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49 | <a href="../index.html" class="icon icon-home"> flex_extract |
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53 | </a> |
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58 | <div class="version"> |
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59 | 7.1 |
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60 | </div> |
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84 | <ul> |
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85 | <li class="toctree-l1"><a class="reference internal" href="../downloads.html">Downloads</a></li> |
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86 | <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li> |
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136 | <li><a href="index.html">Module code</a> »</li> |
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138 | <li>UioFiles</li> |
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149 | </div> |
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150 | <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> |
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151 | <div itemprop="articleBody"> |
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152 | |
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153 | <h1>Source code for UioFiles</h1><div class="highlight"><pre> |
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154 | <span></span><span class="ch">#!/usr/bin/env python</span> |
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155 | <span class="c1"># -*- coding: utf-8 -*-</span> |
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156 | <span class="c1">#*******************************************************************************</span> |
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157 | <span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span> |
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158 | <span class="c1">#</span> |
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159 | <span class="c1"># @Date: October 2014</span> |
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160 | <span class="c1">#</span> |
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161 | <span class="c1"># @Change History:</span> |
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162 | <span class="c1">#</span> |
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163 | <span class="c1"># November 2015 - Leopold Haimberger (University of Vienna):</span> |
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164 | <span class="c1"># - modified method list_files to work with glob instead of listdir</span> |
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165 | <span class="c1"># - added pattern search in method list_files</span> |
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166 | <span class="c1">#</span> |
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167 | <span class="c1"># February - December 2018 - Anne Philipp (University of Vienna):</span> |
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168 | <span class="c1"># - applied PEP8 style guide</span> |
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169 | <span class="c1"># - added documentation</span> |
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170 | <span class="c1"># - optimisation of method list_files since it didn't work correctly</span> |
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171 | <span class="c1"># for sub directories</span> |
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172 | <span class="c1"># - additional speed up of method list_files</span> |
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173 | <span class="c1"># - modified the class so that it is initiated with a pattern instead</span> |
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174 | <span class="c1"># of suffixes. Gives more precision in selection of files.</span> |
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175 | <span class="c1"># - added delete method</span> |
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176 | <span class="c1">#</span> |
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177 | <span class="c1"># @License:</span> |
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178 | <span class="c1"># (C) Copyright 2014-2019.</span> |
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179 | <span class="c1"># Anne Philipp, Leopold Haimberger</span> |
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180 | <span class="c1">#</span> |
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181 | <span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span> |
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182 | <span class="c1"># International License. To view a copy of this license, visit</span> |
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183 | <span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span> |
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184 | <span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span> |
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185 | <span class="c1">#*******************************************************************************</span> |
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186 | |
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187 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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188 | <span class="c1"># MODULES</span> |
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189 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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190 | <span class="kn">import</span> <span class="nn">os</span> |
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191 | <span class="kn">import</span> <span class="nn">sys</span> |
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192 | <span class="kn">import</span> <span class="nn">fnmatch</span> |
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193 | |
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194 | <span class="c1"># software specific modules from flex_extract</span> |
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195 | <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'../'</span><span class="p">)</span> |
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196 | <span class="kn">from</span> <span class="nn">mods.tools</span> <span class="k">import</span> <span class="n">silent_remove</span><span class="p">,</span> <span class="n">get_list_as_string</span> |
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197 | |
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198 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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199 | <span class="c1"># CLASS</span> |
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200 | <span class="c1"># ------------------------------------------------------------------------------</span> |
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201 | |
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202 | <div class="viewcode-block" id="UioFiles"><a class="viewcode-back" href="../api.html#UioFiles.UioFiles">[docs]</a><span class="k">class</span> <span class="nc">UioFiles</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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203 | <span class="sd">'''Collection of files matching a specific pattern.</span> |
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204 | |
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205 | <span class="sd"> The pattern can contain regular expressions for the files.</span> |
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206 | <span class="sd"> The files are listed and can be transformed to a single string or</span> |
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207 | <span class="sd"> they can be deleted.</span> |
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208 | |
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209 | <span class="sd"> Attributes</span> |
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210 | <span class="sd"> ----------</span> |
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211 | <span class="sd"> path : str</span> |
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212 | <span class="sd"> Directory where to list the files.</span> |
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213 | |
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214 | <span class="sd"> pattern : str</span> |
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215 | <span class="sd"> Regular expression pattern. For example: '\*.grb'</span> |
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216 | |
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217 | <span class="sd"> files : list of str</span> |
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218 | <span class="sd"> List of files matching the pattern in the path.</span> |
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219 | <span class="sd"> '''</span> |
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220 | <span class="c1"># --------------------------------------------------------------------------</span> |
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221 | <span class="c1"># CLASS METHODS</span> |
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222 | <span class="c1"># --------------------------------------------------------------------------</span> |
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223 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">pattern</span><span class="p">):</span> |
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224 | <span class="sd">'''Assignes a specific pattern for these files.</span> |
