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[hg] galaxy 1548: Treat EpiGRAPH as a data source much like ucsc...
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ae341e281c89 changeset: 1548:ae341e281c89 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Oct 06 13:34:51 2008 -0400 description: Treat EpiGRAPH as a data source much like ucsc table browser. 6 file(s) affected in this change: lib/galaxy/tools/__init__.py tool_conf.xml.sample tools/data_destination/epigraph.xml tools/data_source/epigraph.py tools/data_source/epigraph_code.py tools/data_source/epigraph_import.xml diffs (174 lines): diff -r 684b78f79f8b -r ae341e281c89 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Oct 06 11:48:35 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Oct 06 13:34:51 2008 -0400 @@ -1070,11 +1070,10 @@ def parse_redirect_url( self, inp_data, param_dict ): """Parse the REDIRECT_URL tool param""" - # Tools that send data to an external application via a redirect must include the following 3 - # tool params: + # Tools that send data to an external application via a redirect must include the following 3 tool params: # REDIRECT_URL - the url to which the data is being sent # DATA_URL - the url to which the receiving application will send an http post to retrieve the Galaxy data - # GALAXY_URL - the to which the external application may post data as a response + # GALAXY_URL - the url to which the external application may post data as a response redirect_url = param_dict.get( 'REDIRECT_URL' ) redirect_url_params = self.build_redirect_url_params( param_dict ) # Add the parameters to the redirect url. We're splitting the param string on '**^**' diff -r 684b78f79f8b -r ae341e281c89 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Oct 06 11:48:35 2008 -0400 +++ b/tool_conf.xml.sample Mon Oct 06 13:34:51 2008 -0400 @@ -10,6 +10,7 @@ <tool file="data_source/biomart_test.xml" /> <tool file="data_source/gbrowse_elegans.xml" /> <tool file="data_source/flymine.xml" /> + <tool file="data_source/epigraph_import.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> diff -r 684b78f79f8b -r ae341e281c89 tools/data_destination/epigraph.xml --- a/tools/data_destination/epigraph.xml Mon Oct 06 11:48:35 2008 -0400 +++ b/tools/data_destination/epigraph.xml Mon Oct 06 13:34:51 2008 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Perform EpiGRAPH" id="epigraph"> - <description> Genome analysis and prediction</description> +<tool name="Perform genome" id="epigraph_export"> + <description> analysis and prediction with EpiGRAPH</description> <redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name} INFO=${input1.info}</redirect_url_params> <inputs> <param format="bed" name="input1" type="data" label="Send this dataset to EpiGRAPH"> diff -r 684b78f79f8b -r ae341e281c89 tools/data_source/epigraph.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/epigraph.py Mon Oct 06 13:34:51 2008 -0400 @@ -0,0 +1,66 @@ +#!/usr/bin/env python +#Retreives data from EpiGRAPH and stores in a file. EpiGRAPH request parameters are provided in the input/output file. +import urllib, sys, os, gzip, tempfile, shutil +from galaxy import eggs +from galaxy.datatypes import data + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def check_gzip( filename ): + temp = open( filename, "U" ) + magic_check = temp.read( 2 ) + temp.close() + if magic_check != data.gzip_magic: + return False + return True + +def __main__(): + filename = sys.argv[1] + params = {} + for line in open( filename, 'r' ): + try: + line = line.strip() + fields = line.split( '\t' ) + params[ fields[0] ] = fields[1] + except: + continue + URL = params.get( 'URL', None ) + if not URL: + open( filename, 'w' ).write( "" ) + stop_err( 'EpiGRAPH has not sent back a URL parameter.' ) + out = open( filename, 'w' ) + CHUNK_SIZE = 2**20 # 1Mb + try: + page = urllib.urlopen( URL, urllib.urlencode( params ) ) + except: + stop_err( 'It appears that the EpiGRAPH server is currently off-line. Please try again later.' ) + while 1: + chunk = page.read( CHUNK_SIZE ) + if not chunk: + break + out.write( chunk ) + out.close() + if check_gzip( filename ): + fd, uncompressed = tempfile.mkstemp() + gzipped_file = gzip.GzipFile( filename ) + while 1: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + gzipped_file.close() + stop_err( 'Problem uncompressing gzipped data, please try retrieving the data uncompressed.' ) + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + # Replace the gzipped file with the uncompressed file + shutil.move( uncompressed, filename ) + +if __name__ == "__main__": __main__() diff -r 684b78f79f8b -r ae341e281c89 tools/data_source/epigraph_code.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/epigraph_code.py Mon Oct 06 13:34:51 2008 -0400 @@ -0,0 +1,41 @@ +#Code for direct connection to EpiGRAPH +from galaxy.datatypes import sniff +import urllib + +def exec_before_job( app, inp_data, out_data, param_dict, tool=None ): + """ + EpiGRAPH sends data to Galaxy by passing the following parameters in the request: + 1. URL - the url to which Galaxy should post a request to retrieve the data + 2. GENOME - the name of the UCSC genome assembly (e.g. hg18), dbkey in Galaxy + 3. NAME - data.name in Galaxy + 4. INFO - data.info in Galaxy + """ + items = out_data.items() + for name, data in items: + NAME = urllib.unquote( param_dict.get( 'NAME', None ) ) + if NAME is not None: + data.name = NAME + INFO = urllib.unquote( param_dict.get( 'INFO', None ) ) + if INFO is not None: + data.info = INFO + GENOME = urllib.unquote( param_dict.get( 'GENOME', None ) ) + if GENOME is not None: + data.dbkey = GENOME + else: + data.dbkey = '?' + # Store EpiGRAPH request parameters temporarily in output file + out = open( data.file_name, 'w' ) + for key, value in param_dict.items(): + print >> out, "%s\t%s" % ( key, value ) + out.close() + out_data[ name ] = data + +def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None ): + """Verifies the datatype after the run""" + name, data = out_data.items()[0] + if data.extension == 'txt': + data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) + data = app.datatypes_registry.change_datatype( data, data_type ) + data.set_peek() + data.set_size() + data.flush() diff -r 684b78f79f8b -r ae341e281c89 tools/data_source/epigraph_import.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/epigraph_import.xml Mon Oct 06 13:34:51 2008 -0400 @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool name="EpiGRAPH" id="epigraph_import"> + <description> server</description> + <command interpreter="python">epigraph.py $output</command> + <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get"> + <display>go to EpiGRAPH server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" /> + </inputs> + <uihints minwidth="800"/> + <code file="epigraph_code.py"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

