: get_mars_data
     64    :members:
     65 
     66prepare_flexpart
     67****************
     68
     69.. automodule:: prepare_flexpart
     70    :members:   
     71   
     72tools
     73*****
     74
     75.. automodule:: tools
     76    :members:
     77
     78disaggregation
     79**************   
     80   
    481.. automodule:: disaggregation
    582    :members:
  • documentation/Sphinx/build/html/_sources/downloads.rst.txt

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    downloads/tar_balls
     13    downloads/git_repo
     14    downloads/history_changes
     15   
  • documentation/Sphinx/build/html/_sources/index.rst.txt

    r708c667 r274f9ef  
    44   contain the root `toctree` directive.
    55
    6 Welcome to flex_extract's documentation!
    7 ========================================
     6Welcome to flex_extract's user documentation!
     7=============================================
     8
     9flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.
     10
     11
     12.. The scripts can be 1) executed locally using the ECMWF WebMARS interface, or 2) on the ECMWF member
     13.. state gateway server or HPC facility using the ecaccess software package. As another option the scripts can 3)
     14.. also be triggered using ecflow scheduling software used by ECMWF for data dissemination.
     15
     16All required second party software and libraries used within flex_extract is open source and free of charge.
     17
     18
    819.. raw:: html
    920
     
    8798
    8899.. toctree::
    89    :maxdepth: 2
     100   :maxdepth: 3
    90101   :caption: Table of Contents:
    91102
  • documentation/Sphinx/build/html/_sources/installation.rst.txt

    r708c667 r274f9ef  
    11Installation
    22============
    3 
    4 Describe installation process flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    installation/requirements
     11    installation/oper_modes
     12    installation/test_install
     13
     14
     15   
  • documentation/Sphinx/build/html/_sources/program_structure.rst.txt

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    program_structure/prog_overview
     13    program_structure/prog_components
     14    program_structure/prog_flow
  • documentation/Sphinx/build/html/_sources/requirements.rst.txt

    r708c667 r274f9ef  
    22============
    33
    4 Describe the requirements to use flex_extract ....
    54 
    65    UNDER CONSTRUCTION
     6   
  • documentation/Sphinx/build/html/_sources/support.rst.txt

    r708c667 r274f9ef  
    22=======
    33
    4 Describe support options ....
    54 
    65    UNDER CONSTRUCTION
     6   
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    support/ticket_system
     13    support/mailing_list
     14    support/known_bugs_issues
     15    support/faq
     16       
  • documentation/Sphinx/build/html/_sources/user_guide.rst.txt

    r708c667 r274f9ef  
    11User Guide
    22==========
    3 
    4 Describe using flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    user_guide/how_to
     11    user_guide/control_templates
     12   
  • documentation/Sphinx/build/html/api.html

    r708c667 r274f9ef  
    3030    <link rel="search" title="Search" href="search.html" />
    3131    <link rel="next" title="Support" href="support.html" />
    32     <link rel="prev" title="User Guide" href="user_guide.html" />
     32    <link rel="prev" title="CONTROL-file templates" href="user_guide/control_templates.html" />
    3333
    3434 
     
    8989<li class="toctree-l1"><a class="reference internal" href="program_structure.html">Program Structure</a></li>
    9090<li class="toctree-l1"><a class="reference internal" href="user_guide.html">User Guide</a></li>
    91 <li class="toctree-l1 current"><a class="current reference internal" href="#">Auto Generated Documentation</a></li>
     91<li class="toctree-l1 current"><a class="current reference internal" href="#">Auto Generated Documentation</a><ul>
     92<li class="toctree-l2"><a class="reference internal" href="#porgrams">Porgrams</a><ul>
     93<li class="toctree-l3"><a class="reference internal" href="#module-install">install</a></li>
     94<li class="toctree-l3"><a class="reference internal" href="#module-submit">submit</a></li>
     95</ul>
     96</li>
     97<li class="toctree-l2"><a class="reference internal" href="#classes">Classes</a><ul>
     98<li class="toctree-l3"><a class="reference internal" href="#module-ControlFile">ControlFile</a></li>
     99<li class="toctree-l3"><a class="reference internal" href="#module-EcFlexpart">EcFlexpart</a></li>
     100<li class="toctree-l3"><a class="reference internal" href="#module-GribTools">GribTools</a></li>
     101<li class="toctree-l3"><a class="reference internal" href="#module-MarsRetrieval">MarsRetrieval</a></li>
     102<li class="toctree-l3"><a class="reference internal" href="#module-UioFiles">UioFiles</a></li>
     103</ul>
     104</li>
     105<li class="toctree-l2"><a class="reference internal" href="#modules">Modules</a><ul>
     106<li class="toctree-l3"><a class="reference internal" href="#module-get_mars_data">get_mars_data</a></li>
     107<li class="toctree-l3"><a class="reference internal" href="#module-prepare_flexpart">prepare_flexpart</a></li>
     108<li class="toctree-l3"><a class="reference internal" href="#module-tools">tools</a></li>
     109<li class="toctree-l3"><a class="reference internal" href="#module-disaggregation">disaggregation</a></li>
     110</ul>
     111</li>
     112</ul>
     113</li>
    92114<li class="toctree-l1"><a class="reference internal" href="support.html">Support</a></li>
    93115</ul>
     
