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commit/galaxy-central: jgoecks: Add generic method for getting track type and use it when saving visualizations.
by Bitbucket 27 Jun '11

27 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b13d16085dfc/ changeset: b13d16085dfc user: jgoecks date: 2011-06-27 22:58:52 summary: Add generic method for getting track type and use it when saving visualizations. affected #: 2 files (861 bytes) --- a/static/scripts/trackster.js Mon Jun 27 15:44:59 2011 -0400 +++ b/static/scripts/trackster.js Mon Jun 27 16:58:52 2011 -0400 @@ -1524,6 +1524,7 @@ * ----> FeatureTrack * -------> ReadTrack * -------> ToolDataFeatureTrack + * -------> VcfTrack */ var Track = function(name, view, parent_element, data_url, data_query_wait) { // @@ -1556,6 +1557,32 @@ this.parent_element.append(this.container_div); }; extend(Track.prototype, { + /** Returns track type. */ + get_type: function() { + // Order is important: start with most-specific classes and go up the track hierarchy. + if (this instanceof LabelTrack) { + return "LabelTrack"; + } + else if (this instanceof ReferenceTrack) { + return "ReferenceTrack"; + } + else if (this instanceof LineTrack) { + return "LineTrack"; + } + else if (this instanceof ReadTrack) { + return "ReadTrack"; + } + else if (this instanceof ToolDataFeatureTrack) { + return "ToolDataFeatureTrack"; + } + else if (this instanceof VcfTrack) { + return "VcfTrack"; + } + else if (this instanceof FeatureTrack) { + return "FeatureTrack"; + } + return ""; + }, /** * Initialize and draw the track. */ --- a/templates/tracks/browser.mako Mon Jun 27 15:44:59 2011 -0400 +++ b/templates/tracks/browser.mako Mon Jun 27 16:58:52 2011 -0400 @@ -59,8 +59,7 @@ converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view; - - + /** * Add bookmark. */ @@ -85,7 +84,7 @@ view.has_changes = true; return new_bookmark; - } + }; $(function() { // Hide bookmarks by default right now. @@ -267,7 +266,7 @@ // Add track. tracks.push( { - "track_type": track.track_type, + "track_type": track.get_type(), "name": track.name, "hda_ldda": track.hda_ldda, "dataset_id": track.dataset_id, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: Rounded the outputs of regression to 10 significant digits.
by Bitbucket 27 Jun '11

27 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a3ef80ad2535/ changeset: a3ef80ad2535 user: guru date: 2011-06-27 21:44:59 summary: Rounded the outputs of regression to 10 significant digits. affected #: 2 files (631 bytes) --- a/test-data/regr_out.tabular Mon Jun 27 11:20:04 2011 -0400 +++ b/test-data/regr_out.tabular Mon Jun 27 15:44:59 2011 -0400 @@ -1,10 +1,10 @@ Y-intercept -28.1169126094 -p-value (Y-intercept) 0.294263204753 -Slope (c1) 5.74713412453 -p-value (c1) 0.0017328770415 -Slope (c2) 0.904274537427 -p-value (c2) 0.114667546826 -R-squared 0.938805439971 -Adjusted R-squared 0.921321279962 -F-statistic {'dendf': 7.0, 'value': 53.694626422997381, 'numdf': 2.0} -Sigma 7.43450071131 +p-value (Y-intercept) 0.2942632048 +Slope (c1) 5.7471341245 +p-value (c1) 0.001732877 +Slope (c2) 0.9042745374 +p-value (c2) 0.1146675468 +R-squared 0.93881 +Adjusted R-squared 0.92132 +F-statistic {'dendf': 7.0, 'value': '53.69463', 'numdf': 2.0} +Sigma 7.4345007113 --- a/tools/regVariation/linear_regression.py Mon Jun 27 11:20:04 2011 -0400 +++ b/tools/regVariation/linear_regression.py Mon Jun 27 15:44:59 2011 -0400 @@ -68,7 +68,6 @@ coeffs=linear_model.as_py()['coefficients'] yintercept= coeffs['(Intercept)'] -print >>fout, "Y-intercept\t%s" %(yintercept) summary = r.summary(linear_model) co = summary.get('coefficients', 'NA') @@ -76,15 +75,23 @@ if len(co) != len(x_vals)+1: stop_err("Stopped performing linear regression on the input data, since one of the predictor columns contains only non-numeric or invalid