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[svn] [2774] Changed a couple constants in sputnik, as per Guru.
by nate＠bx.psu.edu 10 Oct '08

10 Oct '08

Revision: 2774 Author: nate Date: 2008-10-10 14:27:43 -0400 (Fri, 10 Oct 2008) Log Message: ----------- Changed a couple constants in sputnik, as per Guru. Modified Paths: -------------- dependencies/sputnik/sputnik.c Modified: dependencies/sputnik/sputnik.c =================================================================== --- dependencies/sputnik/sputnik.c 2008-09-24 14:26:07 UTC (rev 2773) +++ dependencies/sputnik/sputnik.c 2008-10-10 18:27:43 UTC (rev 2774) @@ -53,9 +53,9 @@ /* this is the point score for each exact match */ #define EXACT_MATCH_POINTS 1 /* this is the point score for a mismatch, insertion or deletion */ -#define ERROR_MATCH_POINTS -6 +#define ERROR_MATCH_POINTS -100 /* this is the minimum score required to be considered a match */ -#define MATCH_MIN_SCORE 8 +#define MATCH_MIN_SCORE 4 /* this is the low score at which we stop trying */ #define MATCH_FAIL_SCORE -1 /* this is the max recursion depth we try to recover errors */

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Re: [galaxy-dev] galaxy-dev Digest, Vol 33, Issue 21
by Ross 06 Oct '08

06 Oct '08

I may be missing something, but right now, and without any changes to Galaxy, there's no reason why a new tool should not wrap an existing (or new) command line executable program that uses web services to do something interesting! I have an rgenetics tool that uses the Haploview java executable in command line mode to prepare image files of LD patterns in the Hapmap populations with an inhouse sample over a region, and then stitches them together into a single image so they can be visually compared - Galaxy doesn't know or care if the tool executable uses web services - the job runner sets up the call and then deals with the resulting tool outputs correctly - as long as the cluster node executing the tool has internet access, it can interact with the web services transparently - as Greg says, the tool will be fragile to changes in the web service call syntax but that's always a problem in the long term. I agree with Greg that bringing web services interfaces *directly* into the existing Galaxy framework does not appear to have a high priority at this time and I'm not even sure that it makes an awful lot of sense in the long term - especially since we can let web service interaction live out in tool space where it already works? Is there a specific use-case anyone has in mind where the web services interface really needs to be brought inside the framework itself? On Tue, Sep 30, 2008 at 2:00 AM, <galaxy-dev-request(a)bx.psu.edu> wrote: > > Today's Topics: > > 1. Re: Galaxy with web services (Greg Von Kuster) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 Sep 2008 09:52:39 -0400 > From: Greg Von Kuster <ghv2(a)psu.edu> > Subject: Re: [galaxy-dev] Galaxy with web services > To: Praveen Agrawal <praveen(a)scfbio-iitd.res.in> > Cc: galaxy-dev(a)bx.psu.edu > Message-ID: <48E0DDA7.1090200(a)psu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Praveen, > > Currently web-based interaction is only used for external data sources > (biomart, UCSC table browser, most other things under "Get Data"). For > the other tools, we generate a command line based on the user input, > which Galaxy then runs. The motivation for this is control and trust. > One of our major goals with Galaxy is to ensure reproducibility, and > relying on web services which can change their interfaces or behavior > makes this very challenging. We are certainly interested in supporting > web services in the Galaxy framework, but implementation is not yet > under way. Several of the methods currently in ~/tools/__init__.py ( > among others ) will need to evolve and grow in order to support a web > services interface for remote tools. We'll certainly keep you informed > as we begin to support this, but it may be a while... > > Greg Von Kuster > Galaxy Development Team > > > Praveen Agrawal wrote: >> Hi, >> I am trying to use Galaxy at my site and cann't figure out Galaxy with web >> services. I understand that it's possible to integrate a data source using >> WSDL/SOAP. Is the same possible for a remote tool as well? -- python -c "foo = map(None,'moc.liamg(a)surazal.ssor'); foo.reverse(); print ''.join(foo)"

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[hg] galaxy 1546: Updating "regional variation' section in tool_...
by Greg Von Kuster 06 Oct '08

06 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d93cf9d961bb changeset: 1546:d93cf9d961bb user: guru date: Mon Oct 06 09:40:47 2008 -0400 description: Updating "regional variation' section in tool_conf.xml.main. 1 file(s) affected in this change: tool_conf.xml.main diffs (33 lines): diff -r cec03ea2d5aa -r d93cf9d961bb tool_conf.xml.main --- a/tool_conf.xml.main Mon Oct 06 09:33:52 2008 -0400 +++ b/tool_conf.xml.main Mon Oct 06 09:40:47 2008 -0400 @@ -122,14 +122,22 @@ <tool file="visualization/build_ucsc_custom_track.xml" /> </section> <section name="Regional Variation" id="regVar"> - <tool file="regVariation/windowSplitter.xml" /> - <tool file="regVariation/featureCounter.xml" /> - <tool file="regVariation/quality_filter.xml" /> + <tool file="regVariation/windowSplitter.xml" /> + <tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/quality_filter.xml" /> <tool file="regVariation/maf_cpg_filter.xml" /> -  + <tool file="regVariation/getIndels_2way.xml" /> + <tool file="regVariation/getIndels_3way.xml" /> + <tool file="regVariation/getIndelRates_3way.xml" /> + <tool file="regVariation/substitutions.xml" /> + <tool file="regVariation/substitution_rates.xml" /> + <tool file="regVariation/microsats_alignment_level.xml" /> + <tool file="regVariation/microsats_mutability.xml" /> + </section> + <section name="Multiple regression" id="multReg"> + <tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/best_regression_subsets.xml" /> + <tool file="regVariation/rcve.xml" /> </section> <section name="Evolution: HyPhy" id="hyphy"> <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />

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[hg] galaxy 1545: Modified help message for indel rate tool.
by Greg Von Kuster 06 Oct '08

06 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cec03ea2d5aa changeset: 1545:cec03ea2d5aa user: guru date: Mon Oct 06 09:33:52 2008 -0400 description: Modified help message for indel rate tool. 1 file(s) affected in this change: tools/regVariation/getIndelRates_3way.xml diffs (25 lines): diff -r 7e2ec07716b8 -r cec03ea2d5aa tools/regVariation/getIndelRates_3way.xml --- a/tools/regVariation/getIndelRates_3way.xml Fri Oct 03 16:06:01 2008 -0400 +++ b/tools/regVariation/getIndelRates_3way.xml Mon Oct 06 09:33:52 2008 -0400 @@ -14,8 +14,8 @@ <conditional name="region"> <param name="type" type="select" label="Estimate rates corresponding to" multiple="false"> - <option value="align" selected="True">Alignment block</option> - <option value="win">Intervals in your history</option> + <option value="win" selected="True">Intervals in your history</option> + <option value="align">Alignment block</option> </param> <when value="win"> <param format="interval" name="input2" type="data" label="Choose intervals"> @@ -45,8 +45,8 @@ **What it does** -This tool estimates the insertion and deletion rates for alignments in a window of specified size. - +This tool estimates the insertion and deletion rates for alignments in a window of specified size. Rates are computed over the total adjusted lengths (adjusted by disregarding masked bases) of all the alignments blocks from the indel file that fall within that window. + ----- .. class:: warningmark

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[hg] galaxy 1544: Add axaj async undelete ability.
by Greg Von Kuster 06 Oct '08

06 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/7e2ec07716b8 changeset: 1544:7e2ec07716b8 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Oct 03 16:06:01 2008 -0400 description: Add axaj async undelete ability. Fix redisplay of dataset when asynchronously deleted under history view showing deleted datasets. 5 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py lib/galaxy/web/controllers/dataset.py templates/root/history.mako templates/root/history_common.mako templates/root/history_item.mako diffs (183 lines): diff -r 45033114f82d -r 7e2ec07716b8 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Thu Oct 02 16:37:32 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Oct 03 16:06:01 2008 -0400 @@ -1052,7 +1052,7 @@ hid = "%s.%d" % ( parent_hid, i + 1 ) else: hid = str( data.hid ) - if not data.deleted and data.state not in [data.states.ERROR] and data.visible: + if not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and data.visible: if self.options and data.get_dbkey() != filter_value: continue if isinstance( data.datatype, self.formats): @@ -1112,7 +1112,7 @@ return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): if self.options and data.get_dbkey() != filter_value: continue most_recent_dataset[0] = data diff -r 45033114f82d -r 7e2ec07716b8 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Oct 02 16:37:32 2008 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Oct 03 16:06:01 2008 -0400 @@ -128,9 +128,8 @@ return open(file_path) except: raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % (filename) ) - - @web.expose - def undelete( self, trans, id ): + + def _undelete( self, trans, id ): history = trans.get_history() data = self.app.model.HistoryDatasetAssociation.get( id ) if data and data.undeletable: @@ -143,4 +142,16 @@ data.mark_undeleted() self.app.model.flush() trans.log_event( "Dataset id %s has been undeleted" % str(id) ) + return True + return False + + @web.expose + def undelete( self, trans, id ): + self._undelete( trans, id ) return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) + + @web.expose + def undelete_async( self, trans, id ): + if self._undelete( trans, id ): + return "OK" + raise "Error undeleting" diff -r 45033114f82d -r 7e2ec07716b8 templates/root/history.mako --- a/templates/root/history.mako Thu Oct 02 16:37:32 2008 -0400 +++ b/templates/root/history.mako Fri Oct 03 16:06:01 2008 -0400 @@ -91,17 +91,41 @@ url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), error: function() { alert( "Delete failed" ) }, success: function() { - q( "#historyItem-" + data_id ).fadeOut( "fast", function() { - q( "div#historyItemContainer-" + data_id ).remove(); - if ( q( "div.historyItemContainer" ).length < 1 ) { - q ( "div#emptyHistoryMessage" ).show(); + if ( "${show_deleted}" == "True" ){ + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); } - }); + else { + q( "#historyItem-" + data_id ).fadeOut( "fast", function() { + q( "div#historyItemContainer-" + data_id ).remove(); + if ( q( "div.historyItemContainer" ).length < 1 ) { + q ( "div#emptyHistoryMessage" ).show(); + } + }); + } } }); return false; }); }); + // Undelete link + q(this).find( "a.historyItemUndelete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + q(this).click( function() { + q( '#progress-' + data_id ).show(); + q.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } + }); + return false; + }); + }); }); }; // Looks for changes in dataset state using an async request. Keeps @@ -143,7 +167,7 @@ setupHistoryItem( container.children( ".historyItemWrapper" ) ); initShowHide(); // If new state was terminal, stop tracking - if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" )) { + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { delete tracked_datasets[ parseInt(id) ]; } else { tracked_datasets[ parseInt(id) ] = val.state; @@ -239,7 +263,7 @@ %for data in reversed( datasets_to_show ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted )} </div> %endif %endfor diff -r 45033114f82d -r 7e2ec07716b8 templates/root/history_common.mako --- a/templates/root/history_common.mako Thu Oct 02 16:37:32 2008 -0400 +++ b/templates/root/history_common.mako Fri Oct 03 16:06:01 2008 -0400 @@ -1,5 +1,5 @@ ## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid )"> +<%def name="render_dataset( data, hid, show_deleted_on_refresh = False )"> <% if data.state in ['no state','',None]: data_state = "queued" @@ -10,7 +10,7 @@ %if data.deleted: <div class="warningmessagesmall"> - <strong>This dataset has been deleted. Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" target="galaxy_history">here</a> to undelete.</strong> + <strong>This dataset has been deleted. Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" class="historyItemUndelete" id="historyItemUndeleter-${data.id}" target="galaxy_history">here</a> to undelete.</strong> </div> %endif ## Header row for history items (name, state, action buttons) @@ -28,7 +28,7 @@ <div style="float: right;"> <a href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"><img src="${h.url_for('/static/images/eye_icon.png')}" rollover="${h.url_for('/static/images/eye_icon_dark.png')}" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a> <a href="${h.url_for( action='edit', id=data.id )}" target="galaxy_main"><img src="${h.url_for('/static/images/pencil_icon.png')}" rollover="${h.url_for('/static/images/pencil_icon_dark.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a> - <a href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted )}" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="${h.url_for('/static/images/delete_icon.png')}" rollover="${h.url_for('/static/images/delete_icon_dark.png')}" width='16' height='16' alt='delete' class='deleteButton' border='0'></a> + <a href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" class="historyItemDelete" id="historyItemDeleter-${data.id}"><img src="${h.url_for('/static/images/delete_icon.png')}" rollover="${h.url_for('/static/images/delete_icon_dark.png')}" width='16' height='16' alt='delete' class='deleteButton' border='0'></a> </div> <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span> </div> @@ -44,6 +44,10 @@ <div> An error occurred running this job: <i>${data.display_info().strip()}</i>, <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a> + </div> + %elif data_state == "discarded": + <div> + The job creating this dataset was cancelled before completion. </div> %elif data_state == "empty": <div>No data: <i>${data.display_info()}</i></div> @@ -95,7 +99,7 @@ <div> There are ${len( children )} secondary datasets. %for idx, child in enumerate(children): - ${render_dataset( child, idx + 1 )} + ${render_dataset( child, idx + 1, show_deleted_on_refresh = show_deleted_on_refresh )} %endfor </div> %endif diff -r 45033114f82d -r 7e2ec07716b8 templates/root/history_item.mako --- a/templates/root/history_item.mako Thu Oct 02 16:37:32 2008 -0400 +++ b/templates/root/history_item.mako Fri Oct 03 16:06:01 2008 -0400 @@ -1,8 +1,3 @@ <%namespace file="history_common.mako" import="render_dataset" /> -## this is necessary because this dataset remains in history.active_datasets -## after deletion, until the history is reloaded -## FIXME: still necessary now that we don't re-pull finished datasets? test. -%if data.deleted is not True: - ${render_dataset( data, hid )} -%endif \ No newline at end of file +${render_dataset( data, hid )}