    155177           <div itemprop="articleBody">
    156178           
    157   <div class="section" id="module-disaggregation">
    158 <span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-disaggregation" title="Permalink to this headline">¶</a></h1>
     179  <div class="section" id="auto-generated-documentation">
     180<h1>Auto Generated Documentation<a class="headerlink" href="#auto-generated-documentation" title="Permalink to this headline">¶</a></h1>
     181<div class="contents local topic" id="contents">
     182<ul class="simple">
     183<li><a class="reference internal" href="#porgrams" id="id1">Porgrams</a><ul>
     184<li><a class="reference internal" href="#module-install" id="id2">install</a></li>
     185<li><a class="reference internal" href="#module-submit" id="id3">submit</a></li>
     186</ul>
     187</li>
     188<li><a class="reference internal" href="#classes" id="id4">Classes</a><ul>
     189<li><a class="reference internal" href="#module-ControlFile" id="id5">ControlFile</a></li>
     190<li><a class="reference internal" href="#module-EcFlexpart" id="id6">EcFlexpart</a></li>
     191<li><a class="reference internal" href="#module-GribTools" id="id7">GribTools</a></li>
     192<li><a class="reference internal" href="#module-MarsRetrieval" id="id8">MarsRetrieval</a></li>
     193<li><a class="reference internal" href="#module-UioFiles" id="id9">UioFiles</a></li>
     194</ul>
     195</li>
     196<li><a class="reference internal" href="#modules" id="id10">Modules</a><ul>
     197<li><a class="reference internal" href="#module-get_mars_data" id="id11">get_mars_data</a></li>
     198<li><a class="reference internal" href="#module-prepare_flexpart" id="id12">prepare_flexpart</a></li>
     199<li><a class="reference internal" href="#module-tools" id="id13">tools</a></li>
     200<li><a class="reference internal" href="#module-disaggregation" id="id14">disaggregation</a></li>
     201</ul>
     202</li>
     203</ul>
     204</div>
     205<div class="section" id="porgrams">
     206<h2><a class="toc-backref" href="#id1">Porgrams</a><a class="headerlink" href="#porgrams" title="Permalink to this headline">¶</a></h2>
     207<div class="section" id="module-install">
     208<span id="install"></span><h3><a class="toc-backref" href="#id2">install</a><a class="headerlink" href="#module-install" title="Permalink to this headline">¶</a></h3>
     209<dl class="function">
     210<dt id="install.delete_convert_build">
     211<code class="descclassname">install.</code><code class="descname">delete_convert_build</code><span class="sig-paren">(</span><em>src_path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#delete_convert_build"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.delete_convert_build" title="Permalink to this definition">¶</a></dt>
     212<dd><p>Clean up the Fortran source directory and remove all
     213build files (e.g. *.o, *.mod and CONVERT2)</p>
     214<table class="docutils field-list" frame="void" rules="none">
     215<col class="field-name" />
     216<col class="field-body" />
     217<tbody valign="top">
     218<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>src_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the fortran source directory.</td>
     219</tr>
     220</tbody>
     221</table>
     222</dd></dl>
     223
     224<dl class="function">
     225<dt id="install.get_install_cmdline_arguments">
     226<code class="descclassname">install.</code><code class="descname">get_install_cmdline_arguments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#get_install_cmdline_arguments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.get_install_cmdline_arguments" title="Permalink to this definition">¶</a></dt>
     227<dd><p>Decomposes the command line arguments and assigns them to variables.
     228Apply default values for non mentioned arguments.</p>
     229<table class="docutils field-list" frame="void" rules="none">
     230<col class="field-name" />
     231<col class="field-body" />
     232<tbody valign="top">
     233<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>args</strong> – Contains the commandline arguments from script/program call.</td>
     234</tr>
     235<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code></td>
     236</tr>
     237</tbody>
     238</table>
     239</dd></dl>
     240
     241<dl class="function">
     242<dt id="install.install_via_gateway">
     243<code class="descclassname">install.</code><code class="descname">install_via_gateway</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#install_via_gateway"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.install_via_gateway" title="Permalink to this definition">¶</a></dt>
     244<dd><p>Perform the actual installation on local machine or prepare data
     245transfer to remote gate and submit a job script which will
     246install everything on the remote gate.</p>
     247<table class="docutils field-list" frame="void" rules="none">
     248<col class="field-name" />
     249<col class="field-body" />
     250<tbody valign="top">
     251<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     252command line.</td>
     253</tr>
     254</tbody>
     255</table>
     256</dd></dl>
     257
     258<dl class="function">
     259<dt id="install.main">
     260<code class="descclassname">install.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.main" title="Permalink to this definition">¶</a></dt>
     261<dd><p>Controls the installation process. Calls the installation function
     262if target is specified.</p>
     263</dd></dl>
     264
     265<dl class="function">
     266<dt id="install.make_convert_build">
     267<code class="descclassname">install.</code><code class="descname">make_convert_build</code><span class="sig-paren">(</span><em>src_path</em>, <em>makefile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#make_convert_build"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.make_convert_build" title="Permalink to this definition">¶</a></dt>
     268<dd><p>Compiles the Fortran code and generates the executable.</p>
     269<table class="docutils field-list" frame="void" rules="none">
     270<col class="field-name" />
     271<col class="field-body" />
     272<tbody valign="top">
     273<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     274<li><strong>src_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the fortran source directory.</li>
     275<li><strong>makefile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the makefile which should be used.</li>
     276</ul>
     277</td>
     278</tr>
     279</tbody>
     280</table>
     281</dd></dl>
     282
     283<dl class="function">
     284<dt id="install.mk_compilejob">
     285<code class="descclassname">install.</code><code class="descname">mk_compilejob</code><span class="sig-paren">(</span><em>makefile</em>, <em>target</em>, <em>ecuid</em>, <em>ecgid</em>, <em>fp_root</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_compilejob"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_compilejob" title="Permalink to this definition">¶</a></dt>
     286<dd><p>Modifies the original job template file so that it is specified
     287for the user and the environment were it will be applied. Result
     288is stored in a new file “job.temp” in the python directory.</p>
     289<table class="docutils field-list" frame="void" rules="none">
     290<col class="field-name" />
     291<col class="field-body" />
     292<tbody valign="top">
     293<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     294<li><strong>makefile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the makefile which should be used to compile FORTRAN
     295CONVERT2 program.</li>
     296<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target where the installation should be done, e.g. the queue.</li>
     297<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     298<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     299<li><strong>fp_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the root directory of FLEXPART environment or flex_extract
     300environment.</li>
     301</ul>
     302</td>
     303</tr>
     304</tbody>
     305</table>
     306</dd></dl>
     307
     308<dl class="function">
     309<dt id="install.mk_env_vars">
     310<code class="descclassname">install.</code><code class="descname">mk_env_vars</code><span class="sig-paren">(</span><em>ecuid</em>, <em>ecgid</em>, <em>gateway</em>, <em>destination</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_env_vars"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_env_vars" title="Permalink to this definition">¶</a></dt>
     311<dd><p>Creates a file named ECMWF_ENV which contains the
     312necessary environmental variables at ECMWF servers.
     313It is based on the template ECMWF_ENV.template.</p>
     314<table class="docutils field-list" frame="void" rules="none">
     315<col class="field-name" />
     316<col class="field-body" />
     317<tbody valign="top">
     318<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     319<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     320<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     321<li><strong>gateway</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The gateway server the user is using.</li>
     322<li><strong>destination</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The remote destination which is used to transfer files
     323from ECMWF server to local gateway server.</li>
     324</ul>
     325</td>
     326</tr>
     327</tbody>
     328</table>
     329</dd></dl>
     330
     331<dl class="function">
     332<dt id="install.mk_job_template">
     333<code class="descclassname">install.</code><code class="descname">mk_job_template</code><span class="sig-paren">(</span><em>ecuid</em>, <em>ecgid</em>, <em>gateway</em>, <em>destination</em>, <em>fp_root</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_job_template"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_job_template" title="Permalink to this definition">¶</a></dt>
     334<dd><p>Modifies the original job template file so that it is specified
     335for the user and the environment were it will be applied. Result
     336is stored in a new file.</p>
     337<table class="docutils field-list" frame="void" rules="none">
     338<col class="field-name" />
     339<col class="field-body" />
     340<tbody valign="top">
     341<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     342<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     343<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     344<li><strong>gateway</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The gateway server the user is using.</li>
     345<li><strong>destination</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The remote destination which is used to transfer files
     346from ECMWF server to local gateway server.</li>
     347<li><strong>fp_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to the root directory of FLEXPART environment or flex_extract
     348environment.</li>
     349</ul>
     350</td>
     351</tr>
     352</tbody>
     353</table>
     354</dd></dl>
     355
     356<dl class="function">
     357<dt id="install.mk_tarball">
     358<code class="descclassname">install.</code><code class="descname">mk_tarball</code><span class="sig-paren">(</span><em>tarball_path</em>, <em>target</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#mk_tarball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_tarball" title="Permalink to this definition">¶</a></dt>
     359<dd><p>Creates a tarball with all necessary files which need to be sent to the
     360installation directory.
     361It does not matter if this is local or remote.
     362Collects all python files, the Fortran source and makefiles,
     363the ECMWF_ENV file, the CONTROL files as well as the
     364template files.</p>
     365<table class="docutils field-list" frame="void" rules="none">
     366<col class="field-name" />
     367<col class="field-body" />
     368<tbody valign="top">
     369<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     370<li><strong>tarball_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The complete path to the tar file which will contain all
     371relevant data for flex_extract.</li>
     372<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The queue where the job is submitted to.</li>
     373</ul>
     374</td>
     375</tr>
     376</tbody>
     377</table>
     378</dd></dl>
     379
     380<dl class="function">
     381<dt id="install.un_tarball">
     382<code class="descclassname">install.</code><code class="descname">un_tarball</code><span class="sig-paren">(</span><em>tarball_path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/install.html#un_tarball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.un_tarball" title="Permalink to this definition">¶</a></dt>
     383<dd><p>Extracts the given tarball into current directory.</p>
     384<table class="docutils field-list" frame="void" rules="none">
     385<col class="field-name" />
     386<col class="field-body" />
     387<tbody valign="top">
     388<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tarball_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The complete path to the tar file which will contain all
     389relevant data for flex_extract.</td>
     390</tr>
     391</tbody>
     392</table>
     393</dd></dl>
     394
     395</div>
     396<div class="section" id="module-submit">
     397<span id="submit"></span><h3><a class="toc-backref" href="#id3">submit</a><a class="headerlink" href="#module-submit" title="Permalink to this headline">¶</a></h3>
     398<dl class="function">
     399<dt id="submit.main">
     400<code class="descclassname">submit.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/submit.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#submit.main" title="Permalink to this definition">¶</a></dt>
     401<dd><p>Get the arguments from script call and from CONTROL file.
     402Decides from the argument “queue” if the local version
     403is done “queue=None” or the gateway version with “queue=ecgate”
     404or “queue=cca”.</p>
     405</dd></dl>
     406
     407<dl class="function">
     408<dt id="submit.submit">
     409<code class="descclassname">submit.</code><code class="descname">submit</code><span class="sig-paren">(</span><em>jtemplate</em>, <em>c</em>, <em>queue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/submit.html#submit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#submit.submit" title="Permalink to this definition">¶</a></dt>
     410<dd><p>Prepares the job script and submit it to the specified queue.</p>
     411<table class="docutils field-list" frame="void" rules="none">
     412<col class="field-name" />
     413<col class="field-body" />
     414<tbody valign="top">
     415<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     416<li><strong>jtemplate</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Job template file from sub-directory “_templates” for
     417submission to ECMWF. It contains all necessary
     418module and variable settings for the ECMWF environment as well as
     419the job call and mail report instructions.
     420Default is “job.temp”.</li>
     421<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     422command line.</li>
     423<li><strong>queue</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of queue for submission to ECMWF (e.g. ecgate or cca )</li>
     424</ul>
     425</td>
     426</tr>
     427</tbody>
     428</table>
     429</dd></dl>
     430
     431</div>
     432</div>
     433<div class="section" id="classes">
     434<h2><a class="toc-backref" href="#id4">Classes</a><a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
     435<div class="section" id="module-ControlFile">
     436<span id="controlfile"></span><h3><a class="toc-backref" href="#id5">ControlFile</a><a class="headerlink" href="#module-ControlFile" title="Permalink to this headline">¶</a></h3>
     437<dl class="class">
     438<dt id="ControlFile.ControlFile">
     439<em class="property">class </em><code class="descclassname">ControlFile.</code><code class="descname">ControlFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile" title="Permalink to this definition">¶</a></dt>
     440<dd><p>Contains the information which are stored in the CONTROL files.</p>
     441<dl class="method">
     442<dt id="ControlFile.ControlFile.assign_args_to_control">
     443<code class="descname">assign_args_to_control</code><span class="sig-paren">(</span><em>args</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.assign_args_to_control"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.assign_args_to_control" title="Permalink to this definition">¶</a></dt>
     444<dd><p>Overwrites the existing ControlFile instance attributes with
     445the command line arguments.</p>
     446<table class="docutils field-list" frame="void" rules="none">
     447<col class="field-name" />
     448<col class="field-body" />
     449<tbody valign="top">
     450<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code>) – Contains the commandline arguments from script/program call.</td>
     451</tr>
     452</tbody>
     453</table>
     454</dd></dl>
     455
     456<dl class="method">
     457<dt id="ControlFile.ControlFile.assign_envs_to_control">
     458<code class="descname">assign_envs_to_control</code><span class="sig-paren">(</span><em>envs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.assign_envs_to_control"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.assign_envs_to_control" title="Permalink to this definition">¶</a></dt>
     459<dd><p>Assigns the ECMWF environment parameter.</p>
     460<table class="docutils field-list" frame="void" rules="none">
     461<col class="field-name" />
     462<col class="field-body" />
     463<tbody valign="top">
     464<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>envs</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">strings</span></code>) – Contains the ECMWF environment parameternames “ECUID”, “ECGID”,
     465“DESTINATION” and “GATEWAY” with its corresponding values.
     466They were read from the file “ECMWF_ENV”.</td>
     467</tr>
     468</tbody>
     469</table>
     470</dd></dl>
     471
     472<dl class="method">
     473<dt id="ControlFile.ControlFile.check_conditions">
     474<code class="descname">check_conditions</code><span class="sig-paren">(</span><em>queue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.check_conditions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.check_conditions" title="Permalink to this definition">¶</a></dt>
     475<dd><p>Checks a couple of necessary attributes and conditions,
     476such as if they exist and contain values.
     477Otherwise set default values.</p>
     478<table class="docutils field-list" frame="void" rules="none">
     479<col class="field-name" />
     480<col class="field-body" />
     481<tbody valign="top">
     482<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>queue</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the queue if submitted to the ECMWF servers.
     483Used to check if ecuid, ecgid, gateway and destination
     484are set correctly and are not empty.</td>
     485</tr>
     486</tbody>
     487</table>
     488</dd></dl>
     489
     490<dl class="method">
     491<dt id="ControlFile.ControlFile.check_install_conditions">
     492<code class="descname">check_install_conditions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.check_install_conditions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.check_install_conditions" title="Permalink to this definition">¶</a></dt>
     493<dd><p>Checks a couple of necessary attributes and conditions
     494for the installation such as if they exist and contain values.
     495Otherwise set default values.</p>
     496</dd></dl>
     497
     498<dl class="method">
     499<dt id="ControlFile.ControlFile.to_list">
     500<code class="descname">to_list</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ControlFile.html#ControlFile.to_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ControlFile.ControlFile.to_list" title="Permalink to this definition">¶</a></dt>
     501<dd><p>Just generates a list of strings containing the attributes and
     502assigned values except the attributes “_expanded”, “exedir”,
     503“ecmwfdatadir” and “flexpart_root_scripts”.</p>
     504<table class="docutils field-list" frame="void" rules="none">
     505<col class="field-name" />
     506<col class="field-body" />
     507<tbody valign="top">
     508<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>l</strong> – A sorted list of the all ControlFile class attributes with
     509their values except the attributes “_expanded”, “exedir”,
     510“ecmwfdatadir” and “flexpart_root_scripts”.</td>
     511</tr>
     512<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></td>
     513</tr>
     514</tbody>
     515</table>
     516</dd></dl>
     517
     518</dd></dl>
     519
     520</div>
     521<div class="section" id="module-EcFlexpart">
     522<span id="ecflexpart"></span><h3><a class="toc-backref" href="#id6">EcFlexpart</a><a class="headerlink" href="#module-EcFlexpart" title="Permalink to this headline">¶</a></h3>
     523<dl class="class">
     524<dt id="EcFlexpart.EcFlexpart">
     525<em class="property">class </em><code class="descclassname">EcFlexpart.</code><code class="descname">EcFlexpart</code><span class="sig-paren">(</span><em>c</em>, <em>fluxes=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart" title="Permalink to this definition">¶</a></dt>
     526<dd><p>Class to retrieve FLEXPART specific ECMWF data.</p>
     527<dl class="method">
     528<dt id="EcFlexpart.EcFlexpart.create">
     529<code class="descname">create</code><span class="sig-paren">(</span><em>inputfiles</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.create" title="Permalink to this definition">¶</a></dt>
     530<dd><p>An index file will be created which depends on the combination
     531of “date”, “time” and “stepRange” values. This is used to iterate
     532over all messages in each grib file which were passed through the
     533parameter “inputfiles” to seperate specific parameters into fort.*
     534files. Afterwards the FORTRAN program is called to convert
     535the data fields all to the same grid and put them in one file
     536per unique time step (combination of “date”, “time” and
     537“stepRange”).</p>
     538<div class="admonition note">
     539<p class="first admonition-title">Note</p>
     540<p class="last">This method is based on the ECMWF example index.py
     541<a class="reference external" href="https://software.ecmwf.int/wiki/display/GRIB/index.py">https://software.ecmwf.int/wiki/display/GRIB/index.py</a></p>
     542</div>
     543<table class="docutils field-list" frame="void" rules="none">
     544<col class="field-name" />
     545<col class="field-body" />
     546<tbody valign="top">
     547<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     548<li><strong>inputfiles</strong> (<a class="reference internal" href="#module-UioFiles" title="UioFiles"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UioFiles</span></code></a>) – Contains a list of files.</li>
     549<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     550command line.</li>
     551</ul>
     552</td>
     553</tr>
     554</tbody>
     555</table>
     556</dd></dl>
     557
     558<dl class="method">
     559<dt id="EcFlexpart.EcFlexpart.deacc_fluxes">
     560<code class="descname">deacc_fluxes</code><span class="sig-paren">(</span><em>inputfiles</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.deacc_fluxes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.deacc_fluxes" title="Permalink to this definition">¶</a></dt>
     561<dd><p>Goes through all flux fields in ordered time and de-accumulate
     562the fields. Afterwards the fields are disaggregated in time.
     563Different versions of disaggregation is provided for rainfall
     564data (darain, modified linear) and the surface fluxes and
     565stress data (dapoly, cubic polynomial).</p>
     566<table class="docutils field-list" frame="void" rules="none">
     567<col class="field-name" />
     568<col class="field-body" />
     569<tbody valign="top">
     570<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     571<li><strong>inputfiles</strong> (<a class="reference internal" href="#module-UioFiles" title="UioFiles"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UioFiles</span></code></a>) – Contains a list of files.</li>
     572<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     573command line.</li>
     574</ul>
     575</td>
     576</tr>
     577</tbody>
     578</table>
     579</dd></dl>
     580
     581<dl class="method">
     582<dt id="EcFlexpart.EcFlexpart.prepare_fp_files">
     583<code class="descname">prepare_fp_files</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.prepare_fp_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.prepare_fp_files" title="Permalink to this definition">¶</a></dt>
     584<dd><p>Conversion of GRIB files to FLEXPART binary format.</p>
     585<table class="docutils field-list" frame="void" rules="none">
     586<col class="field-name" />
     587<col class="field-body" />
     588<tbody valign="top">
     589<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     590command line.</td>
     591</tr>
     592</tbody>
     593</table>
     594</dd></dl>
     595
     596<dl class="method">
     597<dt id="EcFlexpart.EcFlexpart.process_output">
     598<code class="descname">process_output</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.process_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.process_output" title="Permalink to this definition">¶</a></dt>
     599<dd><p>The grib files are postprocessed depending on the selection in
     600CONTROL file. The resulting files are moved to the output
     601directory if its not equal to the input directory.
     602The following modifications might be done if
     603properly switched in CONTROL file:
     604GRIB2 - Conversion to GRIB2
     605ECTRANS - Transfer of files to gateway server
     606ECSTORAGE - Storage at ECMWF server</p>
     607<table class="docutils field-list" frame="void" rules="none">
     608<col class="field-name" />
     609<col class="field-body" />
     610<tbody valign="top">
     611<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     612command line.</td>
     613</tr>
     614</tbody>
     615</table>
     616</dd></dl>
     617
     618<dl class="method">
     619<dt id="EcFlexpart.EcFlexpart.retrieve">
     620<code class="descname">retrieve</code><span class="sig-paren">(</span><em>server</em>, <em>dates</em>, <em>public</em>, <em>request</em>, <em>inputdir='.'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.retrieve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.retrieve" title="Permalink to this definition">¶</a></dt>
     621<dd><p>Finalizing the retrieval information by setting final details
     622depending on grid type.
     623Prepares MARS retrievals per grid type and submits them.</p>
     624<table class="docutils field-list" frame="void" rules="none">
     625<col class="field-name" />
     626<col class="field-body" />
     627<tbody valign="top">
     628<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     629<li><strong>server</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFService</span></code> or <code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFDataServer</span></code>) – The connection to the ECMWF server. This is different
     630for member state users which have full access and non
     631member state users which have only access to the public
     632data sets. The decision is made from command line argument
     633“public”; for public access its True (ECMWFDataServer)
     634for member state users its False (ECMWFService)</li>
     635<li><strong>dates</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains start and end date of the retrieval in the format
     636“YYYYMMDD/to/YYYYMMDD”</li>
     637<li><strong>request</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Selects the mode of retrieval.
     6380: Retrieves the data from ECMWF.
     6391: Prints the mars requests to an output file.
     6402: Retrieves the data and prints the mars request.</li>
     641<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Path to the directory where the retrieved data is about
     642to be stored. The default is the current directory (‘.’).</li>
     643</ul>
     644</td>
     645</tr>
     646</tbody>
     647</table>
     648</dd></dl>
     649
     650<dl class="method">
     651<dt id="EcFlexpart.EcFlexpart.write_namelist">
     652<code class="descname">write_namelist</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/EcFlexpart.html#EcFlexpart.write_namelist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#EcFlexpart.EcFlexpart.write_namelist" title="Permalink to this definition">¶</a></dt>
     653<dd><p>Creates a namelist file in the temporary directory and writes
     654the following values to it: maxl, maxb, mlevel,
     655mlevelist, mnauf, metapar, rlo0, rlo1, rla0, rla1,
     656momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta</p>
     657<table class="docutils field-list" frame="void" rules="none">
     658<col class="field-name" />
     659<col class="field-body" />
     660<tbody valign="top">
     661<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     662<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     663command line.</li>
     664<li><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Name of the namelist file.</li>
     665</ul>
     666</td>
     667</tr>
     668</tbody>
     669</table>
     670</dd></dl>
     671
     672</dd></dl>
     673
     674</div>
     675<div class="section" id="module-GribTools">
     676<span id="gribtools"></span><h3><a class="toc-backref" href="#id7">GribTools</a><a class="headerlink" href="#module-GribTools" title="Permalink to this headline">¶</a></h3>
     677<dl class="class">
     678<dt id="GribTools.GribTools">
     679<em class="property">class </em><code class="descclassname">GribTools.</code><code class="descname">GribTools</code><span class="sig-paren">(</span><em>filenames</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools" title="Permalink to this definition">¶</a></dt>
     680<dd><p>Class for GRIB utilities (new methods) based on GRIB API</p>
     681<dl class="method">
     682<dt id="GribTools.GribTools.copy">
     683<code class="descname">copy</code><span class="sig-paren">(</span><em>filename_in</em>, <em>selectWhere=True</em>, <em>keynames=[]</em>, <em>keyvalues=[]</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.copy" title="Permalink to this definition">¶</a></dt>
     684<dd><p>Add the content of another input grib file to the objects file but
     685only messages corresponding to keys/values passed to the function.
     686The selectWhere switch decides if to copy the keys equal to (True) or
     687different to (False) the keynames/keyvalues list passed to the function.</p>
     688<table class="docutils field-list" frame="void" rules="none">
     689<col class="field-name" />
     690<col class="field-body" />
     691<tbody valign="top">
     692<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     693<li><strong>filename_in</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Filename of the input file to read the grib messages from.</li>
     694<li><strong>selectWhere</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if to copy the keynames and values equal to (True) or
     695different to (False) the keynames/keyvalues list passed to the
     696function. Default is True.</li>
     697<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keynames. Default is an empty list.</li>
     698<li><strong>keyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keynames. Default is an empty list.</li>
     699<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
     700</ul>
     701</td>
     702</tr>
     703</tbody>
     704</table>
     705</dd></dl>
     706
     707<dl class="method">
     708<dt id="GribTools.GribTools.get_keys">
     709<code class="descname">get_keys</code><span class="sig-paren">(</span><em>keynames</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.get_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.get_keys" title="Permalink to this definition">¶</a></dt>
     710<dd><p>Get keyvalues for a given list of keynames a where statement
     711can be given (list of key and list of values)</p>
     712<table class="docutils field-list" frame="void" rules="none">
     713<col class="field-name" />
     714<col class="field-body" />
     715<tbody valign="top">
     716<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     717<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames.</li>
     718<li><strong>wherekeynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     719<li><strong>wherekeyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     720</ul>
     721</td>
     722</tr>
     723<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>return_list</strong> – List of keyvalues for given keynames.</p>
     724</td>
     725</tr>
     726<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     727</td>
     728</tr>
     729</tbody>
     730</table>
     731</dd></dl>
     732
     733<dl class="method">
     734<dt id="GribTools.GribTools.index">
     735<code class="descname">index</code><span class="sig-paren">(</span><em>index_keys=['mars'], index_file='my.idx'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.index" title="Permalink to this definition">¶</a></dt>
     736<dd><p>Create index file from a list of files if it does not exist or
     737read an index file.</p>
     738<table class="docutils field-list" frame="void" rules="none">
     739<col class="field-name" />
     740<col class="field-body" />
     741<tbody valign="top">
     742<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     743<li><strong>index_keys</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Contains the list of key parameter names from
     744which the index is to be created.
     745Default is a list with a single entry string “mars”.</li>
     746<li><strong>index_file</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Filename where the indices are stored.
     747Default is “my.idx”.</li>
     748</ul>
     749</td>
     750</tr>
     751<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>iid</strong> – Grib index id.</p>
     752</td>
     753</tr>
     754<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code></p>
     755</td>
     756</tr>
     757</tbody>
     758</table>
     759</dd></dl>
     760
     761<dl class="method">
     762<dt id="GribTools.GribTools.set_keys">
     763<code class="descname">set_keys</code><span class="sig-paren">(</span><em>fromfile</em>, <em>keynames</em>, <em>keyvalues</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em>, <em>strict=False</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/GribTools.html#GribTools.set_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribTools.GribTools.set_keys" title="Permalink to this definition">¶</a></dt>
     764<dd><p>Opens the file to read the grib messages and then write
     765them to a new output file. By default all messages are
     766written out. Also, the keyvalues of the passed list of
     767keynames are set or only those meeting the where statement.
     768(list of key and list of values).</p>
     769<table class="docutils field-list" frame="void" rules="none">
     770<col class="field-name" />
     771<col class="field-body" />
     772<tbody valign="top">
     773<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     774<li><strong>fromfile</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Filename of the input file to read the grib messages from.</li>
     775<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames. Default is an empty list.</li>
     776<li><strong>keyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – List of keynames. Default is an empty list.</li>
     777<li><strong>wherekeynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     778<li><strong>wherekeyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Default value is an empty list.</li>
     779<li><strong>strict</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if everything from keynames and keyvalues
     780is written out the grib file (False) or only those
     781meeting the where statement (True). Default is False.</li>
     782<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
     783</ul>
     784</td>
     785</tr>
     786</tbody>
     787</table>
     788</dd></dl>
     789
     790</dd></dl>
     791
     792</div>
     793<div class="section" id="module-MarsRetrieval">
     794<span id="marsretrieval"></span><h3><a class="toc-backref" href="#id8">MarsRetrieval</a><a class="headerlink" href="#module-MarsRetrieval" title="Permalink to this headline">¶</a></h3>
     795<dl class="class">
     796<dt id="MarsRetrieval.MarsRetrieval">
     797<em class="property">class </em><code class="descclassname">MarsRetrieval.</code><code class="descname">MarsRetrieval</code><span class="sig-paren">(</span><em>server</em>, <em>public</em>, <em>marsclass='ei'</em>, <em>dataset=''</em>, <em>type=''</em>, <em>levtype=''</em>, <em>levelist=''</em>, <em>repres=''</em>, <em>date=''</em>, <em>resol=''</em>, <em>stream=''</em>, <em>area=''</em>, <em>time=''</em>, <em>step=''</em>, <em>expver='1'</em>, <em>number=''</em>, <em>accuracy=''</em>, <em>grid=''</em>, <em>gaussian=''</em>, <em>target=''</em>, <em>param=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval" title="Permalink to this definition">¶</a></dt>
     798<dd><p>Class for submitting MARS retrievals.</p>
     799<p>A description of MARS keywords/arguments and examples of their
     800values can be found here:
     801<a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/">https://software.ecmwf.int/wiki/display/UDOC/</a>                   Identification+keywords#Identificationkeywords-class</p>
     802<dl class="method">
     803<dt id="MarsRetrieval.MarsRetrieval.data_retrieve">
     804<code class="descname">data_retrieve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.data_retrieve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.data_retrieve" title="Permalink to this definition">¶</a></dt>
     805<dd><p>Submits a MARS retrieval. Depending on the existence of
     806ECMWF Web-API it is submitted via Python or a
     807subprocess in the Shell. The parameter for the mars retrieval
     808are taken from the defined class attributes.</p>
     809</dd></dl>
     810
     811<dl class="method">
     812<dt id="MarsRetrieval.MarsRetrieval.display_info">
     813<code class="descname">display_info</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.display_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.display_info" title="Permalink to this definition">¶</a></dt>
     814<dd><p>Prints all class attributes and their values to the
     815standard output.</p>
     816</dd></dl>
     817
     818<dl class="method">
     819<dt id="MarsRetrieval.MarsRetrieval.print_info">
     820<code class="descname">print_info</code><span class="sig-paren">(</span><em>inputdir</em>, <em>request_number</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.print_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.print_info" title="Permalink to this definition">¶</a></dt>
     821<dd><p>Prints all mars requests to an extra file for debugging and
     822information.</p>
     823<table class="docutils field-list" frame="void" rules="none">
     824<col class="field-name" />
     825<col class="field-body" />
     826<tbody valign="top">
     827<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     828<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path where all data from the retrievals are stored.</li>
     829<li><strong>request_number</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Number of mars requests for flux and non-flux data.</li>
     830</ul>
     831</td>
     832</tr>
     833</tbody>
     834</table>
     835</dd></dl>
     836
     837<dl class="method">
     838<dt id="MarsRetrieval.MarsRetrieval.print_infodata_csv">
     839<code class="descname">print_infodata_csv</code><span class="sig-paren">(</span><em>inputdir</em>, <em>request_number</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MarsRetrieval.html#MarsRetrieval.print_infodata_csv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#MarsRetrieval.MarsRetrieval.print_infodata_csv" title="Permalink to this definition">¶</a></dt>
     840<dd><p>Write all request parameter in alpabetical order into a “csv” file.</p>
     841<table class="docutils field-list" frame="void" rules="none">
     842<col class="field-name" />
     843<col class="field-body" />
     844<tbody valign="top">
     845<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     846<li><strong>inputdir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path where all data from the retrievals are stored.</li>
     847<li><strong>request_number</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code>) – Number of mars requests for flux and non-flux data.</li>
     848</ul>
     849</td>
     850</tr>
     851</tbody>
     852</table>
     853</dd></dl>
     854
     855</dd></dl>
     856
     857</div>
     858<div class="section" id="module-UioFiles">
     859<span id="uiofiles"></span><h3><a class="toc-backref" href="#id9">UioFiles</a><a class="headerlink" href="#module-UioFiles" title="Permalink to this headline">¶</a></h3>
     860<dl class="class">
     861<dt id="UioFiles.UioFiles">
     862<em class="property">class </em><code class="descclassname">UioFiles.</code><code class="descname">UioFiles</code><span class="sig-paren">(</span><em>path</em>, <em>pattern</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/UioFiles.html#UioFiles"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#UioFiles.UioFiles" title="Permalink to this definition">¶</a></dt>
     863<dd><p>Class to manipulate files. At initialisation it has the pattern
     864which stores a regular expression pattern for the files, the path
     865to the files and the files already.</p>
     866<dl class="method">
     867<dt id="UioFiles.UioFiles.delete_files">
     868<code class="descname">delete_files</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/UioFiles.html#UioFiles.delete_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#UioFiles.UioFiles.delete_files" title="Permalink to this definition">¶</a></dt>
     869<dd><p>Deletes the files.</p>
     870</dd></dl>
     871
     872</dd></dl>
     873
     874</div>
     875</div>
     876<div class="section" id="modules">
     877<h2><a class="toc-backref" href="#id10">Modules</a><a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h2>
     878<div class="section" id="module-get_mars_data">
     879<span id="get-mars-data"></span><h3><a class="toc-backref" href="#id11">get_mars_data</a><a class="headerlink" href="#module-get_mars_data" title="Permalink to this headline">¶</a></h3>
     880<dl class="function">
     881<dt id="get_mars_data.do_retrievement">
     882<code class="descclassname">get_mars_data.</code><code class="descname">do_retrievement</code><span class="sig-paren">(</span><em>c</em>, <em>server</em>, <em>start</em>, <em>end</em>, <em>delta_t</em>, <em>fluxes=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#do_retrievement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.do_retrievement" title="Permalink to this definition">¶</a></dt>
     883<dd><p>Divides the complete retrieval period in smaller chunks and
     884retrieves the data from MARS.</p>
     885<table class="docutils field-list" frame="void" rules="none">
     886<col class="field-name" />
     887<col class="field-body" />
     888<tbody valign="top">
     889<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     890<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     891command line.</li>
     892<li><strong>server</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">ECMWFService</span></code>) – The server connection to ECMWF.</li>
     893<li><strong>start</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – The start date of the retrieval.</li>
     894<li><strong>end</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – The end date of the retrieval.</li>
     895<li><strong>delta_t</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">datetime</span></code>) – Delta_t + 1 is the maximal time period of a single
     896retrieval.</li>
     897<li><strong>fluxes</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if the flux parameters are to be retrieved or
     898the rest of the parameter list.
     899Default value is False.</li>
     900</ul>
     901</td>
     902</tr>
     903</tbody>
     904</table>
     905</dd></dl>
     906
     907<dl class="function">
     908<dt id="get_mars_data.get_mars_data">
     909<code class="descclassname">get_mars_data.</code><code class="descname">get_mars_data</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#get_mars_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.get_mars_data" title="Permalink to this definition">¶</a></dt>
     910<dd><p>Retrieves the EC data needed for a FLEXPART simulation.</p>
     911<p>Start and end dates for retrieval period is set. Retrievals
     912are divided into smaller periods if necessary and datechunk parameter
     913is set.</p>
     914<table class="docutils field-list" frame="void" rules="none">
     915<col class="field-name" />
     916<col class="field-body" />
     917<tbody valign="top">
     918<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     919command line.</td>
     920</tr>
     921</tbody>
     922</table>
     923</dd></dl>
     924
     925<dl class="function">
     926<dt id="get_mars_data.main">
     927<code class="descclassname">get_mars_data.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/get_mars_data.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.main" title="Permalink to this definition">¶</a></dt>
     928<dd><p>Controls the program to get data out of mars.</p>
     929<p>This is done if it is called directly from command line.
     930Then it also takes program call arguments and control file input.</p>
     931</dd></dl>
     932
     933</div>
     934<div class="section" id="module-prepare_flexpart">
     935<span id="prepare-flexpart"></span><h3><a class="toc-backref" href="#id12">prepare_flexpart</a><a class="headerlink" href="#module-prepare_flexpart" title="Permalink to this headline">¶</a></h3>
     936<dl class="function">
     937<dt id="prepare_flexpart.main">
     938<code class="descclassname">prepare_flexpart.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/prepare_flexpart.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.main" title="Permalink to this definition">¶</a></dt>
     939<dd><p>Controls the program to prepare flexpart input files from mars data.</p>
     940<p>This is done if it is called directly from command line.
     941Then it also takes program call arguments and control file input.</p>
     942</dd></dl>
     943
     944<dl class="function">
     945<dt id="prepare_flexpart.prepare_flexpart">
     946<code class="descclassname">prepare_flexpart.</code><code class="descname">prepare_flexpart</code><span class="sig-paren">(</span><em>ppid</em>, <em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/prepare_flexpart.html#prepare_flexpart"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.prepare_flexpart" title="Permalink to this definition">¶</a></dt>
     947<dd><p>Converts the mars data into flexpart ready input files.</p>
     948<p>Specific data fields are converted to a different grid and the flux
     949data are going to be disaggregated. The data fields are collected by
     950hour and stored in a file with a specific FLEXPART relevant naming
     951convention.</p>
     952<table class="docutils field-list" frame="void" rules="none">
     953<col class="field-name" />
     954<col class="field-body" />
     955<tbody valign="top">
     956<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     957<li><strong>ppid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>) – Contains the ppid number of the current ECMWF job. It will be None if
     958the method was called within this module.</li>
     959<li><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     960command line.</li>
     961</ul>
     962</td>
     963</tr>
     964</tbody>
     965</table>
     966</dd></dl>
     967
     968</div>
     969<div class="section" id="module-tools">
     970<span id="tools"></span><h3><a class="toc-backref" href="#id13">tools</a><a class="headerlink" href="#module-tools" title="Permalink to this headline">¶</a></h3>
     971<dl class="function">
     972<dt id="tools.clean_up">
     973<code class="descclassname">tools.</code><code class="descname">clean_up</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition">¶</a></dt>
     974<dd><p>Remove all files from intermediate directory (inputdir).</p>
     975<table class="docutils field-list" frame="void" rules="none">
     976<col class="field-name" />
     977<col class="field-body" />
     978<tbody valign="top">
     979<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c</strong> (<a class="reference internal" href="#module-ControlFile" title="ControlFile"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ControlFile</span></code></a>) – Contains all the parameters of CONTROL file and
     980command line.</td>
     981</tr>
     982</tbody>
     983</table>
     984</dd></dl>
     985
     986<dl class="function">
     987<dt id="tools.get_cmdline_arguments">
     988<code class="descclassname">tools.</code><code class="descname">get_cmdline_arguments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#get_cmdline_arguments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_cmdline_arguments" title="Permalink to this definition">¶</a></dt>
     989<dd><p>Decomposes the command line arguments and assigns them to variables.
     990Apply default values for non mentioned arguments.</p>
     991<table class="docutils field-list" frame="void" rules="none">
     992<col class="field-name" />
     993<col class="field-body" />
     994<tbody valign="top">
     995<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><strong>args</strong> – Contains the commandline arguments from script/program call.</td>
     996</tr>
     997<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Namespace</span></code></td>
     998</tr>
     999</tbody>
     1000</table>
     1001</dd></dl>
     1002
     1003<dl class="function">
     1004<dt id="tools.get_list_as_string">
     1005<code class="descclassname">tools.</code><code class="descname">get_list_as_string</code><span class="sig-paren">(</span><em>list_obj</em>, <em>concatenate_sign='</em>, <em>'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#get_list_as_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_list_as_string" title="Permalink to this definition">¶</a></dt>
     1006<dd><p>Converts a list of arbitrary content into a single string.</p>
     1007<table class="docutils field-list" frame="void" rules="none">
     1008<col class="field-name" />
     1009<col class="field-body" />
     1010<tbody valign="top">
     1011<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1012<li><strong>list_obj</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code>) – A list with arbitrary content.</li>
     1013<li><strong>concatenate_sign</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – A string which is used to concatenate the single
     1014list elements. Default value is “, “.</li>
     1015</ul>
     1016</td>
     1017</tr>
     1018<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>str_of_list</strong> – The content of the list as a single string.</p>
     1019</td>
     1020</tr>
     1021<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1022</td>
     1023</tr>
     1024</tbody>
     1025</table>
     1026</dd></dl>
     1027
     1028<dl class="function">
     1029<dt id="tools.init128">
     1030<code class="descclassname">tools.</code><code class="descname">init128</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#init128"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.init128" title="Permalink to this definition">¶</a></dt>
     1031<dd><p>Opens and reads the grib file with table 128 information.</p>
     1032<table class="docutils field-list" frame="void" rules="none">
     1033<col class="field-name" />
     1034<col class="field-body" />
     1035<tbody valign="top">
     1036<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filepath</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to file of ECMWF grib table number 128.</td>
     1037</tr>
     1038<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>table128</strong> – Contains the ECMWF grib table 128 information.
     1039The key is the parameter number and the value is the
     1040short name of the parameter.</td>
     1041</tr>
     1042<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code></td>
     1043</tr>
     1044</tbody>
     1045</table>
     1046</dd></dl>
     1047
     1048<dl class="function">
     1049<dt id="tools.make_dir">
     1050<code class="descclassname">tools.</code><code class="descname">make_dir</code><span class="sig-paren">(</span><em>directory</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#make_dir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.make_dir" title="Permalink to this definition">¶</a></dt>
     1051<dd><p>Creates a directory and gives a warning if the directory
     1052already exists. The program stops only if there is another problem.</p>
     1053<table class="docutils field-list" frame="void" rules="none">
     1054<col class="field-name" />
     1055<col class="field-body" />
     1056<tbody valign="top">
     1057<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>directory</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The directory name including the path which should be created.</td>
     1058</tr>
     1059</tbody>
     1060</table>
     1061</dd></dl>
     1062
     1063<dl class="function">
     1064<dt id="tools.my_error">
     1065<code class="descclassname">tools.</code><code class="descname">my_error</code><span class="sig-paren">(</span><em>users</em>, <em>message='ERROR'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#my_error"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.my_error" title="Permalink to this definition">¶</a></dt>
     1066<dd><p>Prints a specified error message which can be passed to the function
     1067before exiting the program.</p>
     1068<table class="docutils field-list" frame="void" rules="none">
     1069<col class="field-name" />
     1070<col class="field-body" />
     1071<tbody valign="top">
     1072<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     1073<li><strong>user</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains all email addresses which should be notified.
     1074It might also contain just the ecmwf user name which wil trigger
     1075mailing to the associated email address for this user.</li>
     1076<li><strong>message</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Error message. Default value is “ERROR”.</li>
     1077</ul>
     1078</td>
     1079</tr>
     1080</tbody>
     1081</table>
     1082</dd></dl>
     1083
     1084<dl class="function">
     1085<dt id="tools.none_or_int">
     1086<code class="descclassname">tools.</code><code class="descname">none_or_int</code><span class="sig-paren">(</span><em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#none_or_int"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_int" title="Permalink to this definition">¶</a></dt>
     1087<dd><p>Converts the input string into pythons None-type if the string
     1088contains string “None”. Otherwise it is converted to an integer value.</p>
     1089<table class="docutils field-list" frame="void" rules="none">
     1090<col class="field-name" />
     1091<col class="field-body" />
     1092<tbody valign="top">
     1093<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – String to be checked for the “None” word.</td>
     1094</tr>
     1095<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Return depends on the content of the input value. If it was “None”,
     1096then the python type None is returned. Otherwise the string is
     1097converted into an integer value.</td>
     1098</tr>
     1099<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">None or int(value)</td>
     1100</tr>
     1101</tbody>
     1102</table>
     1103</dd></dl>
     1104
     1105<dl class="function">
     1106<dt id="tools.none_or_str">
     1107<code class="descclassname">tools.</code><code class="descname">none_or_str</code><span class="sig-paren">(</span><em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#none_or_str"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_str" title="Permalink to this definition">¶</a></dt>
     1108<dd><p>Converts the input string into pythons None-type if the string
     1109contains string “None”.</p>
     1110<table class="docutils field-list" frame="void" rules="none">
     1111<col class="field-name" />
     1112<col class="field-body" />
     1113<tbody valign="top">
     1114<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – String to be checked for the “None” word.</td>
     1115</tr>
     1116<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Return depends on the content of the input value. If it was “None”,
     1117then the python type None is returned. Otherwise the string itself.</td>
     1118</tr>
     1119<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">None or value</td>
     1120</tr>
     1121</tbody>
     1122</table>
     1123</dd></dl>
     1124
     1125<dl class="function">
     1126<dt id="tools.normal_exit">
     1127<code class="descclassname">tools.</code><code class="descname">normal_exit</code><span class="sig-paren">(</span><em>users</em>, <em>message='Done!'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#normal_exit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.normal_exit" title="Permalink to this definition">¶</a></dt>
     1128<dd><p>Prints a specific exit message which can be passed to the function.</p>
     1129<table class="docutils field-list" frame="void" rules="none">
     1130<col class="field-name" />
     1131<col class="field-body" />
     1132<tbody valign="top">
     1133<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
     1134<li><strong>user</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Contains all email addresses which should be notified.
     1135It might also contain just the ecmwf user name which wil trigger
     1136mailing to the associated email address for this user.</li>
     1137<li><strong>message</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Message for exiting program. Default value is “Done!”.</li>
     1138</ul>
     1139</td>
     1140</tr>
     1141</tbody>
     1142</table>
     1143</dd></dl>
     1144
     1145<dl class="function">
     1146<dt id="tools.product">
     1147<code class="descclassname">tools.</code><code class="descname">product</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.product" title="Permalink to this definition">¶</a></dt>
     1148<dd><p>This method combines the single characters of the passed arguments
     1149with each other. So that each character of each argument value
     1150will be combined with each character of the other arguments as a tuple.</p>
     1151<div class="admonition note">
     1152<p class="first admonition-title">Note</p>
     1153<p class="last">This method is taken from an example at the ECMWF wiki website.
     1154<a class="reference external" href="https://software.ecmwf.int/wiki/display/GRIB/index.py">https://software.ecmwf.int/wiki/display/GRIB/index.py</a>; 2018-03-16</p>
     1155</div>
     1156<p class="rubric">Example</p>
     1157<p>product(‘ABCD’, ‘xy’) –&gt; Ax Ay Bx By Cx Cy Dx Dy</p>
     1158<p>product(range(2), repeat = 3) –&gt; 000 001 010 011 100 101 110 111</p>
     1159<table class="docutils field-list" frame="void" rules="none">
     1160<col class="field-name" />
     1161<col class="field-body" />
     1162<tbody valign="top">
     1163<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1164<li><strong>*args</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code>) – Positional arguments (arbitrary number).</li>
     1165<li><strong>**kwds</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code>) – Contains all the keyword arguments from *args.</li>
     1166</ul>
     1167</td>
     1168</tr>
     1169<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>prod</strong> – Return will be done with “yield”. A tuple of combined arguments.
     1170See example in description above.</p>
     1171</td>
     1172</tr>
     1173<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
     1174</td>
     1175</tr>
     1176</tbody>
     1177</table>
     1178</dd></dl>
     1179
     1180<dl class="function">
     1181<dt id="tools.put_file_to_ecserver">
     1182<code class="descclassname">tools.</code><code class="descname">put_file_to_ecserver</code><span class="sig-paren">(</span><em>ecd</em>, <em>filename</em>, <em>target</em>, <em>ecuid</em>, <em>ecgid</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#put_file_to_ecserver"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.put_file_to_ecserver" title="Permalink to this definition">¶</a></dt>
     1183<dd><p>Uses the ecaccess-file-put command to send a file to the ECMWF servers.</p>
     1184<div class="admonition note">
     1185<p class="first admonition-title">Note</p>
     1186<p class="last">The return value is just for testing reasons. It does not have
     1187to be used from the calling function since the whole error handling
     1188is done in here.</p>
     1189</div>
     1190<table class="docutils field-list" frame="void" rules="none">
     1191<col class="field-name" />
     1192<col class="field-body" />
     1193<tbody valign="top">
     1194<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1195<li><strong>ecd</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The path were the file is stored.</li>
     1196<li><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the file to send to the ECMWF server.</li>
     1197<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target queue where the file should be sent to.</li>
     1198<li><strong>ecuid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The user id on ECMWF server.</li>
     1199<li><strong>ecgid</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The group id on ECMWF server.</li>
     1200</ul>
     1201</td>
     1202</tr>
     1203<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>rcode</strong> – Resulting code of command execution. If successful the string
     1204will be empty.</p>
     1205</td>
     1206</tr>
     1207<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1208</td>
     1209</tr>
     1210</tbody>
     1211</table>
     1212</dd></dl>
     1213
     1214<dl class="function">
     1215<dt id="tools.read_ecenv">
     1216<code class="descclassname">tools.</code><code class="descname">read_ecenv</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#read_ecenv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.read_ecenv" title="Permalink to this definition">¶</a></dt>
     1217<dd><p>Reads the file into a dictionary where the key values are the parameter
     1218names.</p>
     1219<table class="docutils field-list" frame="void" rules="none">
     1220<col class="field-name" />
     1221<col class="field-body" />
     1222<tbody valign="top">
     1223<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Path to file where the ECMWF environment parameters are stored.</td>
     1224</tr>
     1225<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>envs</strong> – Contains the environment parameter ecuid, ecgid, gateway
     1226and destination for ECMWF server environments.</td>
     1227</tr>
     1228<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code></td>
     1229</tr>
     1230</tbody>
     1231</table>
     1232</dd></dl>
     1233
     1234<dl class="function">
     1235<dt id="tools.silent_remove">
     1236<code class="descclassname">tools.</code><code class="descname">silent_remove</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#silent_remove"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.silent_remove" title="Permalink to this definition">¶</a></dt>
     1237<dd><p>Remove file if it exists.
     1238The function does not fail if the file does not exist.</p>
     1239<table class="docutils field-list" frame="void" rules="none">
     1240<col class="field-name" />
     1241<col class="field-body" />
     1242<tbody valign="top">
     1243<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the file to be removed without notification.</td>
     1244</tr>
     1245</tbody>
     1246</table>
     1247</dd></dl>
     1248
     1249<dl class="function">
     1250<dt id="tools.submit_job_to_ecserver">
     1251<code class="descclassname">tools.</code><code class="descname">submit_job_to_ecserver</code><span class="sig-paren">(</span><em>target</em>, <em>jobname</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#submit_job_to_ecserver"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.submit_job_to_ecserver" title="Permalink to this definition">¶</a></dt>
     1252<dd><p>Uses ecaccess-job-submit command to submit a job to the ECMWF server.</p>
     1253<div class="admonition note">
     1254<p class="first admonition-title">Note</p>
     1255<p class="last">The return value is just for testing reasons. It does not have
     1256to be used from the calling function since the whole error handling
     1257is done in here.</p>
     1258</div>
     1259<table class="docutils field-list" frame="void" rules="none">
     1260<col class="field-name" />
     1261<col class="field-body" />
     1262<tbody valign="top">
     1263<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1264<li><strong>target</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The target where the file should be sent to, e.g. the queue.</li>
     1265<li><strong>jobname</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – The name of the jobfile to be submitted to the ECMWF server.</li>
     1266</ul>
     1267</td>
     1268</tr>
     1269<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>rcode</strong> – Resulting code of command execution. If successful the string
     1270will contain an integer number, representing the id of the job
     1271at the ecmwf server.</p>
     1272</td>
     1273</tr>
     1274<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code></p>
     1275</td>
     1276</tr>
     1277</tbody>
     1278</table>
     1279</dd></dl>
     1280
     1281<dl class="function">
     1282<dt id="tools.to_param_id">
     1283<code class="descclassname">tools.</code><code class="descname">to_param_id</code><span class="sig-paren">(</span><em>pars</em>, <em>table</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tools.html#to_param_id"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.to_param_id" title="Permalink to this definition">¶</a></dt>
     1284<dd><p>Transform parameter names to parameter ids with ECMWF grib table 128.</p>
     1285<table class="docutils field-list" frame="void" rules="none">
     1286<col class="field-name" />
     1287<col class="field-body" />
     1288<tbody valign="top">
     1289<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     1290<li><strong>pars</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>) – Addpar argument from CONTROL file in the format of
     1291parameter names instead of ids. The parameter short
     1292names are sepearted with “/” and they are passed as
     1293one single string.</li>
     1294<li><strong>table</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dictionary</span></code>) – Contains the ECMWF grib table 128 information.
     1295The key is the parameter number and the value is the
     1296short name of the parameter.</li>
     1297</ul>
     1298</td>
     1299</tr>
     1300<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>ipar</strong> – List of addpar parameters from CONTROL file transformed to
     1301parameter ids in the format of integer.</p>
     1302</td>
     1303</tr>
     1304<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">integer</span></code></p>
     1305</td>
     1306</tr>
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     1310
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    2741429
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    160165<blockquote>
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    162210<h2 id="D">D</h2>
    163211<table style="width: 100%" class="indextable genindextable"><tr>
     