values.") """ -print >>fout, "p-value (Y-intercept)\t%s" %(co[0][3]) + +try: + yintercept = r.round(float(yintercept), digits=10) + pvaly = r.round(float(co[0][3]), digits=10) +except: + pass + +print >>fout, "Y-intercept\t%s" %(yintercept) +print >>fout, "p-value (Y-intercept)\t%s" %(pvaly) if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable try: - slope = coeffs['x'] + slope = r.round(float(coeffs['x']), digits=10) except: slope = 'NA' try: - pval = co[1][3] + pval = r.round(float(co[1][3]), digits=10) except: pval = 'NA' print >>fout, "Slope (c%d)\t%s" %(x_cols[0]+1,slope) @@ -92,18 +99,36 @@ else: #Multiple regression case with >1 predictors ind=1 while ind < len(coeffs.keys()): - print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,coeffs['x'+str(ind)]) try: - pval = co[ind][3] + slope = r.round(float(coeffs['x'+str(ind)]), digits=10) + except: + slope = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,slope) + try: + pval = r.round(float(co[ind][3]), digits=10) except: pval = 'NA' print >>fout, "p-value (c%d)\t%s" %(x_cols[ind-1]+1,pval) ind+=1 -print >>fout, "R-squared\t%s" %(summary.get('r.squared','NA')) -print >>fout, "Adjusted R-squared\t%s" %(summary.get('adj.r.squared','NA')) -print >>fout, "F-statistic\t%s" %(summary.get('fstatistic','NA')) -print >>fout, "Sigma\t%s" %(summary.get('sigma','NA')) +rsq = summary.get('r.squared','NA') +adjrsq = summary.get('adj.r.squared','NA') +fstat = summary.get('fstatistic','NA') +sigma = summary.get('sigma','NA') + +try: + rsq = r.round(float(rsq), digits=5) + adjrsq = r.round(float(adjrsq), digits=5) + fval = r.round(fstat['value'], digits=5) + fstat['value'] = str(fval) + sigma = r.round(float(sigma), digits=10) +except: + pass + +print >>fout, "R-squared\t%s" %(rsq) +print >>fout, "Adjusted R-squared\t%s" %(adjrsq) +print >>fout, "F-statistic\t%s" %(fstat) +print >>fout, "Sigma\t%s" %(sigma) r.pdf( outfile2, 8, 8 ) if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kellyv: Add missed dbkey setting to Tophat color-space wrapper
by Bitbucket 27 Jun '11

27 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0d9e5403de5b/ changeset: 0d9e5403de5b user: kellyv date: 2011-06-27 17:20:04 summary: Add missed dbkey setting to Tophat color-space wrapper affected #: 2 files (3.4 KB) --- a/tools/ngs_rna/tophat_color_wrapper.xml Fri Jun 24 16:55:43 2011 -0400 +++ b/tools/ngs_rna/tophat_color_wrapper.xml Mon Jun 27 11:20:04 2011 -0400 @@ -391,6 +391,23 @@ ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) ) </filter> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions></data><data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"><filter> @@ -401,9 +418,62 @@ ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) ) </filter> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data></outputs><tests> --- a/tools/ngs_rna/tophat_wrapper.xml Fri Jun 24 16:55:43 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Mon Jun 27 11:20:04 2011 -0400 @@ -386,7 +386,7 @@ ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) - ) + ) </filter><actions><conditional name="refGenomeSource.genomeSource"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 24 Jun '11

24 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d4bedd464938/ changeset: d4bedd464938 user: kellyv date: 2011-06-24 22:13:48 summary: Added new builds to manual builds list affected #: 1 file (209 bytes) --- a/tool-data/shared/ucsc/manual_builds.txt Thu Jun 23 15:39:57 2011 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Fri Jun 24 16:13:48 2011 -0400 @@ -702,3 +702,5 @@ Tcas_3.0 Red Flour Beetle (Tribolium castaneum) chrLG1=X=10877635,chrLG2=20218415,chrLG3=38791480,chrLG4=13894384,chrLG5=19135781,chrLG6=13176827,chrLG7=20532854,chrLG8=18021898,chrLG9=21459655,chrLG10=11386040 hg_g1k_v37 Homo sapiens b37 