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[hg] galaxy 1543: Add the ability to undelete deleted datasets f...
by Greg Von Kuster 06 Oct '08

06 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/45033114f82d changeset: 1543:45033114f82d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 02 16:37:32 2008 -0400 description: Add the ability to undelete deleted datasets from a history. A new selection under History Options allows users to select a history view containing deleted (and undeletable) datasets. Known Issues: 1. When adding a new dataset to a history (tool execution), the history is always refreshed to show only non-deleted datasets. 2. When doing an ajax delete of a dataset while viewing deleted datasets, the newly deleted dataset is still removed from the current view of the history (instead of appearing with the deleted message), a refresh will bring it back. 8 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py templates/history/options.mako templates/root/history.mako templates/root/history_common.mako diffs (190 lines): diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/model/__init__.py Thu Oct 02 16:37:32 2008 -0400 @@ -281,7 +281,15 @@ for child in self.children: child.mark_deleted() - + def mark_undeleted( self, include_children=True ): + self.deleted = False + if include_children: + for child in self.children: + child.mark_undeleted() + def undeletable( self ): + if self.purged: + return False + return True class History( object ): def __init__( self, id=None, name=None, user=None ): diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/model/mapping.py Thu Oct 02 16:37:32 2008 -0400 @@ -288,7 +288,9 @@ assign_mapper( context, History, History.table, properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), - active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) ) ) + active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ), + activatable_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( Dataset.table.c.purged ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) + ) ) assign_mapper( context, User, User.table, properties=dict( histories=relation( History, backref="user", diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/util/__init__.py Thu Oct 02 16:37:32 2008 -0400 @@ -206,7 +206,7 @@ return '' def string_as_bool( string ): - if string.lower() in ( 'true', 'yes', 'on' ): + if str( string ).lower() in ( 'true', 'yes', 'on' ): return True else: return False diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Oct 02 16:37:32 2008 -0400 @@ -128,3 +128,19 @@ return open(file_path) except: raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % (filename) ) + + @web.expose + def undelete( self, trans, id ): + history = trans.get_history() + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data and data.undeletable: + # Walk up parent datasets to find the containing history + topmost_parent = data + while topmost_parent.parent: + topmost_parent = topmost_parent.parent + assert topmost_parent in history.datasets, "Data does not belong to current history" + # Mark undeleted + data.mark_undeleted() + self.app.model.flush() + trans.log_event( "Dataset id %s has been undeleted" % str(id) ) + return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 16:37:32 2008 -0400 @@ -48,7 +48,7 @@ ## ---- Root history display --------------------------------------------- @web.expose - def history( self, trans, as_xml=False ): + def history( self, trans, as_xml=False, show_deleted=False ): """ Display the current history, creating a new history if neccesary. @@ -63,7 +63,7 @@ return trans.fill_template_mako( "root/history_as_xml.mako", history=history ) else: template = "root/history.mako" - return trans.fill_template( "root/history.mako", history=history ) + return trans.fill_template( "root/history.mako", history = history, show_deleted = util.string_as_bool( show_deleted ) ) @web.expose def dataset_state ( self, trans, id=None, stamp=None ): @@ -271,7 +271,7 @@ datatypes=ldatatypes, err=None ) @web.expose - def delete( self, trans, id = None, **kwd): + def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): if id: if isinstance( id, list ): dataset_ids = id @@ -300,7 +300,7 @@ self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job - return self.history( trans ) + return self.history( trans, show_deleted = show_deleted_on_refresh ) @web.expose def delete_async( self, trans, id = None, **kwd): diff -r 20591fa0d05d -r 45033114f82d templates/history/options.mako --- a/templates/history/options.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/history/options.mako Thu Oct 02 16:37:32 2008 -0400 @@ -19,6 +19,7 @@ <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from the current history</li> <li><a href="${h.url_for( action='history_share' )}" target="galaxy_main">Share</a> current history</div> %endif + <li><a href="${h.url_for( action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in history</li> <li><a href="${h.url_for( action='history_delete', id=history.id )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> </ul> diff -r 20591fa0d05d -r 45033114f82d templates/root/history.mako --- a/templates/root/history.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/root/history.mako Thu Oct 02 16:37:32 2008 -0400 @@ -209,7 +209,10 @@ <body class="historyPage"> <div id="top-links" class="historyLinks"> - <a href="${h.url_for('history')}">refresh</a> + <a href="${h.url_for('history', show_deleted=show_deleted)}">refresh</a> + %if show_deleted: + | <a href="${h.url_for('history', show_deleted=False)}">hide deleted</a> + %endif </div> %if history.deleted: @@ -221,11 +224,19 @@ <%namespace file="history_common.mako" import="render_dataset" /> -%if len(history.active_datasets) < 1: +%if ( show_deleted and len( history.datasets ) < 1 ) or len( history.active_datasets ) < 1: <div class="infomessagesmall" id="emptyHistoryMessage"> %else: - ## Render all active (not deleted) datasets, ordered from newest to oldest - %for data in reversed( history.active_datasets ): + <% + if show_deleted: + #all datasets + datasets_to_show = history.activatable_datasets + else: + #active (not deleted) + datasets_to_show = history.active_datasets + %> + ## Render requested datasets, ordered from newest to oldest + %for data in reversed( datasets_to_show ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid )} diff -r 20591fa0d05d -r 45033114f82d templates/root/history_common.mako --- a/templates/root/history_common.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/root/history_common.mako Thu Oct 02 16:37:32 2008 -0400 @@ -8,8 +8,12 @@ %> <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}"> + %if data.deleted: + <div class="warningmessagesmall"> + <strong>This dataset has been deleted. Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" target="galaxy_history">here</a> to undelete.</strong> + </div> + %endif ## Header row for history items (name, state, action buttons) - <div style="overflow: hidden;" class="historyItemTitleBar"> <div style="float: left; padding-right: 3px;"> <div style='display: none;' id="progress-${data.id}"> @@ -24,7 +28,7 @@ <div style="float: right;"> <a href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"><img src="${h.url_for('/static/images/eye_icon.png')}" rollover="${h.url_for('/static/images/eye_icon_dark.png')}" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a> <a href="${h.url_for( action='edit', id=data.id )}" target="galaxy_main"><img src="${h.url_for('/static/images/pencil_icon.png')}" rollover="${h.url_for('/static/images/pencil_icon_dark.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a> - <a href="${h.url_for( action='delete', id=data.id )}" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="${h.url_for('/static/images/delete_icon.png')}" rollover="${h.url_for('/static/images/delete_icon_dark.png')}" width='16' height='16' alt='delete' class='deleteButton' border='0'></a> + <a href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted )}" class="historyItemDelete" id="historyItemDelter-${data.id}"><img src="${h.url_for('/static/images/delete_icon.png')}" rollover="${h.url_for('/static/images/delete_icon_dark.png')}" width='16' height='16' alt='delete' class='deleteButton' border='0'></a> </div> <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span> </div> @@ -100,4 +104,4 @@ </div> </div> -</%def> \ No newline at end of file +</%def>