    165213      <li><a href="api.html#disaggregation.dapoly">dapoly() (in module disaggregation)</a>
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    167   </ul></td>
    168   <td style="width: 33%; vertical-align: top;"><ul>
    169215      <li><a href="api.html#disaggregation.darain">darain() (in module disaggregation)</a>
    170216</li>
     217      <li><a href="api.html#MarsRetrieval.MarsRetrieval.data_retrieve">data_retrieve() (MarsRetrieval.MarsRetrieval method)</a>
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     226</li>
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    172228</li>
     229      <li><a href="api.html#MarsRetrieval.MarsRetrieval.display_info">display_info() (MarsRetrieval.MarsRetrieval method)</a>
     230</li>
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     232</li>
     233  </ul></td>
     234</tr></table>
     235
     236<h2 id="E">E</h2>
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     240
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     247
     248<h2 id="G">G</h2>
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     254</li>
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     256</li>
     257      <li><a href="api.html#tools.get_list_as_string">get_list_as_string() (in module tools)</a>
     258</li>
     259  </ul></td>
     260  <td style="width: 33%; vertical-align: top;"><ul>
     261      <li><a href="api.html#module-get_mars_data">get_mars_data (module)</a>
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     263      <li><a href="api.html#get_mars_data.get_mars_data">get_mars_data() (in module get_mars_data)</a>
     264</li>
     265      <li><a href="api.html#GribTools.GribTools">GribTools (class in GribTools)</a>
     266
     267      <ul>
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     269</li>
     270      </ul></li>
    173271  </ul></td>
    174272</tr></table>
     