1=249250621,2=243199373,3=198022430,4=191154276,5=180915260,6=171115067,7=159138663,8=146364022,9=141213431,10=135534747,11=135006516,12=133851895,13=115169878,14=107349540,15=102531392,16=90354753,17=81195210,18=78077248,19=59128983,20=63025520,21=48129895,22=51304566,X=155270560,Y=59373566,MT=16569,GL000207.1=4262,GL000226.1=15008,GL000229.1=19913,GL000231.1=27386,GL000210.1=27682,GL000239.1=33824,GL000235.1=34474,GL000201.1=36148,GL000247.1=36422,GL000245.1=36651,GL000197.1=37175,GL000203.1=37498,GL000246.1=38154,GL000249.1=38502,GL000196.1=38914,GL000248.1=39786,GL000244.1=39929,GL000238.1=39939,GL000202.1=40103,GL000234.1=40531,GL000232.1=40652,GL000206.1=41001,GL000240.1=41933,GL000236.1=41934,GL000241.1=42152,GL000243.1=43341,GL000242.1=43523,GL000230.1=43691,GL000237.1=45867,GL000233.1=45941,GL000204.1=81310,GL000198.1=90085,GL000208.1=92689,GL000191.1=106433,GL000227.1=128374,GL000228.1=129120,GL000214.1=137718,GL000221.1=155397,GL000209.1=159169,GL000218.1=161147,GL000220.1=161802,GL000213.1=164239,GL000211.1=166566,GL000199.1=169874,GL000217.1=172149,GL000216.1=172294,GL000215.1=172545,GL000205.1=174588,GL000219.1=179198,GL000224.1=179693,GL000223.1=180455,GL000195.1=182896,GL000212.1=186858,GL000222.1=186861,GL000200.1=187035,GL000193.1=189789,GL000194.1=191469,GL000225.1=211173,GL000192.1=547496 Homo_sapiens_nuHg19_mtrCRS Homo sapiens (hg19 with mtDNA replaced with rCRS) chr1=249250621,chr2=243199373,chr3=198022430,chr4=191154276,chr5=180915260,chr6=171115067,chr7=159138663,chr8=146364022,chr9=141213431,chr10=135534747,chr11=135006516,chr12=133851895,chr13=115169878,chr14=107349540,chr15=102531392,chr16=90354753,chr17=81195210,chr18=78077248,chr19=59128983,chr20=63025520,chr21=48129895,chr22=51304566,chrX=155270560,chrY=59373566,chrM=16569,chr1_gl000191_random=106433,chr1_gl000192_random=547496,chr4_ctg9_hap1=590426,chr4_gl000193_random=189789,chr4_gl000194_random=191469,chr6_apd_hap1=4622290,chr6_cox_hap2=4795371,chr6_dbb_hap3=4610396,chr6_mann_hap4=4683263,chr6_mcf_hap5=4833398,chr6_qbl_hap6=4611984,chr6_ssto_hap7=4928567,chr7_gl000195_random=182896,chr8_gl000196_random=38914,chr8_gl000197_random=37175,chr9_gl000198_random=90085,chr9_gl000199_random=169874,chr9_gl000200_random=187035,chr9_gl000201_random=36148,chr11_gl000202_random=40103,chr17_ctg5_hap1=1680828,chr17_gl000203_random=37498,chr17_gl000204_random=81310,chr17_gl000205_random=174588,chr17_gl000206_random=41001,chr18_gl000207_random=4262,chr19_gl000208_random=92689,chr19_gl000209_random=159169,chr21_gl000210_random=27682,chrUn_gl000211=166566,chrUn_gl000212=186858,chrUn_gl000213=164239,chrUn_gl000214=137718,chrUn_gl000215=172545,chrUn_gl000216=172294,chrUn_gl000217=172149,chrUn_gl000218=161147,chrUn_gl000219=179198,chrUn_gl000220=161802,chrUn_gl000221=155397,chrUn_gl000222=186861,chrUn_gl000223=180455,chrUn_gl000224=179693,chrUn_gl000225=211173,chrUn_gl000226=15008,chrUn_gl000227=128374,chrUn_gl000228=129120,chrUn_gl000229=19913,chrUn_gl000230=43691,chrUn_gl000231=27386,chrUn_gl000232=40652,chrUn_gl000233=45941,chrUn_gl000234=40531,chrUn_gl000235=34474,chrUn_gl000236=41934,chrUn_gl000237=45867,chrUn_gl000238=39939,chrUn_gl000239=33824,chrUn_gl000240=41933,chrUn_gl000241=42152,chrUn_gl000242=43523,chrUn_gl000243=43341,chrUn_gl000244=39929,chrUn_gl000245=36651,chrUn_gl000246=38154,chrUn_gl000247=36422,chrUn_gl000248=39786,chrUn_gl000249=38502 +Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) chr1=30427671,chr2=19698289,chr3=23459830,chr4=18585056,chr5=26975502,chrM=366924,chrC=154478 +dp4 D. pseudoobscura (dp4) http://bitbucket.org/galaxy/galaxy-central/changeset/eb26eb407efa/ changeset: eb26eb407efa user: kellyv date: 2011-06-24 22:55:43 summary: Added color-space Tophat wrapper affected #: 21 files (438.5 KB) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Bug fix for change set c996393163e1.
