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[hg] galaxy 1724: upgrade bx-python to rev 460
by Nate Coraor 27 Jan '09

27 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/546e2d835e16 changeset: 1724:546e2d835e16 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 27 14:48:51 2009 -0500 description: upgrade bx-python to rev 460 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 6e88248dcc84 -r 546e2d835e16 eggs.ini --- a/eggs.ini Mon Jan 26 14:48:45 2009 -0500 +++ b/eggs.ini Tue Jan 27 14:48:51 2009 -0500 @@ -55,12 +55,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r459 +bx_python = _dev_r460 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r459.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r460.tar.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 1723: Fix For MAF Filter tool.
by Greg Von Kuster 26 Jan '09

26 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e88248dcc84 changeset: 1723:6e88248dcc84 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jan 26 14:48:45 2009 -0500 description: Fix For MAF Filter tool. Looks like when grouping parameter types were updated to be recursively wrapped properly, this tool was not updated. 1 file(s) affected in this change: tools/maf/maf_filter.xml diffs (32 lines): diff -r 2a81c4b95e20 -r 6e88248dcc84 tools/maf/maf_filter.xml --- a/tools/maf/maf_filter.xml Mon Jan 26 14:41:00 2009 -0500 +++ b/tools/maf/maf_filter.xml Mon Jan 26 14:48:45 2009 -0500 @@ -104,22 +104,22 @@ #if $len( $maf_filter['species1_attributes']['filter_condition'] ) == 0: #continue #end if - primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) if primary_component is not None: #if $maf_filter['species1_attributes']['species1_attribute_type'] == 'attribute_chr': - if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): + if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): #else - if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ): + if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ): #end if #for $filter_condition in $maf_filter['species1_attributes']['filter_condition']: - secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) #if $filter_condition['species2_attributes']['species2_attribute_type'] == 'attribute_chr': if secondary_component is not None: - if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): + if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): return False #else: if secondary_component is not None: - if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ) ): + if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ): return False #end if #end for

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[hg] galaxy 1722: Add a make_dict_copy method to Tool.execute so...
by Greg Von Kuster 26 Jan '09

26 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2a81c4b95e20 changeset: 1722:2a81c4b95e20 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jan 26 14:41:00 2009 -0500 description: Add a make_dict_copy method to Tool.execute so that when wrapping the tool's inputs to display output labels and such, we are not overwriting the incoming param dictionary. Also, yet another fix for tranlsating EOL to <br/> so they can be displayed in the data.info in the histoy. 2 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/tools/actions/__init__.py diffs (77 lines): diff -r 9abb83ad372d -r 2a81c4b95e20 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Sat Jan 24 12:13:47 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Mon Jan 26 14:41:00 2009 -0500 @@ -137,13 +137,14 @@ """Returns formatted html of dataset info""" try: # Change new line chars to html - if dataset.info.find( '\r\n' ) >= 0: - dataset.info = dataset.info.replace( '\r\n', '<br/>' ) - if dataset.info.find( '\r' ) >= 0: - dataset.info = dataset.info.replace( '\r', '<br/>' ) - if dataset.info.find( '\n' ) >= 0: - dataset.info = dataset.info.replace( '\n', '<br/>' ) - return escape( dataset.info ) + info = escape( dataset.info ) + if info.find( '\r\n' ) >= 0: + info = info.replace( '\r\n', '<br/>' ) + if info.find( '\r' ) >= 0: + info = info.replace( '\r', '<br/>' ) + if info.find( '\n' ) >= 0: + info = info.replace( '\n', '<br/>' ) + return info except: return "info unavailable" def validate(self, dataset): diff -r 9abb83ad372d -r 2a81c4b95e20 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Sat Jan 24 12:13:47 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Mon Jan 26 14:41:00 2009 -0500 @@ -6,6 +6,7 @@ from galaxy.web import url_for from galaxy.jobs import JOB_OK import galaxy.tools +from types import * import logging log = logging.getLogger( __name__ ) @@ -65,8 +66,21 @@ param_values[input.name] = input_datasets[ prefix + input.name ] tool.visit_inputs( param_values, visitor ) return input_datasets - + def execute(self, tool, trans, incoming={}, set_output_hid=True ): + def make_dict_copy( from_dict ): + """ + Makes a copy of input dictionary from_dict such that all values that are dictionaries + result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle + other complex types ( e.g., lists, etc ), but not sure... + """ + copy_from_dict = {} + for key, value in from_dict.items(): + if type( value ).__name__ == 'dict': + copy_from_dict[ key ] = make_dict_copy( value ) + else: + copy_from_dict[ key ] = value + return copy_from_dict def wrap_values( inputs, input_values ): # Wrap tool inputs as necessary for input in inputs.itervalues(): @@ -75,7 +89,7 @@ wrap_values( input.inputs, d ) elif isinstance( input, Conditional ): values = input_values[ input.name ] - current = values["__current_case__"] + current = values[ "__current_case__" ] wrap_values( input.cases[current].inputs, values ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ @@ -172,7 +186,7 @@ data.blurb = "queued" # Set output label if output.label: - params = dict( incoming ) + params = make_dict_copy( incoming ) # wrapping the params allows the tool config to contain things like # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" />