    178276  <td style="width: 33%; vertical-align: top;"><ul>
    179277      <li><a href="api.html#disaggregation.IA3">IA3() (in module disaggregation)</a>
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     279      <li><a href="api.html#GribTools.GribTools.index">index() (GribTools.GribTools method)</a>
     280</li>
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     282  <td style="width: 33%; vertical-align: top;"><ul>
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     286</li>
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     288</li>
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     291
     292<h2 id="M">M</h2>
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     294  <td style="width: 33%; vertical-align: top;"><ul>
     295      <li><a href="api.html#get_mars_data.main">main() (in module get_mars_data)</a>
     296
     297      <ul>
     298        <li><a href="api.html#install.main">(in module install)</a>
     299</li>
     300        <li><a href="api.html#prepare_flexpart.main">(in module prepare_flexpart)</a>
     301</li>
     302        <li><a href="api.html#submit.main">(in module submit)</a>
     303</li>
     304      </ul></li>
     305      <li><a href="api.html#install.make_convert_build">make_convert_build() (in module install)</a>
     306</li>
     307      <li><a href="api.html#tools.make_dir">make_dir() (in module tools)</a>
     308</li>
     309  </ul></td>
     310  <td style="width: 33%; vertical-align: top;"><ul>
     311      <li><a href="api.html#MarsRetrieval.MarsRetrieval">MarsRetrieval (class in MarsRetrieval)</a>
     312
     313      <ul>
     314        <li><a href="api.html#module-MarsRetrieval">(module)</a>
     315</li>
     316      </ul></li>
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     318</li>
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     320</li>
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     322</li>
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     326</li>
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     329
     330<h2 id="N">N</h2>
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     333      <li><a href="api.html#tools.none_or_int">none_or_int() (in module tools)</a>
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     337      <li><a href="api.html#tools.none_or_str">none_or_str() (in module tools)</a>
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     340</li>
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     344<h2 id="P">P</h2>
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     350</li>
     351      <li><a href="api.html#EcFlexpart.EcFlexpart.prepare_fp_files">prepare_fp_files() (EcFlexpart.EcFlexpart method)</a>
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     358</li>
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     362</li>
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     364</li>
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     368<h2 id="R">R</h2>
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     376</li>
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     380<h2 id="S">S</h2>
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     394</li>
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     398<h2 id="T">T</h2>
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     423      <li><a href="api.html#install.un_tarball">un_tarball() (in module install)</a>
     424</li>
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     428<h2 id="W">W</h2>
     429<table style="width: 100%" class="indextable genindextable"><tr>
     430  <td style="width: 33%; vertical-align: top;"><ul>
     431      <li><a href="api.html#EcFlexpart.EcFlexpart.write_namelist">write_namelist() (EcFlexpart.EcFlexpart method)</a>
    180432</li>
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  • documentation/Sphinx/build/html/index.html

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    1010 
    11   <title>Welcome to flex_extract’s documentation! &mdash; flex_extract 7.1 alpha documentation</title>
     11  <title>Welcome to flex_extract’s user documentation! &mdash; flex_extract 7.1 alpha documentation</title>
    1212 
    1313
     
    135135      <li><a href="#">Docs</a> &raquo;</li>
    136136       
    137       <li>Welcome to flex_extract’s documentation!</li>
     137      <li>Welcome to flex_extract’s user documentation!</li>
    138138   
    139139   
     
    154154           <div itemprop="articleBody">
    155155           
    156   <div class="section" id="welcome-to-flex-extract-s-documentation">
    157 <h1>Welcome to flex_extract’s documentation!<a class="headerlink" href="#welcome-to-flex-extract-s-documentation" title="Permalink to this headline">¶</a></h1>
     156  <div class="section" id="welcome-to-flex-extract-s-user-documentation">
     157<h1>Welcome to flex_extract’s user documentation!<a class="headerlink" href="#welcome-to-flex-extract-s-user-documentation" title="Permalink to this headline">¶</a></h1>
     158<p>flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.</p>
     159<p>All required second party software and libraries used within flex_extract is open source and free of charge.</p>
    158160<table style="width:100%;">
    159161  <tr>
     
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    156163<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
    157 <p>Describe installation process flex_extract ….</p>
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    159165<div>UNDER CONSTRUCTION</div></blockquote>
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    155164  <div class="section" id="requirements">
    156165<h1>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h1>
    157 <p>Describe the requirements to use flex_extract ….</p>
    158166<blockquote>
    159167<div>UNDER CONSTRUCTION</div></blockquote>
     
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     91<li class="toctree-l2"><a class="reference internal" href="user_guide/how_to.html">How to use flex_extract</a></li>
     92<li class="toctree-l2"><a class="reference internal" href="user_guide/control_templates.html">CONTROL-file templates</a></li>
     93</ul>
     94</li>
    9195<li class="toctree-l1"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
    9296<li class="toctree-l1"><a class="reference internal" href="support.html">Support</a></li>
     
    157161  <div class="section" id="user-guide">
    158162<h1>User Guide<a class="headerlink" href="#user-guide" title="Permalink to this headline">¶</a></h1>
    159 <p>Describe using flex_extract ….</p>
    160163<blockquote>
    161164<div>UNDER CONSTRUCTION</div></blockquote>
     165<div class="toctree-wrapper compound">
     166</div>
    162167</div>
    163168
     
    170175    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
    171176     
    172         <a href="api.html" class="btn btn-neutral float-right" title="Auto Generated Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
    173      
    174      
    175         <a href="program_structure.html" class="btn btn-neutral" title="Program Structure" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
     177        <a href="user_guide/how_to.html" class="btn btn-neutral float-right" title="How to use flex_extract" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
     178     
     179     
     180        <a href="program_structure/prog_flow.html" class="btn btn-neutral" title="Program Flow" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
    176181     
    177182    </div>
  • documentation/Sphinx/source/api.rst

    r708c667 r274f9ef  
    22============================
    33
     4.. contents::
     5    :local:
     6   
     7Porgrams
     8--------
     9
     10install
     11*******
     12
     13.. automodule:: install
     14    :members:
     15   
     16submit
     17******
     18
     19.. automodule:: submit
     20    :members:
     21   
     22Classes
     23-------
     24
     25ControlFile
     26***********
     27
     28.. automodule:: ControlFile
     29    :members:
     30   
     31EcFlexpart
     32**********
     33
     34.. automodule:: EcFlexpart
     35    :members:
     36   
     37GribTools
     38*********
     39
     40.. automodule:: GribTools
     41    :members:
     42
     43MarsRetrieval
     44*************
     45
     46.. automodule:: MarsRetrieval
     47    :members:
     48
     49UioFiles
     50********
     51
     52.. automodule:: UioFiles
     53    :members:
     54
     55
     56
     57Modules
     58-------
     59
     60get_mars_data
     61*************
     62
     63.. automodule:: get_mars_data
     64    :members:
     65 
     66prepare_flexpart
     67****************
     68
     69.. automodule:: prepare_flexpart
     70    :members:   
     71   
     72tools
     73*****
     74
     75.. automodule:: tools
     76    :members:
     77
     78disaggregation
     79**************   
     80   
    481.. automodule:: disaggregation
    582    :members:
  • documentation/Sphinx/source/downloads.rst