by Bitbucket 23 Jun '11

23 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0966a9170e68/ changeset: 0966a9170e68 user: greg date: 2011-06-23 21:39:57 summary: Bug fix for change set c996393163e1. affected #: 1 file (28 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jun 23 15:32:07 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jun 23 15:39:57 2011 -0400 @@ -117,7 +117,7 @@ model.User.table.c.email == column_filter ) ) class EmailAlertsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - if trans.user.email in from_json_string( repository.email_alerts ): + if repository.email_alerts and trans.user.email in from_json_string( repository.email_alerts ): return 'yes' return '' # Grid definition Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to select Galaxy tool shed repositories to receive email alerts when they are updated. Also remove a broken link on the Galaxy tool shed Help menu.
by Bitbucket 23 Jun '11

23 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c996393163e1/ changeset: c996393163e1 user: greg date: 2011-06-23 21:32:07 summary: Add the ability to select Galaxy tool shed repositories to receive email alerts when they are updated. Also remove a broken link on the Galaxy tool shed Help menu. affected #: 12 files (10.3 KB) --- a/lib/galaxy/webapps/community/config.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Thu Jun 23 15:32:07 2011 -0400 @@ -54,6 +54,9 @@ self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) + self.smtp_username = kwargs.get( 'smtp_username', None ) + self.smtp_password = kwargs.get( 'smtp_password', None ) + self.email_alerts_from = kwargs.get( 'email_alerts_from', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' ) --- a/lib/galaxy/webapps/community/controllers/common.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Thu Jun 23 15:32:07 2011 -0400 @@ -1,4 +1,7 @@ -import os, tarfile, tempfile, shutil +import os, tarfile, tempfile, shutil, string, socket +from time import strftime +from datetime import * +from galaxy.util.json import from_json_string, to_json_string from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -9,6 +12,25 @@ import logging log = logging.getLogger( __name__ ) +email_alert_template = """ +GALAXY TOOL SHED REPOSITORY UPDATE ALERT +----------------------------------------------------------------------------- +You received this alert because you registered to receive email whenever +changes were made to the repository named "${repository_name}". +----------------------------------------------------------------------------- + +Date of change: ${display_date} +Changed by: ${username} + +Revision: ${revision} +Change description: +${description} + +----------------------------------------------------------------------------- +This change alert was sent from the Galaxy tool shed hosted on the server +"${host}" +""" + # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" @@ -95,6 +117,42 @@ os.chdir( cloned_repo_dir ) os.system( cmd ) os.chdir( current_working_dir ) + smtp_server = trans.app.config.smtp_server + if smtp_server and repository.email_alerts: + # Send email alert to users that want them. + if trans.app.config.email_alerts_from is not None: + email_alerts_from = trans.app.config.email_alerts_from + elif trans.request.host.split( ':' )[0] == 'localhost': + email_alerts_from = 'galaxy-no-reply@' + socket.getfqdn() + else: + email_alerts_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0] + tip_changeset = repo.changelog.tip() + ctx = repo.changectx( tip_changeset ) + t, tz = ctx.date() + date = datetime( *time.gmtime( float( t ) - tz )[:6] ) + display_date = date.strftime( "%Y-%m-%d" ) + try: + username = ctx.user().split()[0] + except: + username = ctx.user() + # Build the email message + body = string.Template( email_alert_template ) \ + .safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username ) + frm = email_alerts_from + subject = "Galaxy tool shed repository update alert" + email_alerts = from_json_string( repository.email_alerts ) + for email in email_alerts: + to = email.strip() + # Send it + try: + util.send_mail( frm, to, subject, body, trans.app.config ) + except Exception, e: + log.exception( "An error occurred sending a tool shed repository update alert by email." ) def hg_remove( file_path, current_working_dir, cloned_repo_dir ): # Remove a file path from a cloned repository. Since mercurial doesn't track # directories (only files), directories are automatically removed when they --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jun 23 15:32:07 2011 -0400 @@ -5,9 +5,11 @@ from galaxy