1 0

fresh (this morning) security hg pull -u: OperationalError: (OperationalError) no such column: dataset.purged - same error with a new, empty db
by Ross 05 Oct '08

05 Oct '08

URL: http://localhost:8080/user/create File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/debug/prints.py', line 98 in __call__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg/beaker/session.py', line 103 in __call__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/rossl/py/galaxy_security/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/rossl/py/galaxy_security/lib/galaxy/web/controllers/user.py', line 120 in create trans.app.security_agent.setup_new_user( user ) File '/home/rossl/py/galaxy_security/lib/galaxy/security/__init__.py', line 42 in setup_new_user self.user_set_default_access( user, history = True, dataset = True ) File '/home/rossl/py/galaxy_security/lib/galaxy/security/__init__.py', line 196 in user_set_default_access for history in user.active_histories: File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/attributes.py', line 44 in __get__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/attributes.py', line 279 in get File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/strategies.py', line 466 in __call__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/query.py', line 878 in all File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/query.py', line 938 in __iter__ File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/query.py', line 941 in _execute_and_instances File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/session.py', line 628 in execute File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 844 in execute File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 895 in execute_clauseelement File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 907 in _execute_compiled File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 916 in __execute_raw File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 960 in _cursor_execute File '/home/rossl/py/galaxy_security/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py', line 942 in _handle_dbapi_exception OperationalError: (OperationalError) no such column: dataset.purged u'SELECT history.id AS history_id, history.create_time AS history_create_time, history.update_time AS history_update_time, history.user_id AS history_user_id, history.name AS history_name, history.hid_counter AS history_hid_counter, history.deleted AS history_deleted, history.purged AS history_purged, history.genome_build AS history_genome_build, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, history_dataset_association_1.id AS history_dataset_association_1_id, history_dataset_association_1.history_id AS history_dataset_association_1_history_id, history_dataset_association_1.dataset_id AS history_dataset_association_1_dataset_id, history_dataset_association_1.create_time AS history_dataset_association_1_create_time, history_dataset_association_1.update_time AS history_dataset_association_1_update_time, history_dataset_association_1.copied_from_history_dataset_association_id AS history_dataset_association_1_copied_from_history_dataset_association_id, history_dataset_association_1.copied_from_library_folder_dataset_association_id AS history_dataset_association_1_copied_from_library_folder_dataset_association_id, history_dataset_association_1.hid AS history_dataset_association_1_hid, history_dataset_association_1.name AS history_dataset_association_1_name, history_dataset_association_1.info AS history_dataset_association_1_info, history_dataset_association_1.blurb AS history_dataset_association_1_blurb, history_dataset_association_1.peek AS history_dataset_association_1_peek, history_dataset_association_1.extension AS history_dataset_association_1_extension, history_dataset_association_1.metadata AS history_dataset_association_1_metadata, history_dataset_association_1.parent_id AS history_dataset_association_1_parent_id, history_dataset_association_1.designation AS history_dataset_association_1_designation, history_dataset_association_1.deleted AS history_dataset_association_1_deleted, history_dataset_association_1.visible AS history_dataset_association_1_visible, dataset_2.id AS dataset_2_id, dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time AS dataset_2_update_time, dataset_2.state AS dataset_2_state, dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS dataset_2_purged, dataset_2.purgable AS dataset_2_purgable, dataset_2.external_filename AS dataset_2_external_filename, dataset_2._extra_files_path AS dataset_2__extra_files_path, dataset_2.file_size AS dataset_2_file_size, history_dataset_association_2.id AS history_dataset_association_2_id, history_dataset_association_2.history_id AS history_dataset_association_2_history_id, history_dataset_association_2.dataset_id AS history_dataset_association_2_dataset_id, history_dataset_association_2.create_time AS history_dataset_association_2_create_time, history_dataset_association_2.update_time AS history_dataset_association_2_update_time, history_dataset_association_2.copied_from_history_dataset_association_id AS history_dataset_association_2_copied_from_history_dataset_association_id, history_dataset_association_2.copied_from_library_folder_dataset_association_id AS history_dataset_association_2_copied_from_library_folder_dataset_association_id, history_dataset_association_2.hid AS history_dataset_association_2_hid, history_dataset_association_2.name AS history_dataset_association_2_name, history_dataset_association_2.info AS history_dataset_association_2_info, history_dataset_association_2.blurb AS history_dataset_association_2_blurb, history_dataset_association_2.peek AS history_dataset_association_2_peek, history_dataset_association_2.extension AS history_dataset_association_2_extension, history_dataset_association_2.metadata AS history_dataset_association_2_metadata, history_dataset_association_2.parent_id AS history_dataset_association_2_parent_id, history_dataset_association_2.designation AS history_dataset_association_2_designation, history_dataset_association_2.deleted AS history_dataset_association_2_deleted, history_dataset_association_2.visible AS history_dataset_association_2_visible \nFROM history LEFT OUTER JOIN history_dataset_association AS history_dataset_association_1 ON history_dataset_association_1.history_id = history.id AND NOT history_dataset_association_1.deleted LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association_1.dataset_id LEFT OUTER JOIN history_dataset_association AS history_dataset_association_2 ON history_dataset_association_2.history_id = history.id AND NOT dataset.purged LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id = history_dataset_association_2.dataset_id \nWHERE history.user_id = ? AND NOT history.deleted ORDER BY history.update_time DESC, history_dataset_association_1.hid ASC, dataset_1.oid, history_dataset_association_2.hid ASC, dataset_2.oid' [1]