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225 | |
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226 | <span class="sd"> Parameters</span> |
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227 | <span class="sd"> ----------</span> |
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228 | <span class="sd"> path : str</span> |
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229 | <span class="sd"> Directory where to list the files.</span> |
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230 | |
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231 | <span class="sd"> pattern : str</span> |
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232 | <span class="sd"> Regular expression pattern. For example: '\*.grb'</span> |
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233 | |
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234 | <span class="sd"> Return</span> |
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235 | <span class="sd"> ------</span> |
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236 | |
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237 | <span class="sd"> '''</span> |
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238 | |
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239 | <span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span> |
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240 | <span class="bp">self</span><span class="o">.</span><span class="n">pattern</span> <span class="o">=</span> <span class="n">pattern</span> |
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241 | <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">[]</span> |
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242 | |
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243 | <span class="bp">self</span><span class="o">.</span><span class="n">_list_files</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">)</span> |
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244 | |
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245 | <span class="k">return</span> |
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246 | |
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247 | |
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248 | <span class="k">def</span> <span class="nf">_list_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span> |
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249 | <span class="sd">'''Lists all files in the directory with the matching</span> |
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250 | <span class="sd"> regular expression pattern.</span> |
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251 | |
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252 | <span class="sd"> Parameters</span> |
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253 | <span class="sd"> ----------</span> |
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254 | <span class="sd"> path : str</span> |
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255 | <span class="sd"> Path to the files.</span> |
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256 | |
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257 | <span class="sd"> Return</span> |
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258 | <span class="sd"> ------</span> |
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259 | |
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260 | <span class="sd"> '''</span> |
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261 | <span class="c1"># Get the absolute path</span> |
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262 | <span class="n">path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> |
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263 | |
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264 | <span class="c1"># get all files in the dir and subdir as absolut path</span> |
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265 | <span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> |
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266 | <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">filenames</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pattern</span><span class="p">):</span> |
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267 | <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">root</span><span class="p">,</span> <span class="n">filename</span><span class="p">))</span> |
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268 | |
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269 | <span class="k">return</span> |
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270 | |
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271 | |
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272 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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273 | <span class="sd">'''Converts the list of files into a single string.</span> |
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274 | <span class="sd"> The entries are sepereated by "," sign.</span> |
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275 | |
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276 | <span class="sd"> Parameters</span> |
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277 | <span class="sd"> ----------</span> |
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278 | |
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279 | <span class="sd"> Return</span> |
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280 | <span class="sd"> ------</span> |
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281 | <span class="sd"> files_string : str</span> |
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282 | <span class="sd"> The content of the list as a single string.</span> |
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283 | <span class="sd"> '''</span> |
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284 | |
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285 | <span class="n">filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">]</span> |
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286 | <span class="n">files_string</span> <span class="o">=</span> <span class="n">get_list_as_string</span><span class="p">(</span><span class="n">filenames</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">', '</span><span class="p">)</span> |
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287 | |
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288 | <span class="k">return</span> <span class="n">files_string</span> |
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289 | |
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290 | |
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291 | <div class="viewcode-block" id="UioFiles.delete_files"><a class="viewcode-back" href="../api.html#UioFiles.UioFiles.delete_files">[docs]</a> <span class="k">def</span> <span class="nf">delete_files</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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292 | <span class="sd">'''Deletes the files.</span> |
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293 | |
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294 | <span class="sd"> Parameters</span> |
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295 | <span class="sd"> ----------</span> |
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296 | |
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297 | <span class="sd"> Return</span> |
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298 | <span class="sd"> ------</span> |
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299 | |
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300 | <span class="sd"> '''</span> |
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301 | |
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302 | <span class="k">for</span> <span class="n">old_file</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">:</span> |
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303 | <span class="n">silent_remove</span><span class="p">(</span><span class="n">old_file</span><span class="p">)</span> |
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304 | |
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305 | <span class="k">return</span></div></div> |
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306 | </pre></div> |
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307 | |
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308 | </div> |
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309 | |
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310 | </div> |
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311 | <footer> |
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312 | |
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313 | |
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314 | <hr/> |
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315 | |
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316 | <div role="contentinfo"> |
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317 | <p> |
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318 | © Copyright 2018, Anne Philipp and Leopold Haimberger |
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319 | |
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320 | </p> |
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321 | </div> |
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322 | Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. |
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