import util from galaxy.datatypes.checkers import * from galaxy.web.base.controller import * +from galaxy.web.form_builder import CheckboxField from galaxy.webapps.community import model from galaxy.webapps.community.model import directory_hash_id from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * from common import * from mercurial import hg, ui, patch @@ -113,6 +115,11 @@ return query return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + class EmailAlertsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): + if trans.user.email in from_json_string( repository.email_alerts ): + return 'yes' + return '' # Grid definition title = "Repositories" model_class = model.Repository @@ -139,6 +146,8 @@ key="username" ), grids.CommunityRatingColumn( "Average Rating", key="rating" ), + EmailAlertsColumn( "Alert", + attach_popup=False ), # Columns that are valid for filtering but are not visible. EmailColumn( "Email", model_class=model.User, @@ -154,7 +163,10 @@ key="free-text-search", visible=False, filterable="standard" ) ) - operations = [] + operations = [ grids.GridOperation( "Receive email alerts", + allow_multiple=True, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] standard_filters = [] default_filter = {} num_rows_per_page = 50 @@ -248,6 +260,10 @@ category_id = kwd.get( 'id', None ) category = get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name + elif operation == "receive email alerts": + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) # Render the list view return self.repository_list_grid( trans, **kwd ) @web.expose @@ -485,6 +501,30 @@ tip = get_repository_tip( repo ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) + alerts = params.get( 'alerts', '' ) + alerts_checked = CheckboxField.is_checked( alerts ) + if repository.email_alerts: + email_alerts = from_json_string( repository.email_alerts ) + else: + email_alerts = [] + user = trans.user + if params.get( 'receive_email_alerts_button', False ): + flush_needed = False + if alerts_checked: + if user.email not in email_alerts: + email_alerts.append( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + else: + if user.email in email_alerts: + email_alerts.remove( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + if flush_needed: + trans.sa_session.add( repository ) + trans.sa_session.flush() + checked = alerts_checked or user.email in email_alerts + alerts_check_box = CheckboxField( 'alerts', checked=checked ) return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, @@ -492,6 +532,7 @@ avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, + alerts_check_box=alerts_check_box, message=message, status=status ) @web.expose @@ -507,11 +548,18 @@ description = util.restore_text( params.get( 'description', repository.description ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) + alerts = params.get( 'alerts', '' ) + alerts_checked = CheckboxField.is_checked( alerts ) + if repository.email_alerts: + email_alerts = from_json_string( repository.email_alerts ) + else: + email_alerts = [] allow_push = params.get( 'allow_push', '' ) error = False + user = trans.user if params.get( 'edit_repository_button', False ): flush_needed = False - if trans.user != repository.user: + if user != repository.user: message = "You are not the owner of this repository, so you cannot manage it." status = error return trans.response.send_redirect( web.url_for( controller='repository', @@ -520,7 +568,7 @@ message=message, status=status ) ) if repo_name != repository.name: - message = self.__validate_repository_name( repo_name, trans.user ) + message = self.__validate_repository_name( repo_name, user ) if message: error = True else: @@ -545,10 +593,27 @@ usernames.append( user.username ) usernames = ','.join( usernames ) self.__set_allow_push( repository, usernames, remove_auth=remove_auth ) + elif params.get( 'receive_email_alerts_button', False ): + flush_needed = False + if alerts_checked: + if user.email not in email_alerts: + email_alerts.append( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + else: + if user.email in email_alerts: + email_alerts.remove( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + if flush_needed: + trans.sa_session.add( repository ) + trans.sa_session.flush() if error: status = 'error' current_allow_push_list = self.