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    downloads/tar_balls
     13    downloads/git_repo
     14    downloads/history_changes
     15   
  • documentation/Sphinx/source/index.rst

    r708c667 r274f9ef  
    44   contain the root `toctree` directive.
    55
    6 Welcome to flex_extract's documentation!
    7 ========================================
     6Welcome to flex_extract's user documentation!
     7=============================================
     8
     9flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.
     10
     11
     12.. The scripts can be 1) executed locally using the ECMWF WebMARS interface, or 2) on the ECMWF member
     13.. state gateway server or HPC facility using the ecaccess software package. As another option the scripts can 3)
     14.. also be triggered using ecflow scheduling software used by ECMWF for data dissemination.
     15
     16All required second party software and libraries used within flex_extract is open source and free of charge.
     17
    818.. raw:: html
    919
     
    8797
    8898.. toctree::
    89    :maxdepth: 2
     99   :maxdepth: 3
    90100   :caption: Table of Contents:
    91101
  • documentation/Sphinx/source/installation.rst

    r708c667 r274f9ef  
    11Installation
    22============
    3 
    4 Describe installation process flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    installation/requirements
     11    installation/oper_modes
     12    installation/test_install
     13
     14
     15   
  • documentation/Sphinx/source/program_structure.rst

    r708c667 r274f9ef  
    55 
    66    UNDER CONSTRUCTION
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    program_structure/prog_overview
     13    program_structure/prog_components
     14    program_structure/prog_flow
  • documentation/Sphinx/source/support.rst

    r708c667 r274f9ef  
    22=======
    33
    4 Describe support options ....
    54 
    65    UNDER CONSTRUCTION
     6   
     7   
     8.. toctree::
     9    :hidden:
     10    :maxdepth: 2
     11   
     12    support/ticket_system
     13    support/mailing_list
     14    support/known_bugs_issues
     15    support/faq
     16       
  • documentation/Sphinx/source/user_guide.rst

    r708c667 r274f9ef  
    11User Guide
    22==========
    3 
    4 Describe using flex_extract ....
    53 
    64    UNDER CONSTRUCTION
     5   
     6.. toctree::
     7    :hidden:
     8    :maxdepth: 2
     9   
     10    user_guide/how_to
     11    user_guide/control_templates
     12   
  • source/python/classes/ControlFile.py

    r708c667 r274f9ef  
    7171
    7272    def __init__(self, filename):
    73         '''
    74         @Description:
    75             Initialises the instance of ControlFile class and defines
    76             all class attributes with default values. Afterwards calls
    77             function __read_controlfile__ to read parameter from
    78             Control file.
    79 
    80         @Input:
    81             self: instance of ControlFile class
    82                 Description see class documentation.
    83 
    84             filename: string
    85                 Name of CONTROL file.
    86 
    87         @Return:
    88             <nothing>
     73        '''Initialises the instance of ControlFile class and defines
     74        all class attributes with default values. Afterwards calls
     75        function __read_controlfile__ to read parameter from Control file.
     76
     77        Parameters
     78        ----------
     79        filename : :obj:`string`
     80            Name of CONTROL file.
     81
     82        Return
     83        ------
     84
    8985        '''
    9086
     
    162158
    163159    def __read_controlfile__(self):
    164         '''
    165         @Description:
    166             Read CONTROL file and assign all CONTROL file variables.
    167 
    168         @Input:
    169             self: instance of ControlFile class
    170                 Description see class documentation.
    171 
    172         @Return:
    173             <nothing>
     160        '''Read CONTROL file and assign all CONTROL file variables.
     161
     162        Parameters
     163        ----------
     164
     165        Return
     166        ------
     167
    174168        '''
    175169
     
    235229
    236230    def __str__(self):
    237         '''
    238         @Description:
    239             Prepares a string which have all the ControlFile
    240             class attributes with its associated values.
    241             Each attribute is printed in one line and in
    242             alphabetical order.
    243 
    244             Example:
    245             'age': 10
    246             'color': 'Spotted'
    247             'kids': 0
    248             'legs': 2
    249             'name': 'Dog'
    250             'smell': 'Alot'
    251 
    252         @Input:
    253             self: instance of ControlFile class
    254                 Description see class documentation.
    255 
    256         @Return:
    257             string of ControlFile class attributes with their values
     231        '''Prepares a string which have all the ControlFile class attributes
     232        with its associated values. Each attribute is printed in one line and
     233        in alphabetical order.
     234
     235        Example
     236        -------
     237        'age': 10
     238        'color': 'Spotted'
     239        'kids': 0
     240        'legs': 2
     241        'name': 'Dog'
     242        'smell': 'Alot'
     243
     244        Parameters
     245        ----------
     246
     247        Return
     248        ------
     249        string
     250            Single string of concatenated ControlFile class attributes
     251            with their values
    258252        '''
    259253        import collections
     
    265259
    266260    def assign_args_to_control(self, args):
    267         '''
    268         @Description:
    269             Overwrites the existing ControlFile instance attributes with
    270             the command line arguments.
    271 
    272         @Input:
    273             self: instance of ControlFile class
    274                 Description see class documentation.
    275 
    276             args: instance of ArgumentParser
    277                 Contains the commandline arguments from script/program call.
    278 
    279         @Return:
    280             <nothing>
     261        '''Overwrites the existing ControlFile instance attributes with
     262        the command line arguments.
     263
     264        Parameters
     265        ----------
     266        args : :obj:`Namespace`
     267            Contains the commandline arguments from script/program call.
     268
     269        Return
     270        ------
     271
    281272        '''
    282273
     
    294285
    295286    def assign_envs_to_control(self, envs):
    296         '''
    297         @Description:
    298             Assigns the ECMWF environment parameter.
    299 
    300         @Input:
    301             envs: dict of strings
    302                 Contains the ECMWF environment parameternames "ECUID", "ECGID",
    303                 "DESTINATION" and "GATEWAY" with its corresponding values.
    304                 They were read from the file "ECMWF_ENV".
    305 
    306         @Return:
    307             <nothing>
     287        '''Assigns the ECMWF environment parameter.
     288
     289        Parameters
     290        ----------
     291        envs : :obj:`dictionary` of :obj:`strings`
     292            Contains the ECMWF environment parameternames "ECUID", "ECGID",
     293            "DESTINATION" and "GATEWAY" with its corresponding values.
     294            They were read from the file "ECMWF_ENV".
     295
     296        Return
     297        ------
     298
    308299        '''
    309300
     
    314305
    315306    def check_conditions(self, queue):
    316         '''
    317         @Description:
    318             Checks a couple of necessary attributes and conditions,
    319             such as if they exist and contain values.
    320             Otherwise set default values.
    321 
    322         @Input:
    323             self: instance of ControlFile class
    324                 Description see class documentation.
    325 
    326             queue: string
    327                 Name of the queue if submitted to the ECMWF servers.
    328                 Used to check if ecuid, ecgid, gateway and destination
    329                 are set correctly and are not empty.
    330 
    331         @Return:
    332             <nothing>
     307        '''Checks a couple of necessary attributes and conditions,
     308        such as if they exist and contain values.
     309        Otherwise set default values.
     310
     311        Parameters
     312        ----------
     313        queue : :obj:`string`
     314            Name of the queue if submitted to the ECMWF servers.
     315            Used to check if ecuid, ecgid, gateway and destination
     316            are set correctly and are not empty.
     317
     318        Return
     319        ------
     320
    333321        '''
    334322        from mods.tools import my_error
     
    501489
    502490    def check_install_conditions(self):
    503         '''
    504         @Description:
    505             Checks a couple of necessary attributes and conditions
    506             for the installation such as if they exist and contain values.
    507             Otherwise set default values.
    508 
    509         @Input:
    510             self: instance of ControlFile class
    511                 Description see class documentation.
    512 
    513         @Return:
    514             <nothing>
     491        '''Checks a couple of necessary attributes and conditions
     492        for the installation such as if they exist and contain values.
     493        Otherwise set default values.
     494
     495        Parameters
     496        ----------
     497
     498        Return
     499        ------
     500
    515501        '''
    516502
     
    549535
    550536    def to_list(self):
    551         '''
    552         @Description:
    553             Just generates a list of strings containing the attributes and
    554             assigned values except the attributes "_expanded", "exedir",
     537        '''Just generates a list of strings containing the attributes and
     538        assigned values except the attributes "_expanded", "exedir",
     539        "ecmwfdatadir" and "flexpart_root_scripts".
     540
     541        Parameters
     542        ----------
     543
     544        Return
     545        ------
     546        l : :obj:`list`
     547            A sorted list of the all ControlFile class attributes with
     548            their values except the attributes "_expanded", "exedir",
    555549            "ecmwfdatadir" and "flexpart_root_scripts".
    556 
    557         @Input:
    558             self: instance of ControlFile class
    559                 Description see class documentation.
    560 
    561         @Return:
    562             l: list
    563                 A sorted list of the all ControlFile class attributes with
    564                 their values except the attributes "_expanded", "exedir",
    565                 "ecmwfdatadir" and "flexpart_root_scripts".
    566550        '''
    567551
  • source/python/classes/EcFlexpart.py

    r0934db1 r274f9ef  
    111111    # --------------------------------------------------------------------------
    112112    def __init__(self, c, fluxes=False):
    113         '''
    114         @Description:
    115             Creates an object/instance of EcFlexpart with the
    116             associated settings of its attributes for the retrieval.
    117 
    118         @Input:
    119             self: instance of EcFlexpart
    120                 The current object of the class.
    121 
    122             c: instance of class ControlFile
    123                 Contains all the parameters of CONTROL file and
    124                 command line.
    125                 For more information about format and content of the parameter
    126                 see documentation.
    127 
    128             fluxes: boolean, optional
    129                 Decides if the flux parameter settings are stored or
    130                 the rest of the parameter list.
    131                 Default value is False.
    132 
    133         @Return:
    134             <nothing>
     113        '''Creates an object/instance of EcFlexpart with the associated
     114        settings of its attributes for the retrieval.
     115
     116        Parameters:
     117        -----------
     118        c : :obj:`ControlFile`
     119            Contains all the parameters of CONTROL file and
     120            command line.
     121
     122        fluxes : :obj:`boolean`, optional
     123            Decides if the flux parameter settings are stored or
     124            the rest of the parameter list.
     125            Default value is False.
     126
     127        Return
     128        ------
     129
    135130        '''
    136131        # set a counter for the number of mars requests generated
     
    306301
    307302    def _mk_targetname(self, ftype, param, date):
    308         '''
    309         @Description:
    310             Creates the filename for the requested grib data to be stored in.
    311             This name is passed as the "target" parameter in the request.
    312 
    313         @Input:
    314             ftype: string
    315                 Shortcut name of the type of the field. E.g. AN, FC, PF, ...
    316 
    317             param: string
    318                 Shortcut of the grid type. E.g. SH__ML, SH__SL, GG__ML,
    319                 GG__SL, OG__ML, OG__SL, OG_OROLSM_SL, OG_acc_SL
    320 
    321             date: string
    322                 The date period of the grib data to be stored in this file.
    323 
    324         @Return:
    325             targetname: string
    326                 The target filename for the grib data.
     303        '''Creates the filename for the requested grib data to be stored in.
     304        This name is passed as the "target" parameter in the request.
     305
     306        Parameters
     307        ----------
     308        ftype : :obj:`string`
     309            Shortcut name of the type of the field. E.g. AN, FC, PF, ...
     310
     311        param : :obj:`string`
     312            Shortcut of the grid type. E.g. SH__ML, SH__SL, GG__ML,
     313            GG__SL, OG__ML, OG__SL, OG_OROLSM_SL, OG_acc_SL
     314
     315        date : :obj:`string`
     316            The date period of the grib data to be stored in this file.
     317
     318        Return
     319        ------
     320        targetname : :obj:`string`
     321            The target filename for the grib data.
    327322        '''
    328323        targetname = (self.inputdir + '/' + ftype + param + '.' + date + '.' +
     
    333328
    334329    def _start_retrievement(self, request, par_dict):
    335         '''
    336         @Description:
    337             Creates the Mars Retrieval and prints or submits the request
    338             depending on the status of the request variable.
    339 
    340         @Input:
    341             self: instance of EcFlexpart
    342                 The current object of the class.
    343 
    344             request: integer
    345                 Selects the mode of retrieval.
    346                 0: Retrieves the data from ECMWF.
    347                 1: Prints the mars requests to an output file.
    348                 2: Retrieves the data and prints the mars request.
    349 
    350             par_dict: dictionary
    351                 Contains all parameter which have to be set for creating the
    352                 Mars Retrievals. The parameter are:
    353                 marsclass, dataset, stream, type, levtype, levelist, resol,
    354                 gaussian, accuracy, grid, target, area, date, time, number,
    355                 step, expver, param
    356 
    357         @Return:
    358             <nothing>
     330        '''Creates the Mars Retrieval and prints or submits the request
     331        depending on the status of the request variable.
     332
     333        Parameters
     334        ----------
     335        request : :obj:`integer`
     336            Selects the mode of retrieval.
     337            0: Retrieves the data from ECMWF.
     338            1: Prints the mars requests to an output file.
     339            2: Retrieves the data and prints the mars request.
     340
     341        par_dict : :obj:`dictionary`
     342            Contains all parameter which have to be set for creating the
     343            Mars Retrievals. The parameter are:
     344            marsclass, dataset, stream, type, levtype, levelist, resol,
     345            gaussian, accuracy, grid, target, area, date, time, number,
     346            step, expver, param
     347
     348        Return
     349        ------
     350
    359351        '''
    360352        # increase number of mars requests
     
    398390
    399391    def _mk_index_values(self, inputdir, inputfiles, keys):
    400         '''
    401         @Description:
    402             Creates an index file for a set of grib parameter keys.
    403             The values from the index keys are returned in a list.
    404 
    405         @Input:
    406             keys: dictionary
    407                 List of parameter names which serves as index.
    408 
    409             inputfiles: instance of UioFiles
    410                 Contains a list of files.
    411 
    412         @Return:
    413             iid: grib_index
    414                 This is a grib specific index structure to access
    415                 messages in a file.
    416 
    417             index_vals: list
    418                 Contains the values from the keys used for a distinct selection
    419                 of grib messages in processing  the grib files.
    420                 Content looks like e.g.:
    421                 index_vals[0]: ('20171106', '20171107', '20171108') ; date
    422                 index_vals[1]: ('0', '1200', '1800', '600') ; time
    423                 index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange
     392        '''Creates an index file for a set of grib parameter keys.
     393        The values from the index keys are returned in a list.
     394
     395        Parameters
     396        ----------
     397        keys : :obj:`dictionary`
     398            List of parameter names which serves as index.
     399
     400        inputfiles : :obj:`UioFiles`
     401            Contains a list of files.
     402
     403        Return
     404        ------
     405        iid : :obj:`grib_index`
     406            This is a grib specific index structure to access
     407            messages in a file.
     408
     409        index_vals : :obj:`list`
     410            Contains the values from the keys used for a distinct selection
     411            of grib messages in processing  the grib files.
     412            Content looks like e.g.:
     413            index_vals[0]: ('20171106', '20171107', '20171108') ; date
     414            index_vals[1]: ('0', '1200', '1800', '600') ; time
     415            index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange
    424416        '''
    425417        iid = None
     