1 0

[hg] galaxy 1542: Reverting to rev 1459.
by Greg Von Kuster 02 Oct '08

02 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/20591fa0d05d changeset: 1542:20591fa0d05d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 02 15:51:17 2008 -0400 description: Reverting to rev 1459. 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (458 lines): diff -r 993bed7b5e26 -r 20591fa0d05d lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 02 13:18:50 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 15:51:17 2008 -0400 @@ -21,7 +21,9 @@ @web.expose def index(self, trans, id=None, tool_id=None, mode=None, m_c=None, m_a=None, **kwd): - return trans.fill_template( "root/index.mako", tool_id=tool_id, m_c=m_c, m_a=m_a ) + return trans.fill_template( "root/index.mako", + tool_id=tool_id, + m_c=m_c, m_a=m_a ) ## ---- Tool related ----------------------------------------------------- @@ -66,10 +68,10 @@ @web.expose def dataset_state ( self, trans, id=None, stamp=None ): if id is not None: - try: - data = self.app.model.Dataset.get( id ) + try: + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return trans.show_error_message( "Unable to check dataset id %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) trans.response.headers['X-Dataset-State'] = data.state trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -80,13 +82,13 @@ @web.expose def dataset_code( self, trans, id=None, hid=None, stamp=None ): if id is not None: - try: - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + try: + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return trans.show_error_message( "Unable to check dataset id %s." % str( id ) ) + return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return trans.fill_template( "root/history_item.mako", data=hda.dataset, hid=hid ) + return trans.fill_template("root/history_item.mako", data=data, hid=hid) else: return trans.show_error_message( "Must specify a dataset id.") @@ -101,11 +103,11 @@ ids = map( int, ids.split( "," ) ) states = states.split( "," ) for id, state in zip( ids, states ): - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda.dataset.state != state: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data.state != state: rval[id] = { - "state": hda.dataset.state, - "html": trans.fill_template( "root/history_item.mako", data=hda, hid=hda.hid ) + "state": data.state, + "html": trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ) } return rval @@ -123,36 +125,36 @@ except: return "hid '%s' is invalid" %str( hid ) history = trans.get_history() - for hda in history.datasets: - if hda.hid == hid: - history_dataset_assoc = hda + for dataset in history.datasets: + if dataset.hid == hid: + data = dataset break else: - raise Exception( "History_dataset_association with hid '%s' does not exist." % str( hid ) ) + raise Exception( "No dataset with hid '%d'" % hid ) else: try: - history_dataset_assoc = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return "Dataset id '%s' is invalid." %str( id ) - if history_dataset_assoc: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( history_dataset_assoc.extension.lower() ) + return "Dataset id '%s' is invalid" %str( id ) + if data: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) if tofile: - fStat = os.stat(history_dataset_assoc.file_name) + fStat = os.stat(data.file_name) trans.response.headers['Content-Length'] = int(fStat.st_size) if toext[0:1] != ".": toext = "." + toext valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = history_dataset_assoc.name + fname = data.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (history_dataset_assoc.hid, fname, toext) - trans.log_event( "Display dataset id: '%s'." % str(id) ) + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) + trans.log_event( "Display dataset id: %s" % str(id) ) try: - return open( history_dataset_assoc.file_name ) + return open( data.file_name ) except: - return "Dataset id '%s' contains no content." % str( id ) + return "This dataset contains no content" else: - return "Dataset id '%s' does not exist." % str( id ) + return "No dataset with id '%s'" % str( id ) @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"): @@ -160,36 +162,36 @@ Returns child data directly into the browser, based upon parent_id and designation. """ try: - hda = self.app.model.HistoryDatasetAssociation.get( parent_id ) - if hda: - child = hda.get_child_by_designation( designation ) + data = self.app.model.HistoryDatasetAssociation.get( parent_id ) + if data: + child = data.get_child_by_designation(designation) if child: return self.display(trans, id=child.id, tofile=tofile, toext=toext) except Exception: pass - return "A child named '%s' could not be found for history_dataset_association id '%s'" % ( designation, str( parent_id ) ) + return "A child named %s could not be found for data %s" % ( designation, parent_id ) @web.expose def display_as( self, trans, id=None, display_app=None, **kwd ): """Returns a file in a format that can successfully be displayed in display_app""" - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: - trans.response.set_content_type( hda.get_mime() ) + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: + trans.response.set_content_type(data.get_mime()) trans.log_event( "Formatted dataset id %s for display at %s" % ( str(id), display_app ) ) - return hda.as_display_type( display_app, **kwd ) + return data.as_display_type(display_app, **kwd) else: - return "Dataset 'id' %s does not exist." % str( id ) + return "No data with id=%d" % id @web.expose def peek(self, trans, id=None): """Returns a 'peek' at the data""" - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: yield "<html><body><pre>" - yield hda.peek + yield data.peek yield "</pre></body></html>" else: - yield "Dataset 'id' %s does not exist." % str( id ) + yield "No data with id=%d" % id @web.expose def