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[hg] galaxy 1721: Apparently I only committed these fixes to sec...
by Nate Coraor 24 Jan '09

24 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9abb83ad372d changeset: 1721:9abb83ad372d user: Nate Coraor <nate(a)bx.psu.edu> date: Sat Jan 24 12:13:47 2009 -0500 description: Apparently I only committed these fixes to security. Recommit of changeset 2015:7a447128f2cd from security, Make UCSC build update scripts find elementtree properly 3 file(s) affected in this change: cron/parse_builds.py cron/parse_builds_3_sites.py cron/updateucsc.sh.sample diffs (55 lines): diff -r f27a815ae734 -r 9abb83ad372d cron/parse_builds.py --- a/cron/parse_builds.py Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/parse_builds.py Sat Jan 24 12:13:47 2009 -0500 @@ -8,8 +8,12 @@ import sys import urllib -import pkg_resources; pkg_resources.require( "elementtree" ) -from elementtree import ElementTree +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.ElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree URL = "http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" diff -r f27a815ae734 -r 9abb83ad372d cron/parse_builds_3_sites.py --- a/cron/parse_builds_3_sites.py Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/parse_builds_3_sites.py Sat Jan 24 12:13:47 2009 -0500 @@ -5,8 +5,12 @@ import sys import urllib -import pkg_resources; pkg_resources.require( "elementtree" ) -from elementtree import ElementTree +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.ElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree sites = ['http://genome.ucsc.edu/cgi-bin/', 'http://archaea.ucsc.edu/cgi-bin/', diff -r f27a815ae734 -r 9abb83ad372d cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/updateucsc.sh.sample Sat Jan 24 12:13:47 2009 -0500 @@ -6,7 +6,7 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/modules:${GALAXY}/eggs:${GALAXY}/lib +export PYTHONPATH=${GALAXY}/lib # setup directories mkdir ${GALAXY}/tool-data/shared/ucsc/new @@ -57,4 +57,4 @@ echo "Manual addition was successful." else echo "Manual addition failed" >&2 -fi \ No newline at end of file +fi

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Alignment Extractors - in batch?
by Abhi Ratnakumar 23 Jan '09

23 Jan '09

Hello, I have multiple sequence alignment files in the *maf format, containing whole genome alignments from 6 species. I'm interested in extracting the sequence surrounding the exons of ~16,000 genes. I was wondering if it would be possible to run the Alignment Extractors tool in batch? Would it be possible for me to run it on the command line? Thanks ins Advance Abhi Ratnakumar By the way I'm a PhD student at Uppsala University, so any executables that you provide will be used for academic purposes only.

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[hg] galaxy 1720: in JobWrapper.fail(), save the traceback befor...
by Nate Coraor 23 Jan '09

23 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f27a815ae734 changeset: 1720:f27a815ae734 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 23 14:12:52 2009 -0500 description: in JobWrapper.fail(), save the traceback before doing anything else that might result in a traceback 1 file(s) affected in this change: lib/galaxy/jobs/__init__.py diffs (24 lines): diff -r 4fa4d0ddbf1f -r f27a815ae734 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Jan 23 12:55:35 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Jan 23 14:12:52 2009 -0500 @@ -381,6 +381,10 @@ job.refresh() # if the job was deleted, don't fail it if not job.state == model.Job.states.DELETED: + # If the failure is due to a Galaxy framework exception, save the traceback + # Do this first in case we generate a traceback below + if exception: + job.traceback = traceback.format_exc() for dataset_assoc in job.output_datasets: if self.app.config.outputs_to_working_directory: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.dataset.id ) ) @@ -399,9 +403,6 @@ job.state = model.Job.states.ERROR job.command_line = self.command_line job.info = message - # If the failure is due to a Galaxy framework exception, save the traceback - if exception: - job.traceback = traceback.format_exc() job.flush() # If the job was deleted, just clean up self.cleanup()