    455447
    456448    def retrieve(self, server, dates, public, request, inputdir='.'):
    457         '''
    458         @Description:
    459             Finalizing the retrieval information by setting final details
    460             depending on grid type.
    461             Prepares MARS retrievals per grid type and submits them.
    462 
    463         @Input:
    464             self: instance of EcFlexpart
    465                 The current object of the class.
    466 
    467             server: instance of ECMWFService or ECMWFDataServer
    468                 The connection to the ECMWF server. This is different
    469                 for member state users which have full access and non
    470                 member state users which have only access to the public
    471                 data sets. The decision is made from command line argument
    472                 "public"; for public access its True (ECMWFDataServer)
    473                 for member state users its False (ECMWFService)
    474 
    475             dates: string
    476                 Contains start and end date of the retrieval in the format
    477                 "YYYYMMDD/to/YYYYMMDD"
    478 
    479             request: integer
    480                 Selects the mode of retrieval.
    481                 0: Retrieves the data from ECMWF.
    482                 1: Prints the mars requests to an output file.
    483                 2: Retrieves the data and prints the mars request.
    484 
    485             inputdir: string, optional
    486                 Path to the directory where the retrieved data is about
    487                 to be stored. The default is the current directory ('.').
    488 
    489         @Return:
    490             <nothing>
     449        '''Finalizing the retrieval information by setting final details
     450        depending on grid type.
     451        Prepares MARS retrievals per grid type and submits them.
     452
     453        Parameters
     454        ----------
     455        server : :obj:`ECMWFService` or :obj:`ECMWFDataServer`
     456            The connection to the ECMWF server. This is different
     457            for member state users which have full access and non
     458            member state users which have only access to the public
     459            data sets. The decision is made from command line argument
     460            "public"; for public access its True (ECMWFDataServer)
     461            for member state users its False (ECMWFService)
     462
     463        dates : :obj:`string`
     464            Contains start and end date of the retrieval in the format
     465            "YYYYMMDD/to/YYYYMMDD"
     466
     467        request : :obj:`integer`
     468            Selects the mode of retrieval.
     469            0: Retrieves the data from ECMWF.
     470            1: Prints the mars requests to an output file.
     471            2: Retrieves the data and prints the mars request.
     472
     473        inputdir : :obj:`string`, optional
     474            Path to the directory where the retrieved data is about
     475            to be stored. The default is the current directory ('.').
     476
     477        Return
     478        ------
     479
    491480        '''
    492481        self.dates = dates
     
    665654
    666655    def write_namelist(self, c):
    667         '''
    668         @Description:
    669             Creates a namelist file in the temporary directory and writes
    670             the following values to it: maxl, maxb, mlevel,
    671             mlevelist, mnauf, metapar, rlo0, rlo1, rla0, rla1,
    672             momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta
    673 
    674         @Input:
    675             self: instance of EcFlexpart
    676                 The current object of the class.
    677 
    678             c: instance of class ControlFile
    679                 Contains all the parameters of CONTROL file and
    680                 command line.
    681                 For more information about format and content of the parameter
    682                 see documentation.
    683 
    684             filename: string
     656        '''Creates a namelist file in the temporary directory and writes
     657        the following values to it: maxl, maxb, mlevel,
     658        mlevelist, mnauf, metapar, rlo0, rlo1, rla0, rla1,
     659        momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta
     660
     661        Parameters
     662        ----------
     663        c : :obj:`ControlFile`
     664            Contains all the parameters of CONTROL file and
     665            command line.
     666
     667        filename : :obj:`string`
    685668                Name of the namelist file.
    686669
    687         @Return:
    688             <nothing>
     670        Return
     671        ------
     672
    689673        '''
    690674
     
    734718
    735719    def deacc_fluxes(self, inputfiles, c):
    736         '''
    737         @Description:
    738             Goes through all flux fields in ordered time and de-accumulate
    739             the fields. Afterwards the fields are disaggregated in time.
    740             Different versions of disaggregation is provided for rainfall
    741             data (darain, modified linear) and the surface fluxes and
    742             stress data (dapoly, cubic polynomial).
    743 
    744         @Input:
    745             self: instance of EcFlexpart
    746                 The current object of the class.
    747 
    748             inputfiles: instance of UioFiles
    749                 Contains a list of files.
    750 
    751             c: instance of class ControlFile
    752                 Contains all the parameters of CONTROL file and
    753                 command line.
    754                 For more information about format and content of the parameter
    755                 see documentation.
    756 
    757         @Return:
    758             <nothing>
     720        '''Goes through all flux fields in ordered time and de-accumulate
     721        the fields. Afterwards the fields are disaggregated in time.
     722        Different versions of disaggregation is provided for rainfall
     723        data (darain, modified linear) and the surface fluxes and
     724        stress data (dapoly, cubic polynomial).
     725
     726        Parameters
     727        ----------
     728        inputfiles : :obj:`UioFiles`
     729            Contains a list of files.
     730
     731        c : :obj:`ControlFile`
     732            Contains all the parameters of CONTROL file and
     733            command line.
     734
     735        Return
     736        ------
     737
    759738        '''
    760739
     
    952931
    953932    def create(self, inputfiles, c):
    954         '''
    955         @Description:
    956             This method is based on the ECMWF example index.py
    957             https://software.ecmwf.int/wiki/display/GRIB/index.py
    958 
    959             An index file will be created which depends on the combination
    960             of "date", "time" and "stepRange" values. This is used to iterate
    961             over all messages in each grib file which were passed through the
    962             parameter "inputfiles" to seperate specific parameters into fort.*
    963             files. Afterwards the FORTRAN program is called to convert
    964             the data fields all to the same grid and put them in one file
    965             per unique time step (combination of "date", "time" and
    966             "stepRange").
    967 
    968         @Input:
    969             self: instance of EcFlexpart
    970                 The current object of the class.
    971 
    972             inputfiles: instance of UioFiles
    973                 Contains a list of files.
    974 
    975             c: instance of class ControlFile
    976                 Contains all the parameters of CONTROL file and
    977                 command line.
    978                 For more information about format and content of the parameter
    979                 see documentation.
    980 
    981         @Return:
    982             <nothing>
     933        '''An index file will be created which depends on the combination
     934        of "date", "time" and "stepRange" values. This is used to iterate
     935        over all messages in each grib file which were passed through the
     936        parameter "inputfiles" to seperate specific parameters into fort.*
     937        files. Afterwards the FORTRAN program is called to convert
     938        the data fields all to the same grid and put them in one file
     939        per unique time step (combination of "date", "time" and
     940        "stepRange").
     941
     942        Note
     943        ----
     944        This method is based on the ECMWF example index.py
     945        https://software.ecmwf.int/wiki/display/GRIB/index.py
     946
     947        Parameters
     948        ----------
     949        inputfiles : :obj:`UioFiles`
     950            Contains a list of files.
     951
     952        c : :obj:`ControlFile`
     953            Contains all the parameters of CONTROL file and
     954            command line.
     955
     956        Return
     957        ------
     958
    983959        '''
    984960
     
    11831159
    11841160    def process_output(self, c):
    1185         '''
    1186         @Description:
    1187             The grib files are postprocessed depending on the selection in
    1188             CONTROL file. The resulting files are moved to the output
    1189             directory if its not equal to the input directory.
    1190             The following modifications might be done if
    1191             properly switched in CONTROL file:
    1192             GRIB2 - Conversion to GRIB2
    1193             ECTRANS - Transfer of files to gateway server
    1194             ECSTORAGE - Storage at ECMWF server
    1195 
    1196         @Input:
    1197             self: instance of EcFlexpart
    1198                 The current object of the class.
    1199 
    1200             c: instance of class ControlFile
    1201                 Contains all the parameters of CONTROL file and
    1202                 command line.
    1203                 For more information about format and content of the parameter
    1204                 see documentation.
    1205 
    1206         @Return:
    1207             <nothing>
     1161        '''The grib files are postprocessed depending on the selection in
     1162        CONTROL file. The resulting files are moved to the output
     1163        directory if its not equal to the input directory.
     1164        The following modifications might be done if
     1165        properly switched in CONTROL file:
     1166        GRIB2 - Conversion to GRIB2
     1167        ECTRANS - Transfer of files to gateway server
     1168        ECSTORAGE - Storage at ECMWF server
     1169
     1170        Parameters
     1171        ----------
     1172        c : :obj:`ControlFile`
     1173            Contains all the parameters of CONTROL file and
     1174            command line.
     1175
     1176        Return
     1177        ------
    12081178
    12091179        '''
     
    12471217
    12481218    def prepare_fp_files(self, c):
    1249         '''
    1250         @Description:
    1251             Conversion of GRIB files to FLEXPART binary format.
    1252 
    1253         @Input:
    1254             c: instance of class ControlFile
    1255                 Contains all the parameters of CONTROL file and
    1256                 command line.
    1257                 For more information about format and content of the parameter
    1258                 see documentation.
    1259 
    1260 
    1261         @Return:
    1262             <nothing>
     1219        '''Conversion of GRIB files to FLEXPART binary format.
     1220
     1221        Parameters
     1222        ----------
     1223        c : :obj:`ControlFile`
     1224            Contains all the parameters of CONTROL file and
     1225            command line.
     1226
     1227        Return
     1228        ------
     1229
    12631230        '''
    12641231        # generate AVAILABLE file
  • source/python/classes/GribTools.py

    r0934db1 r274f9ef  
    6666    # --------------------------------------------------------------------------
    6767    def __init__(self, filenames):
    68         '''
    69         @Description:
    70             Initialise an object of GribTools and assign a list
    71             of filenames.
    72 
    73         @Input:
    74             filenames: list of strings
    75                 A list of filenames.
    76 
    77         @Return:
    78             <nothing>
     68        '''Initialise an object of GribTools and assign a list of filenames.
     69
     70        Parameters
     71        ----------
     72        filenames : :obj:`list` of :obj:`strings`
     73             A list of filenames.
     74
     75        Return
     76        ------
     77
    7978        '''
    8079
     
    8584
    8685    def get_keys(self, keynames, wherekeynames=[], wherekeyvalues=[]):
    87         '''
    88         @Description:
    89             get keyvalues for a given list of keynames
    90             a where statement can be given (list of key and list of values)
    91 
    92         @Input:
    93             keynames: list of strings
    94                 List of keynames.
    95 
    96             wherekeynames: list of strings, optional
    97                 Default value is an empty list.
    98 
    99             wherekeyvalues: list of strings, optional
    100                 Default value is an empty list.
    101 
    102         @Return:
    103             return_list: list of strings
    104                 List of keyvalues for given keynames.
     86        '''Get keyvalues for a given list of keynames a where statement
     87        can be given (list of key and list of values)
     88
     89        Parameters
     90        ----------
     91        keynames : :obj:`list` of :obj:`string`
     92            List of keynames.
     93
     94        wherekeynames : :obj:`list` of :obj:`string`, optional
     95            Default value is an empty list.
     96
     97        wherekeyvalues : :obj:`list` of :obj:`string`, optional
     98            Default value is an empty list.
     99
     100        Return
     101        ------
     102        return_list : :obj:`list` of :obj:`string`
     103            List of keyvalues for given keynames.
    105104        '''
    106105
     
    144143    def set_keys(self, fromfile, keynames, keyvalues, wherekeynames=[],
    145144                 wherekeyvalues=[], strict=False, filemode='w'):
    146         '''
    147         @Description:
    148             Opens the file to read the grib messages and then write
    149             them to a new output file. By default all messages are
    150             written out. Also, the keyvalues of the passed list of
    151             keynames are set or only those meeting the where statement.
    152             (list of key and list of values).
    153 
    154         @Input:
    155             fromfile: string
    156                 Filename of the input file to read the grib messages from.
    157 
    158             keynames: list of strings
    159                 List of keynames. Default is an empty list.
    160 
    161             keyvalues: list of strings
    162                 List of keynames. Default is an empty list.
    163 
    164             wherekeynames: list of strings, optional
    165                 Default value is an empty list.
    166 
    167             wherekeyvalues: list of strings, optional
    168                 Default value is an empty list.
    169 
    170             strict: boolean, optional
    171                 Decides if everything from keynames and keyvalues
    172                 is written out the grib file (False) or only those
    173                 meeting the where statement (True). Default is False.
    174 
    175             filemode: string, optional
    176                 Sets the mode for the output file. Default is "w".
    177 
    178         @Return:
    179             <nothing>
     145        '''Opens the file to read the grib messages and then write
     146        them to a new output file. By default all messages are
     147        written out. Also, the keyvalues of the passed list of
     148        keynames are set or only those meeting the where statement.
     149        (list of key and list of values).
     150
     151        Parameters
     152        ----------
     153        fromfile : :obj:`string`
     154            Filename of the input file to read the grib messages from.
     155
     156        keynames : :obj:`list` of :obj:`string`
     157            List of keynames. Default is an empty list.
     158
     159        keyvalues : :obj:`list` of :obj:`string`
     160            List of keynames. Default is an empty list.
     161
     162        wherekeynames : :obj:`list` of :obj:`string`, optional
     163            Default value is an empty list.
     164
     165        wherekeyvalues : :obj:`list` of :obj:`string`, optional
     166            Default value is an empty list.
     167
     168        strict : :obj:`boolean`, optional
     169            Decides if everything from keynames and keyvalues
     170            is written out the grib file (False) or only those
     171            meeting the where statement (True). Default is False.
     172
     173        filemode : :obj:`string`, optional
     174            Sets the mode for the output file. Default is "w".
     175
     176        Return
     177        ------
    180178
    181179        '''
     
    219217    def copy(self, filename_in, selectWhere=True,
    220218             keynames=[], keyvalues=[], filemode='w'):
    221         '''
    222         Add the content of another input grib file to the objects file but
     219        '''Add the content of another input grib file to the objects file but
    223220        only messages corresponding to keys/values passed to the function.
    224221        The selectWhere switch decides if to copy the keys equal to (True) or
    225222        different to (False) the keynames/keyvalues list passed to the function.
    226223
    227         @Input:
    228             filename_in: string
    229                 Filename of the input file to read the grib messages from.
    230 
    231             selectWhere: boolean, optional
    232                 Decides if to copy the keynames and values equal to (True) or
    233                 different to (False) the keynames/keyvalues list passed to the
    234                 function. Default is True.
    235 
    236             keynames: list of strings, optional
    237                 List of keynames. Default is an empty list.
    238 
    239             keyvalues: list of strings, optional
    240                 List of keynames. Default is an empty list.
    241 
    242             filemode: string, optional
    243                 Sets the mode for the output file. Default is "w".
    244 
    245         @Return:
    246             <nothing>
     224        Parameters
     225        ----------
     226        filename_in : :obj:`string`
     227            Filename of the input file to read the grib messages from.
     228
     229        selectWhere : :obj:`boolean`, optional
     230            Decides if to copy the keynames and values equal to (True) or
     231            different to (False) the keynames/keyvalues list passed to the
     232            function. Default is True.
     233
     234        keynames : :obj:`list` of :obj:`string`, optional
     235            List of keynames. Default is an empty list.
     236
     237        keyvalues : :obj:`list` of :obj:`string`, optional
     238            List of keynames. Default is an empty list.
     239
     240        filemode : :obj:`string`, optional
     241            Sets the mode for the output file. Default is "w".
     242
     243        Return
     244        ------
     245
    247246        '''
    248247
     
    284283
    285284    def index(self, index_keys=["mars"], index_file="my.idx"):
    286         '''
    287         @Description:
    288             Create index file from a list of files if it does not exist or
    289             read an index file.
    290 
    291         @Input:
    292             index_keys: list of strings, optional
    293                 Contains the list of key parameter names from
    294                 which the index is to be created.
    295                 Default is a list with a single entry string "mars".
    296 
    297             index_file: string, optional
    298                 Filename where the indices are stored.
    299                 Default is "my.idx".
    300 
    301         @Return:
    302             iid: integer
    303                 Grib index id.
     285        '''Create index file from a list of files if it does not exist or
     286        read an index file.
     287
     288        Parameters
     289        ----------
     290        index_keys: :obj:`list` of :obj:`string`, optional
     291            Contains the list of key parameter names from
     292            which the index is to be created.
     293            Default is a list with a single entry string "mars".
     294
     295        index_file: :obj:`string`, optional
     296            Filename where the indices are stored.
     297            Default is "my.idx".
     298
     299        Return
     300        ------
     301        iid: :obj:`integer`
     302            Grib index id.
    304303        '''
    305304        print("... index will be done")
  • source/python/classes/MarsRetrieval.py

    r70fee58 r274f9ef  
    7373# ------------------------------------------------------------------------------
    7474class MarsRetrieval(object):
    75     '''
    76     Class for submitting MARS retrievals.
     75    '''Class for submitting MARS retrievals.
    7776
    7877    A description of MARS keywords/arguments and examples of their
     
    8079    https://software.ecmwf.int/wiki/display/UDOC/\
    8180                   Identification+keywords#Identificationkeywords-class
    82 
    8381    '''
    8482
     