edit(self, trans, id=None, hid=None, **kwd): @@ -197,75 +199,76 @@ if hid is not None: history = trans.get_history() # TODO: hid handling - hda = history.datasets[ int( hid ) - 1 ] + data = history.datasets[ int( hid ) - 1 ] elif id is None: - return trans.show_error_message( "Problem loading dataset id '%s' with history id '%s'." % ( str( id ), str( hid ) ) ) + return trans.show_error_message( "Problem loading dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) else: - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda is None: - return trans.show_error_message( "Problem retrieving dataset 'id' %s with history id '%s'." % ( str( id ), str( hid ) ) ) + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data is None: + return trans.show_error_message( "Problem retrieving dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) p = util.Params(kwd, safe=False) if p.change: # The user clicked the Save button on the 'Change data type' form - trans.app.datatypes_registry.change_datatype( hda, p.datatype ) + trans.app.datatypes_registry.change_datatype( data, p.datatype ) trans.app.model.flush() elif p.save: # The user clicked the Save button on the 'Edit Attributes' form - hda.name = p.name - hda.info = p.info + data.name = p.name + data.info = p.info # The following for loop will save all metadata_spec items - for name, spec in hda.datatype.metadata_spec.items(): + for name, spec in data.datatype.metadata_spec.items(): if spec.get("readonly"): continue optional = p.get("is_"+name, None) if optional and optional == 'true': # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( hda.metadata, name, None ) + setattr(data.metadata,name,None) else: - setattr( hda.metadata, name, spec.unwrap( p.get( name, None ), p ) ) + setattr(data.metadata,name,spec.unwrap(p.get(name, None), p)) - hda.datatype.after_edit( hda ) + data.datatype.after_edit( data ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in hda.datatype.metadata_spec.items(): + for name, spec in data.datatype.metadata_spec.items(): # We need to be careful about the attributes we are resetting if name != 'name' and name != 'info' and name != 'dbkey': if spec.get( 'default' ): - setattr( hda.metadata, name, spec.unwrap( spec.get( 'default' ), spec ) ) - hda.datatype.set_meta( hda ) - hda.datatype.after_edit( hda ) + setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec )) + data.datatype.set_meta( data ) + data.datatype.after_edit( data ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.convert_data: """The user clicked the Convert button on the 'Convert to new format' form""" target_type = kwd.get("target_type", None) if target_type: - msg = hda.datatype.convert_dataset(trans, hda, target_type) + msg = data.datatype.convert_dataset(trans, data, target_type) return trans.show_ok_message( msg, refresh_frames=['history'] ) - hda.datatype.before_edit( hda ) + data.datatype.before_edit( data ) - if "dbkey" in hda.datatype.metadata_spec and not hda.metadata.dbkey: + if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability # This looks like it does nothing, but getting the dbkey # returns the metadata dbkey unless it is None, in which # case it resorts to the old dbkey. Setting the dbkey # sets it properly in the metadata - hda.metadata.dbkey = hda.dbkey + data.metadata.dbkey = data.dbkey metadata = list() # a list of MetadataParemeters - for name, spec in hda.datatype.metadata_spec.items(): + for name, spec in data.datatype.metadata_spec.items(): if spec.visible: - metadata.append( spec.wrap( hda.metadata.get( name ), hda ) ) + metadata.append( spec.wrap( data.metadata.get(name), data ) ) # let's not overwrite the imported datatypes module with the variable datatypes? ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()] ldatatypes.sort() - trans.log_event( "Opened edit view on dataset id '%s'" % str( id ) ) - return trans.fill_template( "/dataset/edit_attributes.mako", data=hda, metadata=metadata, datatypes=ldatatypes, err=None ) + trans.log_event( "Opened edit view on dataset %s" % str(id) ) + return trans.fill_template( "/dataset/edit_attributes.mako", data=data, metadata=metadata, + datatypes=ldatatypes, err=None ) @web.expose def delete( self, trans, id = None, **kwd): @@ -280,21 +283,21 @@ int( id ) except: continue - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: - # Walk up parent hdas to find the containing history - topmost_parent = hda + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: + # Walk up parent datasets to find the containing history + topmost_parent = data while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - hda.mark_deleted() - hda.clear_associated_files() + data.mark_deleted() + data.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id '%s' marked as deleted" % str( id ) ) - if hda.parent_id is None: + trans.log_event( "Dataset id %s marked as deleted" % str(id) ) + if data.parent_id is None: try: - self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) + self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return self.history( trans ) @@ -307,21 +310,21 @@ except: return "Dataset id '%s' is invalid" %str( id ) history = trans.get_history() - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: # Walk up parent datasets to find the containing history - topmost_parent = hda + topmost_parent = data while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - hda.mark_deleted() - hda.clear_associated_files() + data.mark_deleted() + data.