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[hg] galaxy 1719: Fix an infinite loop in eggs.require()
by Nate Coraor 23 Jan '09

23 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4fa4d0ddbf1f changeset: 1719:4fa4d0ddbf1f user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 23 12:55:35 2009 -0500 description: Fix an infinite loop in eggs.require() 1 file(s) affected in this change: lib/galaxy/eggs/__init__.py diffs (31 lines): diff -r 520c6e39b3d0 -r 4fa4d0ddbf1f lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Thu Jan 22 12:46:37 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Fri Jan 23 12:55:35 2009 -0500 @@ -530,7 +530,7 @@ return except pkg_resources.VersionConflict, e: # there's a conflicting egg on the pythonpath, remove it - dist = pkg_resources.get_distribution( name ) + dist = e.args[0] working_set = pkg_resources.working_set # use the canonical path for comparisons location = os.path.realpath( dist.location ) @@ -543,18 +543,6 @@ del working_set.by_key[dist.key] working_set.entry_keys[entry] = [] sys.path.remove(entry) - # get - egg.find() - if not egg.have: - if not egg.fetch(): - raise EggNotFetchable( egg.name ) - pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) - if dist.project_name in sys.modules: - try: - mod = sys.modules[dist.project_name] - reload( mod ) - except: - raise NewEgg( "Galaxy downloaded a new egg (%s) but was unable to reload the module it contained. Please try starting Galaxy again." % egg.name ) except pkg_resources.DistributionNotFound, e: # the initial require itself is the first dep, but it can have # multiple deps, which will be fetched by the require below.

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[hg] galaxy 1718: Changed grouping output to tabular
by Nate Coraor 23 Jan '09

23 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/520c6e39b3d0 changeset: 1718:520c6e39b3d0 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 22 12:46:37 2009 -0500 description: Changed grouping output to tabular 1 file(s) affected in this change: tools/stats/grouping.xml diffs (12 lines): diff -r 4004ab767cf6 -r 520c6e39b3d0 tools/stats/grouping.xml --- a/tools/stats/grouping.xml Thu Jan 22 12:29:44 2009 -0500 +++ b/tools/stats/grouping.xml Thu Jan 22 12:46:37 2009 -0500 @@ -33,7 +33,7 @@ </repeat> </inputs> <outputs> - <data format="input" name="out_file1" metadata_source="input1" /> + <data format="tabular" name="out_file1" /> </outputs> <requirements> <requirement type="python-module">rpy</requirement>

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[hg] galaxy 1717: Update welcome page with Anton's copy from sec...
by Nate Coraor 22 Jan '09