    8886                 number="", accuracy="", grid="", gaussian="", target="",
    8987                 param=""):
    90         '''
    91         @Description:
    92             Initialises the instance of the MarsRetrieval class and
    93             defines and assigns a set of the necessary retrieval parameters
    94             for the FLEXPART input data.
    95             A description of MARS keywords/arguments, their dependencies
    96             on each other and examples of their values can be found here:
    97 
    98             https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords
    99 
    100         @Input:
    101             self: instance of MarsRetrieval
    102                 For description see class documentation.
    103 
    104             server: instance of ECMWFService (from ECMWF Web-API)
    105                 This is the connection to the ECMWF data servers.
    106                 It is needed for the pythonic access of ECMWF data.
    107 
    108             public: integer
    109                 Decides which Web API version is used:
    110                 0: member-state users and full archive access
    111                 1: public access and limited access to the public server and
    112                    datasets. Needs the parameter dataset.
    113                 Default is "0" and for member-state users.
    114 
    115             marsclass: string, optional
    116                 Characterisation of dataset. E.g. EI (ERA-Interim),
    117                 E4 (ERA40), OD (Operational archive), ea (ERA5).
    118                 Default is the ERA-Interim dataset "ei".
    119 
    120             dataset: string, optional
    121                 For public datasets there is the specific naming and parameter
    122                 dataset which has to be used to characterize the type of
    123                 data. Usually there is less data available, either in times,
    124                 domain or parameter.
    125                 Default is an empty string.
    126 
    127             type: string, optional
    128                 Determines the type of fields to be retrieved.
    129                 Selects between observations, images or fields.
    130                 Examples for fields: Analysis (an), Forecast (fc),
    131                 Perturbed Forecast (pf), Control Forecast (cf) and so on.
    132                 Default is an empty string.
    133 
    134             levtype: string, optional
    135                 Denotes type of level. Has a direct implication on valid
    136                 levelist values!
    137                 E.g. model level (ml), pressure level (pl), surface (sfc),
    138                 potential vorticity (pv), potential temperature (pt)
    139                 and depth (dp).
    140                 Default is an empty string.
    141 
    142             levelist: string, optional
    143                 Specifies the required levels. It has to have a valid
    144                 correspondence to the selected levtype.
    145                 Examples: model level: 1/to/137, pressure levels: 500/to/1000
    146                 Default is an empty string.
    147 
    148             repres: string, optional
    149                 Selects the representation of the archived data.
    150                 E.g. sh - spherical harmonics, gg - Gaussian grid,
    151                 ll - latitude/longitude, ...
    152                 Default is an empty string.
    153 
    154             date: string, optional
    155                 Specifies the Analysis date, the Forecast base date or
    156                 Observations date. Valid formats are:
    157                 Absolute as YYYY-MM-DD or YYYYMMDD.
    158                 Default is an empty string.
    159 
    160             resol: string, optional
    161                 Specifies the desired triangular truncation of retrieved data,
    162                 before carrying out any other selected post-processing.
    163                 The default is automatic truncation (auto), by which the lowest
    164                 resolution compatible with the value specified in grid is
    165                 automatically selected for the retrieval.
    166                 Users wanting to perform post-processing from full spectral
    167                 resolution should specify Archived Value (av).
    168                 The following are examples of existing resolutions found in
    169                 the archive: 63, 106, 159, 213, 255, 319, 399, 511, 799 or 1279.
    170                 This keyword has no meaning/effect if the archived data is
    171                 not in spherical harmonics representation.
    172                 The best selection can be found here:
    173                 https://software.ecmwf.int/wiki/display/UDOC/\
    174                       Retrieve#Retrieve-Truncationbeforeinterpolation
    175                 Default is an empty string.
    176 
    177             stream: string, optional
    178                 Identifies the forecasting system used to generate the data.
    179                 E.g. oper (Atmospheric model), enfo (Ensemble forecats), ...
    180                 Default is an empty string.
    181 
    182             area: string, optional
    183                 Specifies the desired sub-area of data to be extracted.
    184                 Areas can be defined to wrap around the globe.
    185 
    186                 Latitude values must be given as signed numbers, with:
    187                     north latitudes (i.e. north of the equator)
    188                         being positive (e.g: 40.5)
    189                     south latitutes (i.e. south of the equator)
    190                         being negative (e.g: -50.5)
    191                 Longtitude values must be given as signed numbers, with:
    192                     east longitudes (i.e. east of the 0 degree meridian)
    193                         being positive (e.g: 35.0)
    194                     west longitudes (i.e. west of the 0 degree meridian)
    195                         being negative (e.g: -20.5)
    196 
    197                 E.g.: North/West/South/East
    198                 Default is an empty string.
    199 
    200             time: string, optional
    201                 Specifies the time of the data in hours and minutes.
    202                 Valid values depend on the type of data: Analysis time,
    203                 Forecast base time or First guess verification time
    204                 (all usually at synoptic hours: 00, 06, 12 and 18 ).
    205                 Observation time (any combination in hours and minutes is valid,
    206                 subject to data availability in the archive).
    207                 The syntax is HHMM or HH:MM. If MM is omitted it defaults to 00.
    208                 Default is an empty string.
    209 
    210             step: string, optional
    211                 Specifies the forecast time step from forecast base time.
    212                 Valid values are hours (HH) from forecast base time. It also
    213                 specifies the length of the forecast which verifies at
    214                 First Guess time.
    215                 E.g. 1/3/6-hourly
    216                 Default is an empty string.
    217 
    218             expver: string, optional
    219                 The version of the dataset. Each experiment is assigned a
    220                 unique code (version). Production data is assigned 1 or 2,
    221                 and experimental data in Operations 11, 12 ,...
    222                 Research or Member State's experiments have a four letter
    223                 experiment identifier.
    224                 Default is "1".
    225 
    226             number: string, optional
    227                 Selects the member in ensemble forecast run. (Only then it
    228                 is necessary.) It has a different meaning depending on
    229                 the type of data.
    230                 E.g. Perturbed Forecasts: specifies the Ensemble forecast member
    231                 Default is an empty string.
    232 
    233             accuracy: string, optional
    234                 Specifies the number of bits per value to be used in the
    235                 generated GRIB coded fields.
    236                 A positive integer may be given to specify the preferred number
    237                 of bits per packed value. This must not be greater than the
    238                 number of bits normally used for a Fortran integer on the
    239                 processor handling the request (typically 32 or 64 bit).
    240                 Within a compute request the accuracy of the original fields
    241                 can be passed to the result field by specifying accuracy=av.
    242                 Default is an empty string.
    243 
    244             grid: string, optional
    245                 Specifies the output grid which can be either a Gaussian grid
    246                 or a Latitude/Longitude grid. MARS requests specifying
    247                 grid=av will return the archived model grid.
    248 
    249                 Lat/Lon grid: The grid spacing needs to be an integer
    250                 fraction of 90 degrees e.g. grid = 0.5/0.5
    251 
    252                 Gaussian grid: specified by a letter denoting the type of
    253                 Gaussian grid followed by an integer (the grid number)
    254                 representing the number of lines between the Pole and Equator,
    255                 e.g.
    256                 grid = F160 - full (or regular) Gaussian grid with
    257                        160 latitude lines between the pole and equator
    258                 grid = N320 - ECMWF original reduced Gaussian grid with
    259                        320 latitude lines between the pole and equator,
    260                        see Reduced Gaussian Grids for grid numbers used at ECMWF
    261                 grid = O640 - ECMWF octahedral (reduced) Gaussian grid with
    262                        640 latitude lines between the pole and equator
    263                 Default is an empty string.
    264 
    265             gaussian: string, optional
    266                 This parameter is deprecated and should no longer be used.
    267                 Specifies the desired type of Gaussian grid for the output.
    268                 Valid Gaussian grids are quasi-regular (reduced) or regular.
    269                 Keyword gaussian can only be specified together with
    270                 keyword grid. Gaussian without grid has no effect.
    271                 Default is an empty string.
    272 
    273             target: string, optional
    274                 Specifies a file into which data is to be written after
    275                 retrieval or manipulation. Path names should always be
    276                 enclosed in double quotes. The MARS client supports automatic
    277                 generation of multiple target files using MARS keywords
    278                 enclosed in square brackets [ ].  If the environment variable
    279                 MARS_MULTITARGET_STRICT_FORMAT is set to 1 before calling mars,
    280                 the keyword values will be used in the filename as shown by
    281                 the ecCodes GRIB tool grib_ls -m, e.g. with
    282                 MARS_MULTITARGET_STRICT_FORMAT set to 1 the keywords time,
    283                 expver and param will be formatted as 0600, 0001 and 129.128
    284                 rather than 600, 1 and 129.
    285                 Default is an empty string.
    286 
    287             param: string, optional
    288                 Specifies the meteorological parameter.
    289                 The list of meteorological parameters in MARS is extensive.
    290                 Their availability is directly related to their meteorological
    291                 meaning and, therefore, the rest of directives specified
    292                 in the MARS request.
    293                 Meteorological parameters can be specified by their
    294                 GRIB code (param=130), their mnemonic (param=t) or
    295                 full name (param=temperature).
    296                 The list of parameter should be seperated by a "/"-sign.
    297                 E.g. 130/131/133
    298                 Default is an empty string.
    299 
    300         @Return:
    301             <nothing>
     88        '''Initialises the instance of the MarsRetrieval class and
     89        defines and assigns a set of the necessary retrieval parameters
     90        for the FLEXPART input data.
     91        A description of MARS keywords/arguments, their dependencies
     92        on each other and examples of their values can be found here:
     93
     94        https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords
     95
     96        Parameters
     97        ----------
     98        server : :obj:`ECMWFService`
     99            This is the connection to the ECMWF data servers.
     100            It is needed for the pythonic access of ECMWF data.
     101
     102        public : :obj:`integer`
     103            Decides which Web API version is used:
     104            0: member-state users and full archive access
     105            1: public access and limited access to the public server and
     106               datasets. Needs the parameter dataset.
     107            Default is "0" and for member-state users.
     108
     109        marsclass : :obj:`string`, optional
     110            Characterisation of dataset. E.g. EI (ERA-Interim),
     111            E4 (ERA40), OD (Operational archive), ea (ERA5).
     112            Default is the ERA-Interim dataset "ei".
     113
     114        dataset : :obj:`string`, optional
     115            For public datasets there is the specific naming and parameter
     116            dataset which has to be used to characterize the type of
     117            data. Usually there is less data available, either in times,
     118            domain or parameter.
     119            Default is an empty string.
     120
     121        type : :obj:`string`, optional
     122            Determines the type of fields to be retrieved.
     123            Selects between observations, images or fields.
     124            Examples for fields: Analysis (an), Forecast (fc),
     125            Perturbed Forecast (pf), Control Forecast (cf) and so on.
     126            Default is an empty string.
     127
     128        levtype : :obj:`string`, optional
     129            Denotes type of level. Has a direct implication on valid
     130            levelist values!
     131            E.g. model level (ml), pressure level (pl), surface (sfc),
     132            potential vorticity (pv), potential temperature (pt)
     133            and depth (dp).
     134            Default is an empty string.
     135
     136        levelist : :obj:`string`, optional
     137            Specifies the required levels. It has to have a valid
     138            correspondence to the selected levtype.
     139            Examples: model level: 1/to/137, pressure levels: 500/to/1000
     140            Default is an empty string.
     141
     142        repres : :obj:`string`, optional
     143            Selects the representation of the archived data.
     144            E.g. sh - spherical harmonics, gg - Gaussian grid,
     145            ll - latitude/longitude, ...
     146            Default is an empty string.
     147
     148        date : :obj:`string`, optional
     149            Specifies the Analysis date, the Forecast base date or
     150            Observations date. Valid formats are:
     151            Absolute as YYYY-MM-DD or YYYYMMDD.
     152            Default is an empty string.
     153
     154        resol : :obj:`string`, optional
     155            Specifies the desired triangular truncation of retrieved data,
     156            before carrying out any other selected post-processing.
     157            The default is automatic truncation (auto), by which the lowest
     158            resolution compatible with the value specified in grid is
     159            automatically selected for the retrieval.
     160            Users wanting to perform post-processing from full spectral
     161            resolution should specify Archived Value (av).
     162            The following are examples of existing resolutions found in
     163            the archive: 63, 106, 159, 213, 255, 319, 399, 511, 799 or 1279.
     164            This keyword has no meaning/effect if the archived data is
     165            not in spherical harmonics representation.
     166            The best selection can be found here:
     167            https://software.ecmwf.int/wiki/display/UDOC/\
     168                  Retrieve#Retrieve-Truncationbeforeinterpolation
     169            Default is an empty string.
     170
     171        stream : :obj:`string`, optional
     172            Identifies the forecasting system used to generate the data.
     173            E.g. oper (Atmospheric model), enfo (Ensemble forecats), ...
     174            Default is an empty string.
     175
     176        area : :obj:`string`, optional
     177            Specifies the desired sub-area of data to be extracted.
     178            Areas can be defined to wrap around the globe.
     179
     180            Latitude values must be given as signed numbers, with:
     181                north latitudes (i.e. north of the equator)
     182                    being positive (e.g: 40.5)
     183                south latitutes (i.e. south of the equator)
     184                    being negative (e.g: -50.5)
     185            Longtitude values must be given as signed numbers, with:
     186                east longitudes (i.e. east of the 0 degree meridian)
     187                    being positive (e.g: 35.0)
     188                west longitudes (i.e. west of the 0 degree meridian)
     189                    being negative (e.g: -20.5)
     190
     191            E.g.: North/West/South/East
     192            Default is an empty string.
     193
     194        time : :obj:`string`, optional
     195            Specifies the time of the data in hours and minutes.
     196            Valid values depend on the type of data: Analysis time,
     197            Forecast base time or First guess verification time
     198            (all usually at synoptic hours: 00, 06, 12 and 18 ).
     199            Observation time (any combination in hours and minutes is valid,
     200            subject to data availability in the archive).
     201            The syntax is HHMM or HH:MM. If MM is omitted it defaults to 00.
     202            Default is an empty string.
     203
     204        step : :obj:`string`, optional
     205            Specifies the forecast time step from forecast base time.
     206            Valid values are hours (HH) from forecast base time. It also
     207            specifies the length of the forecast which verifies at
     208            First Guess time.
     209            E.g. 1/3/6-hourly
     210            Default is an empty string.
     211
     212        expver : :obj:`string`, optional
     213            The version of the dataset. Each experiment is assigned a
     214            unique code (version). Production data is assigned 1 or 2,
     215            and experimental data in Operations 11, 12 ,...
     216            Research or Member State's experiments have a four letter
     217            experiment identifier.
     218            Default is "1".
     219
     220        number : :obj:`string`, optional
     221            Selects the member in ensemble forecast run. (Only then it
     222            is necessary.) It has a different meaning depending on
     223            the type of data.
     224            E.g. Perturbed Forecasts: specifies the Ensemble forecast member
     225            Default is an empty string.
     226
     227        accuracy : :obj:`string`, optional
     228            Specifies the number of bits per value to be used in the
     229            generated GRIB coded fields.
     230            A positive integer may be given to specify the preferred number
     231            of bits per packed value. This must not be greater than the
     232            number of bits normally used for a Fortran integer on the
     233            processor handling the request (typically 32 or 64 bit).
     234            Within a compute request the accuracy of the original fields
     235            can be passed to the result field by specifying accuracy=av.
     236            Default is an empty string.
     237
     238        grid : :obj:`string`, optional
     239            Specifies the output grid which can be either a Gaussian grid
     240            or a Latitude/Longitude grid. MARS requests specifying
     241            grid=av will return the archived model grid.
     242
     243            Lat/Lon grid: The grid spacing needs to be an integer
     244            fraction of 90 degrees e.g. grid = 0.5/0.5
     245
     246            Gaussian grid: specified by a letter denoting the type of
     247            Gaussian grid followed by an integer (the grid number)
     248            representing the number of lines between the Pole and Equator,
     249            e.g.
     250            grid = F160 - full (or regular) Gaussian grid with
     251                   160 latitude lines between the pole and equator
     252            grid = N320 - ECMWF original reduced Gaussian grid with
     253                   320 latitude lines between the pole and equator,
     254                   see Reduced Gaussian Grids for grid numbers used at ECMWF
     255            grid = O640 - ECMWF octahedral (reduced) Gaussian grid with
     256                   640 latitude lines between the pole and equator
     257            Default is an empty string.
     258
     259        gaussian : :obj:`string`, optional
     260            This parameter is deprecated and should no longer be used.
     261            Specifies the desired type of Gaussian grid for the output.
     262            Valid Gaussian grids are quasi-regular (reduced) or regular.
     263            Keyword gaussian can only be specified together with
     264            keyword grid. Gaussian without grid has no effect.
     265            Default is an empty string.
     266
     267        target : :obj:`string`, optional
     268            Specifies a file into which data is to be written after
     269            retrieval or manipulation. Path names should always be
     270            enclosed in double quotes. The MARS client supports automatic
     271            generation of multiple target files using MARS keywords
     272            enclosed in square brackets [ ].  If the environment variable
     273            MARS_MULTITARGET_STRICT_FORMAT is set to 1 before calling mars,
     274            the keyword values will be used in the filename as shown by
     275            the ecCodes GRIB tool grib_ls -m, e.g. with
     276            MARS_MULTITARGET_STRICT_FORMAT set to 1 the keywords time,
     277            expver and param will be formatted as 0600, 0001 and 129.128
     278            rather than 600, 1 and 129.
     279            Default is an empty string.
     280
     281        param : :obj:`string`, optional
     282            Specifies the meteorological parameter.
     283            The list of meteorological parameters in MARS is extensive.
     284            Their availability is directly related to their meteorological
     285            meaning and, therefore, the rest of directives specified
     286            in the MARS request.
     287            Meteorological parameters can be specified by their
     288            GRIB code (param=130), their mnemonic (param=t) or
     289            full name (param=temperature).
     290            The list of parameter should be seperated by a "/"-sign.
     291            E.g. 130/131/133
     292            Default is an empty string.
     293
     294        Return
     295        ------
     296
    302297        '''
    303298
     