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id '%s' marked as deleted async" % str( id ) ) - if hda.parent_id is None: + trans.log_event( "Dataset id %s marked as deleted async" % str(id) ) + if data.parent_id is None: try: - self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) + self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return "OK" @@ -331,7 +334,8 @@ @web.expose def history_options( self, trans ): """Displays a list of history related actions""" - return trans.fill_template( "/history/options.mako", user=trans.get_user(), history=trans.get_history() ) + return trans.fill_template( "/history/options.mako", + user = trans.get_user(), history = trans.get_history() ) @web.expose def history_delete( self, trans, id=None, **kwd): @@ -363,16 +367,16 @@ trans.log_event( "History id %s marked as deleted" % str(hid) ) else: return trans.show_message( "You must select at least one history to delete." ) - return trans.show_message( "History deleted: %s" % ",".join(history_names), refresh_frames=['history'] ) + return trans.show_message( "History deleted: %s" % ",".join(history_names), + refresh_frames=['history']) @web.expose def clear_history( self, trans ): """Clears the history for a user""" history = trans.get_history() - for hda in history.datasets: - hda.deleted = True - hda.dataset.deleted = True - hda.clear_associated_files() + for dataset in history.datasets: + dataset.deleted = True + dataset.clear_associated_files() self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @@ -420,7 +424,9 @@ if not isinstance( id, list ): id = [ id ] trans.log_event( "History id %s available" % str( id ) ) - return trans.fill_template( "/history/list.mako", ids=id, user=trans.get_user(), current_history=trans.get_history() ) + return trans.fill_template( "/history/list.mako", ids=id, + user=trans.get_user(), + current_history=trans.get_history() ) @web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): @@ -546,23 +552,23 @@ """Adds a POSTed file to a History""" try: history = trans.app.model.History.get( history_id ) - hda = trans.app.model.HistoryDatasetAssociation( name=name, info=info, extension=ext, dbkey=dbkey, create_dataset=True ) - hda.flush() - data_file = open( hda.file_name, "wb" ) + data = trans.app.model.HistoryDatasetAssociation( name = name, info = info, extension = ext, dbkey = dbkey, create_dataset = True ) + data.flush() + data_file = open( data.file_name, "wb" ) file_data.file.seek( 0 ) data_file.write( file_data.file.read() ) data_file.close() - hda.dataset.state = hda.dataset.states.OK - hda.init_meta() - hda.set_meta() - hda.flush() - history.add_dataset( hda ) + data.state = data.states.OK + data.init_meta() + data.set_meta() + data.flush() + history.add_dataset( data ) history.flush() - hda.set_peek() - hda.set_size() - hda.flush() - trans.log_event( "Added dataset id '%s' to history id '%s'." % ( str( hda.dataset_id ), str( history_id ) ) ) - return trans.show_ok_message( "Dataset id " + str( hda.dataset_id ) + " added to history id " + str( history_id ) + "." ) + data.set_peek() + data.set_size() + data.flush() + trans.log_event("Added dataset %d to history %d" %(data.id, trans.history.id)) + return trans.show_ok_message("Dataset "+str(data.hid)+" added to history "+str(history_id)+".") except: return trans.show_error_message("Adding File to History has Failed") @@ -570,11 +576,13 @@ def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" try: - old_hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - new_hda = old_hda.copy() + old_data = self.app.model.HistoryDatasetAssociation.get( id ) + new_data = old_data.copy() + ## new_data.parent = None + ## history = trans.app.model.History.get( old_data.history_id ) history = trans.get_history() - history.add_dataset( new_hda ) - new_hda.flush() + history.add_dataset(new_data) + new_data.flush() return trans.show_message( "<p>Secondary dataset has been made primary.</p>", refresh_frames=['history'] ) except: return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) @@ -594,7 +602,7 @@ @web.expose def dataset_errors( self, trans, id=None, **kwd ): """View/fix errors associated with dataset""" - hda = trans.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + data = trans.app.model.HistoryDatasetAssociation.get( id ) p = kwd if p.get("fix_errors", None): # launch tool to create new, (hopefully) error free dataset @@ -602,19 +610,18 @@ tool_params["tool_id"] = 'fix_errors' tool_params["runtool_btn"] = 'T' tool_params["input"] = id - tool_params["ext"] = hda.ext + tool_params["ext"] = data.ext # send methods selected - repair_methods = hda.datatype.repair_methods( hda ) + repair_methods = data.datatype.repair_methods( data ) methods = [] for method, description in repair_methods: - if method in p: - methods.append( method ) + if method in p: methods.append(method) tool_params["methods"] = ",".join(methods) url = "/tool_runner/index?" + urllib.urlencode(tool_params) trans.response.send_redirect(url) else: - history = trans.app.model.History.get( hda.history_id ) - return trans.fill_template('dataset/validation.tmpl', data=hda, history=history) + history = trans.app.model.History.get( data.history_id ) + return trans.fill_template('dataset/validation.tmpl', data=data, history=history) # ---- Debug methods ----------------------------------------------------

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[hg] galaxy 1541: Remove a debug statement from root controller...
by Greg Von Kuster 02 Oct '08

02 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/993bed7b5e26 changeset: 1541:993bed7b5e26 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 02 13:18:50 2008 -0400 description: Remove a debug statement from root controller... 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (11 lines): diff -r 0041f2ba49ed -r 993bed7b5e26 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 02 12:45:03 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 13:18:50 2008 -0400 @@ -281,7 +281,6 @@ except: continue hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - log.debug("***hda.dataset_id: %s" % str( hda.dataset_id)) if hda: # Walk up parent hdas to find the containing history topmost_parent = hda

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