22 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4004ab767cf6 changeset: 1717:4004ab767cf6 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jan 22 12:29:44 2009 -0500 description: Update welcome page with Anton's copy from security 1 file(s) affected in this change: static/welcome.html diffs (116 lines): diff -r 19d18731ce19 -r 4004ab767cf6 static/welcome.html --- a/static/welcome.html Thu Jan 22 11:22:39 2009 -0500 +++ b/static/welcome.html Thu Jan 22 12:29:44 2009 -0500 @@ -6,48 +6,80 @@ <meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> <title></title> <link rel="stylesheet" href="style/base.css" type="text/css" /> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> + <title></title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/"/> + <script src="http://www.apple.com/library/quicktime/scripts/ac_quicktime.js" language="JavaScript" type="text/javascript"></script> + <script src="http://www.apple.com/library/quicktime/scripts/qtp_library.js" language="JavaScript" type="text/javascript"></script> + <link href="http://www.apple.com/library/quicktime/stylesheets/qtp_library.css" rel="StyleSheet" type="text/css" /> + <link rel="stylesheet" href="style/base.css" type="text/css" /> + </head> + </head> <body> <div class="document"> -<div class="warningmessage"> - <strong>Galaxy and 2008 Meeting Season</strong> - <hr> - <ul> - <li><a target="_blank" href="http://www.beyondgenome.com/08Personalized_Medicine_Day1.asp">Beyond Genome</a> | San Francisco | June 9 - 11</li> - <li>ISMB 2008 | Toronto | July 19 - 23</li> - <li>Genome Informatics | Hinxton, UK | September 10 - 14</li> - <li><a target="_blank" href="http://www.ashg.org/2008meeting/pages/workshops.shtml#4">ASHG</a> | Philadelphia | November 11 - 15</li> - </ul> - <hr> - Download <strong>new</strong> Galaxy brochure <a href="/static/images/brochure.pdf">here</a>. +<div class="infomessage"> + <strong>We are hiring!</strong> + <hr> + Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click <a target="_blank" href="https://www.bx.psu.edu/cgi-bin/trac.cgi/galaxy/wiki/PythonDeveloper">here</a>. </div> <hr> -<div class="section" align="center"> - <strong>Unsequenced Genomes of the World</strong> | June 2008 - <br> - <br> - <img src="images/welcomePhoto.jpg" border="0"> - <br> - Przewalski's Horse (<i>Equus przewalskii</i>) | Escondido, California - <br> - <br> -</div> +<div class="welcomeBlue" id="screencasts" align="center"> +<strong>Introducing Galactic Quickies</strong> + <hr> + Galactic quickies are <i>super-short</i> screencasts that are <i>always</i> under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly. + <hr> + <table width="100%" border="0" height="100%"> + <tr> + <td valign="middle" align="center"> + + <br> + <script type="text/javascript"> + + </script> + <noscript> + <object width="640" height="480" classid="clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B" codebase="http://www.apple.com/qtactivex/qtplugin.cab"> + <param name="src" value="http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.jpg" /> + <param name="href" value="http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.mov" /> + <param name="target" value="myself" /> + <param name="controller" value="false" /> + <param name="autoplay" value="false" /> + <param name="scale" value="aspect" /> + <embed width="640" height="480" type="video/quicktime" pluginspage="http://www.apple.com/quicktime/download/" + src="http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.jpg" + href="http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.mov" + target="myself" + controller="false" + autoplay="false" + scale="aspect"> + </embed> + </object> + </noscript> + + </td> + </tr> + </table> + <br> + For a high resolution version <a target="_blank" class="reference" href="http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/">click here</a>. + <br> + <hr> + </div> <hr> -<div class="welcomeBlue"> - <strong>Galaxy is for Biologists</strong> - <br> - Use this site to access popular sources of data like the UCSC Table Browser. Run analyses right on the spot using a variety of integrated tools. Your results are always available and can be easily shared with others. Just <a target="_blank" href="http://g2.trac.bx.psu.edu/wiki/ScreenCasts">watch</a> how. -</div> -<br> -<div class="welcomeRed"> - <strong>Galaxy is for Developers</strong> - <br> - Galaxy is an easy-to-use, open-source, scalable framework for tool and data integration. Stop wasting time writing interfaces and get your tools used by biologists! Galaxy includes everything you need to get started, so <a target="_blank" href="http://g2.trac.bx.psu.edu/wiki/HowToInstall">download</a> and start <a target="_blank" href="http://g2.trac.bx.psu.edu/wiki/HowToInstall">integrating</a>! -</div> + <p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> <hr class="docutils" /> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a> and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. <p><small>Galaxy build: <b>$Rev$</b></small></p>

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[hg] galaxy 1716: Fixes in the upload tool for removing temporar...
by Nate Coraor 22 Jan '09

22 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/19d18731ce19 changeset: 1716:19d18731ce19 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Jan 22 11:22:39 2009 -0500 description: Fixes in the upload tool for removing temporary files. 1 file(s) affected in this change: lib/galaxy/tools/actions/upload.py diffs (81 lines): diff -r 5c293dbf0726 -r 19d18731ce19 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Jan 22 08:50:52 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Thu Jan 22 11:22:39 2009 -0500 @@ -13,7 +13,11 @@ def __init__( self ): self.empty = False self.line_count = None - + def remove_tempfile( self, filename ): + try: + os.unlink( filename ) + except: + log.exception( 'failure removing temporary file: %s' % filename ) def execute( self, tool, trans, incoming={}, set_output_hid = True ): data_file = incoming['file_data'] file_type = incoming['file_type'] @@ -48,6 +52,7 @@ data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) ) + self.remove_tempfile( data_file.local_filename ) return self.upload_empty( trans, job, "Error:", str( e ) ) elif 'filename' in dir( data_file ): file_name = data_file.filename @@ -57,16 +62,13 @@ temp_name = sniff.stream_to_file( data_file.file, prefix='upload' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) if url_paste not in [ None, "" ]: if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0: @@ -78,16 +80,13 @@ temp_name = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, line, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) ) except Exception, e: log.exception( 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) else: is_valid = False @@ -101,16 +100,13 @@ temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) except Exception, e: log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) - try: - # Attempt to remove temporary file - os.unlink( temp_name ) - except: - log.exception( 'failure removing temporary file: %s' % temp_name ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) try: data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) ) except Exception, e: log.excception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) + self.remove_tempfile( temp_name ) return self.upload_empty( trans, job, "Error:", str( e ) ) else: return self.upload_empty( trans, job, "No data error:", "you pasted no data." )

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