    328323
    329324    def display_info(self):
    330         '''
    331         @Description:
    332             Prints all class attributes and their values to the
    333             standard output.
    334 
    335         @Input:
    336             self: instance of MarsRetrieval
    337                 For description see class documentation.
    338 
    339         @Return:
    340             <nothing>
     325        '''Prints all class attributes and their values to the
     326        standard output.
     327
     328        Parameters
     329        ----------
     330
     331        Return
     332        ------
     333
    341334        '''
    342335        # Get all class attributes and their values as a dictionary
     
    355348
    356349    def print_info(self, inputdir, request_number):
    357         '''
    358         @Description:
    359             Prints all mars requests to an extra file for debugging and
    360             information.
    361 
    362         @Input:
    363             self: instance of MarsRetrieval
    364                 For description see class documentation.
    365 
    366             inputdir: string
    367                 The path where all data from the retrievals are stored.
    368 
    369             request_number: integer
    370                 Number of mars requests for flux and non-flux data.
    371 
    372             @Return:
    373             <nothing>
     350        '''Prints all mars requests to an extra file for debugging and
     351        information.
     352
     353        Parameters
     354        ----------
     355        inputdir : :obj:`string`
     356            The path where all data from the retrievals are stored.
     357
     358        request_number : :obj:`integer`
     359            Number of mars requests for flux and non-flux data.
     360
     361        Return
     362        ------
     363
    374364        '''
    375365        # Get all class attributes and their values as a dictionary
     
    393383
    394384    def print_infodata_csv(self, inputdir, request_number):
    395         '''
    396         @Description:
    397             Write all request parameter in alpabetical order into a "csv" file.
    398 
    399         @Input:
    400             self: instance of MarsRetrieval
    401                 For description see class documentation.
    402 
    403             inputdir: string
    404                 The path where all data from the retrievals are stored.
    405 
    406             request_number: integer
    407                 Number of mars requests for flux and non-flux data.
    408 
    409         @Return:
    410             <nothing>
     385        '''Write all request parameter in alpabetical order into a "csv" file.
     386
     387        Parameters
     388        ----------
     389        inputdir : :obj:`string`
     390            The path where all data from the retrievals are stored.
     391
     392        request_number : :obj:`integer`
     393            Number of mars requests for flux and non-flux data.
     394
     395        Return
     396        ------
     397
    411398        '''
    412399
     
    427414
    428415    def data_retrieve(self):
    429         '''
    430         @Description:
    431             Submits a MARS retrieval. Depending on the existence of
    432             ECMWF Web-API it is submitted via Python or a
    433             subprocess in the Shell. The parameter for the mars retrieval
    434             are taken from the defined class attributes.
    435 
    436         @Input:
    437             self: instance of MarsRetrieval
    438                 For description see class documentation.
    439 
    440         @Return:
    441             <nothing>
     416        '''Submits a MARS retrieval. Depending on the existence of
     417        ECMWF Web-API it is submitted via Python or a
     418        subprocess in the Shell. The parameter for the mars retrieval
     419        are taken from the defined class attributes.
     420
     421        Parameters
     422        ----------
     423
     424        Return
     425        ------
     426
    442427        '''
    443428        # Get all class attributes and their values as a dictionary
  • source/python/classes/UioFiles.py

    rca867de r274f9ef  
    6161
    6262class UioFiles(object):
    63     '''
    64     Class to manipulate files. At initialisation it has the pattern
     63    '''Class to manipulate files. At initialisation it has the pattern
    6564    which stores a regular expression pattern for the files, the path
    6665    to the files and the files already.
     
    7069    # --------------------------------------------------------------------------
    7170    def __init__(self, path, pattern):
    72         '''
    73         @Description:
    74             Assignes a specific pattern for these files.
     71        '''Assignes a specific pattern for these files.
    7572
    76         @Input:
    77             self: instance of UioFiles
    78                 Description see class documentation.
     73        Parameters
     74        ----------
     75        path : :obj:`string`
     76            Directory where to list the files.
    7977
    80             path: string
    81                 Directory where to list the files.
     78        pattern : :obj:`string`
     79            Regular expression pattern. For example: '\*.grb'
    8280
    83             pattern: string
    84                 Regular expression pattern. For example: '*.grb'
     81        Return
     82        ------
    8583
    86         @Return:
    87             <nothing>
    8884        '''
    8985
     
    9894    #@profiling.timefn
    9995    def __list_files__(self, path):
    100         '''
    101         @Description:
    102             Lists all files in the directory with the matching
    103             regular expression pattern.
     96        '''Lists all files in the directory with the matching
     97        regular expression pattern.
    10498
    105         @Input:
    106             self: instance of UioFiles
    107                 Description see class documentation.
     99        Parameters
     100        ----------
     101        path : :obj:`string`
     102            Path to the files.
    108103
    109             path: string
    110                 Path to the files.
     104        Return
     105        ------
    111106
    112         @Return:
    113             <nothing>
    114107        '''
    115108        # Get the absolute path
     
    124117
    125118    def __str__(self):
    126         '''
    127         @Description:
    128             Converts the list of files into a single string.
    129             The entries are sepereated by "," sign.
     119        '''Converts the list of files into a single string.
     120        The entries are sepereated by "," sign.
    130121
    131         @Input:
    132             self: instance of UioFiles
    133                 Description see class documentation.
     122        Parameters
     123        ----------
    134124
    135         @Return:
    136             files_string: string
    137                 The content of the list as a single string.
     125        Return
     126        ------
     127        files_string : :obj:`string`
     128            The content of the list as a single string.
    138129        '''
    139130
     
    144135
    145136    def delete_files(self):
    146         '''
    147         @Description:
    148             Deletes the files.
     137        '''Deletes the files.
    149138
    150         @Input:
    151             self: instance of UioFiles
    152                 Description see class documentation.
     139        Parameters
     140        ----------
    153141
    154         @Return:
    155             <nothing>
     142        Return
     143        ------
     144
    156145        '''
    157146
  • source/python/install.py

    rc5074d2 r274f9ef  
    6666# ------------------------------------------------------------------------------
    6767def main():
    68     '''
    69     @Description:
    70         Controls the installation process. Calls the installation function
    71         if target is specified.
    72 
    73     @Intput:
    74         <nothing>
    75 
    76     @Return:
    77         <nothing>
     68    '''Controls the installation process. Calls the installation function
     69    if target is specified.
     70
     71    Parameters
     72    ----------
     73
     74    Return
     75    ------
    7876    '''
    7977
     
    8886
    8987def get_install_cmdline_arguments():
    90     '''
    91     @Description:
    92         Decomposes the command line arguments and assigns them to variables.
    93         Apply default values for non mentioned arguments.
    94 
    95     @Input:
    96         <nothing>
    97 
    98     @Return:
    99         args: instance of ArgumentParser
    100             Contains the commandline arguments from script/program call.
     88    '''Decomposes the command line arguments and assigns them to variables.
     89    Apply default values for non mentioned arguments.
     90
     91    Parameters
     92    ----------
     93
     94    Return
     95    ------
     96    args : :obj:`Namespace`
     97        Contains the commandline arguments from script/program call.
    10198    '''
    10299    parser = ArgumentParser(description='Install flex_extract software locally or \
     
    139136
    140137def install_via_gateway(c):
    141     '''
    142     @Description:
    143         Perform the actual installation on local machine or prepare data
    144         transfer to remote gate and submit a job script which will
    145         install everything on the remote gate.
    146 
    147     @Input:
    148         c: instance of class ControlFile
    149             Contains all the parameters of CONTROL file and
    150             command line.
    151             For more information about format and content of the parameter
    152             see documentation.
    153 
    154     @Return:
    155         <nothing>
     138    '''Perform the actual installation on local machine or prepare data
     139    transfer to remote gate and submit a job script which will
     140    install everything on the remote gate.
     141
     142    Parameters
     143    ----------
     144    c : :obj:`ControlFile`
     145        Contains all the parameters of CONTROL file and
     146        command line.
     147
     148    Return
     149    ------
     150
    156151    '''
    157152    import tarfile
     
    224219
    225220def mk_tarball(tarball_path, target):
    226     '''
    227     @Description:
    228         Creates a tarball with all necessary files which need to be sent to the
    229         installation directory.
    230         It does not matter if this is local or remote.
    231         Collects all python files, the Fortran source and makefiles,
    232         the ECMWF_ENV file, the CONTROL files as well as the
    233         template files.
    234 
    235     @Input:
    236         tarball_path: string
    237             The complete path to the tar file which will contain all
    238             relevant data for flex_extract.
    239 
    240         target: string
    241             The queue where the job is submitted to.
    242 
    243     @Return:
    244         <nothing>
     221    '''Creates a tarball with all necessary files which need to be sent to the
     222    installation directory.
     223    It does not matter if this is local or remote.
     224    Collects all python files, the Fortran source and makefiles,
     225    the ECMWF_ENV file, the CONTROL files as well as the
     226    template files.
     227
     228    Parameters
     229    ----------
     230    tarball_path : :obj:`string`
     231        The complete path to the tar file which will contain all
     232        relevant data for flex_extract.
     233
     234    target : :obj:`string`
     235        The queue where the job is submitted to.
     236
     237    Return
     238    ------
     239
    245240    '''
    246241    import tarfile
     
    294289
    295290def un_tarball(tarball_path):
    296     '''
    297     @Description:
    298         Extracts the given tarball into current directory.
    299 
    300     @Input:
    301         tarball_path: string
    302             The complete path to the tar file which will contain all
    303             relevant data for flex_extract.
    304 
    305     @Return:
    306         <nothing>
     291    '''Extracts the given tarball into current directory.
     292
     293    Parameters
     294    ----------
     295    tarball_path : :obj:`string`
     296        The complete path to the tar file which will contain all
     297        relevant data for flex_extract.
     298
     299    Return
     300    ------
     301
    307302    '''
    308303    import tarfile
     
    316311
    317312def mk_env_vars(ecuid, ecgid, gateway, destination):
    318     '''
    319     @Description:
    320         Creates a file named ECMWF_ENV which contains the
    321         necessary environmental variables at ECMWF servers.
    322         It is based on the template ECMWF_ENV.template.
    323 
    324     @Input:
    325         ecuid: string
    326             The user id on ECMWF server.
    327 
    328         ecgid: string
    329             The group id on ECMWF server.
    330 
    331         gateway: string
    332             The gateway server the user is using.
    333 
    334         destination: string
    335             The remote destination which is used to transfer files
    336             from ECMWF server to local gateway server.
    337 
    338     @Return:
    339         <nothing>
     313    '''Creates a file named ECMWF_ENV which contains the
     314    necessary environmental variables at ECMWF servers.
     315    It is based on the template ECMWF_ENV.template.
     316
     317    Parameters
     318    ----------
     319    ecuid : :obj:`string`
     320        The user id on ECMWF server.
     321
     322    ecgid : :obj:`string`
     323        The group id on ECMWF server.
     324
     325    gateway : :obj:`string`
     326        The gateway server the user is using.
     327
     328    destination : :obj:`string`
     329        The remote destination which is used to transfer files
     330        from ECMWF server to local gateway server.
     331
     332    Return
     333    ------
     334
    340335    '''
    341336    from genshi.template.text import NewTextTemplate
     
    358353
    359354def mk_compilejob(makefile, target, ecuid, ecgid, fp_root):
    360     '''
    361     @Description:
    362         Modifies the original job template file so that it is specified
    363         for the user and the environment were it will be applied. Result
    364         is stored in a new file "job.temp" in the python directory.
    365 
    366     @Input:
    367         makefile: string
    368             Name of the makefile which should be used to compile FORTRAN
    369             CONVERT2 program.
    370 
    371         target: string
    372             The target where the installation should be done, e.g. the queue.
    373 
    374         ecuid: string
    375             The user id on ECMWF server.
    376 
    377         ecgid: string
    378             The group id on ECMWF server.
    379 
    380         fp_root: string
    381            Path to the root directory of FLEXPART environment or flex_extract
    382            environment.
    383 
    384     @Return:
    385         <nothing>
     355    '''Modifies the original job template file so that it is specified
     356    for the user and the environment were it will be applied. Result
     357    is stored in a new file "job.temp" in the python directory.
     358
     359    Parameters
     360    ----------
     361    makefile : :obj:`string`
     362        Name of the makefile which should be used to compile FORTRAN
     363        CONVERT2 program.
     364
     365    target : :obj:`string`
     366        The target where the installation should be done, e.g. the queue.
     367
     368    ecuid : :obj:`string`
     369        The user id on ECMWF server.
     370
     371    ecgid : :obj:`string`
     372        The group id on ECMWF server.
     373
     374    fp_root : :obj:`string`
     375       Path to the root directory of FLEXPART environment or flex_extract
     376       environment.
     377
     378    Return
     379    ------
     380
    386381    '''
    387382    from genshi.template.text import NewTextTemplate
     
    413408
    414409def mk_job_template(ecuid, ecgid, gateway, destination, fp_root):
    415     '''
    416     @Description:
    417         Modifies the original job template file so that it is specified
    418         for the user and the environment were it will be applied. Result
    419         is stored in a new file.
    420 
    421     @Input:
    422         ecuid: string
    423             The user id on ECMWF server.
    424 
    425         ecgid: string
    426             The group id on ECMWF server.
    427 
    428         gateway: string
    429             The gateway server the user is using.
    430 
    431         destination: string
    432             The remote destination which is used to transfer files
    433             from ECMWF server to local gateway server.
    434 
    435         fp_root: string
    436            Path to the root directory of FLEXPART environment or flex_extract
    437            environment.
    438 
    439     @Return:
    440         <nothing>
     410    '''Modifies the original job template file so that it is specified
     411    for the user and the environment were it will be applied. Result
     412    is stored in a new file.
     413
     414    Parameters
     415    ----------
     416    ecuid : :obj:`string`
     417        The user id on ECMWF server.
     418
     419    ecgid : :obj:`string`
     420        The group id on ECMWF server.
     421
     422    gateway : :obj:`string`
     423        The gateway server the user is using.
     424
     425    destination : :obj:`string`
     426        The remote destination which is used to transfer files
     427        from ECMWF server to local gateway server.
     428
     429    fp_root : :obj:`string`
     430       Path to the root directory of FLEXPART environment or flex_extract
     431       environment.
     432
     433    Return
     434    ------
     435
    441436    '''
    442437    from genshi.template.text import NewTextTemplate
     
    467462
    468463def delete_convert_build(src_path):
    469     '''
    470     @Description:
    471         Clean up the Fortran source directory and remove all
    472         build files (e.g. *.o, *.mod and CONVERT2)
    473 
    474     @Input:
    475         src_path: string
    476             Path to the fortran source directory.
    477 
    478     @Return:
    479         <nothing>
     464    '''Clean up the Fortran source directory and remove all
     465    build files (e.g. \*.o, \*.mod and CONVERT2)
     466
     467    Parameters
     468    ----------
     469    src_path : :obj:`string`
     470        Path to the fortran source directory.
     471
     472    Return
     473    ------
     474
    480475    '''
    481476
     
    491486
    492487def make_convert_build(src_path, makefile):
    493     '''
    494     @Description:
    495         Compiles the Fortran code and generates the executable.
    496 
    497     @Input:
    498         src_path: string
    499             Path to the fortran source directory.
    500 
    501         makefile: string
    502             The name of the makefile which should be used.
    503 
    504     @Return:
    505         <nothing>
     488    '''Compiles the Fortran code and generates the executable.