__get_allow_push( repository ).split( ',' ) allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) + checked = alerts_checked or user.email in email_alerts + alerts_check_box = CheckboxField( 'alerts', checked=checked ) return trans.fill_template( '/webapps/community/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -560,6 +625,7 @@ avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, + alerts_check_box=alerts_check_box, message=message, status=status ) @web.expose @@ -666,6 +732,42 @@ message=message, status=status ) @web.expose + def set_email_alerts( self, trans, **kwd ): + # Set email alerts for selected repositories + params = util.Params( kwd ) + user = trans.user + repository_ids = util.listify( kwd.get( 'id', '' ) ) + total_alerts_added = 0 + total_alerts_removed = 0 + for repository_id in repository_ids: + flush_needed = False + repository = get_repository( trans, repository_id ) + if repository.email_alerts: + email_alerts = from_json_string( repository.email_alerts ) + else: + email_alerts = [] + if user.email in email_alerts: + email_alerts.remove( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + trans.sa_session.add( repository ) + flush_needed = True + total_alerts_removed += 1 + else: + email_alerts.append( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + trans.sa_session.add( repository ) + flush_needed = True + total_alerts_added += 1 + if flush_needed: + trans.sa_session.flush() + message = 'Total alerts added: %d, total alerts removed: %d' % ( total_alerts_added, total_alerts_removed ) + kwd[ 'message' ] = message + kwd[ 'status' ] = 'done' + del( kwd[ 'operation' ] ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) + @web.expose def download( self, trans, repository_id, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) --- a/lib/galaxy/webapps/community/model/__init__.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Thu Jun 23 15:32:07 2011 -0400 @@ -19,8 +19,6 @@ self.deleted = False self.purged = False self.username = None - # Relationships - self.tools = [] def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" self.password = new_secure_hash( text_type=cleartext ) @@ -90,11 +88,12 @@ MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, name=None, description=None, user_id=None, private=False ): + def __init__( self, name=None, description=None, user_id=None, private=False, email_alerts=None ): self.name = name or "Unnamed repository" self.description = description self.user_id = user_id self.private = private + self.email_alerts = email_alerts @property def repo_path( self ): # Repository locations on disk are defined in the hgweb.config file --- a/lib/galaxy/webapps/community/model/mapping.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Thu Jun 23 15:32:07 2011 -0400 @@ -106,7 +106,8 @@ Column( "description" , TEXT ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "private", Boolean, default=False ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "email_alerts", JSONType, nullable=True ) ) RepositoryRatingAssociation.table = Table( "repository_rating_association", metadata, Column( "id", Integer, primary_key=True ), --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Thu Jun 23 15:32:07 2011 -0400 @@ -11,8 +11,14 @@ # Need our custom types, but don't import anything else from model from galaxy.model.custom_types import * -import logging +import sys, logging log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) metadata = MetaData( migrate_engine ) --- a/lib/galaxy/webapps/community/model/migrate/versions/0002_add_tool_suite_column.py Thu Jun 23 11:03:45 2011 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0002_add_tool_suite_column.py Thu Jun 23 15:32:07 2011 -0400 @@ -7,8 +7,14 @@ from migrate import * from migrate.changeset import * -import logging +import sys, logging log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) @@ -16,7 +22,6 @@ def upgrade(): print __doc__ metadata.reflect() - # Create and initialize imported column in job table. Tool_table = Table( "tool", metadata, autoload=True ) c = Column( "suite", Boolean, default=False, index=True ) @@ -24,22 +29,19 @@ # Create c.create( Tool_table ) assert c is Tool_table.c.suite - # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" elif migrate_engine.name == 'postgres': default_false = "false" db_session.execute( "UPDATE tool SET suite=%s" % default_false ) - except Exception, e: print "Adding suite column to the tool table failed: %s" % str( e ) log.debug( "Adding suite column to the tool table failed: %s" % str( e ) ) def downgrade(): metadata.reflect() - - # Drop imported column from job table. + # Drop suite column from tool table. Tool_table = Table( "tool", metadata, autoload=True ) try: Tool_table.c.suite.drop() --- a/templates/display_common.mako Thu Jun 23 11:03:45 2011 -0400 +++ b/templates/display_common.mako Thu Jun 23 15:32:07 2011 -0400 @@ -2,6 +2,8 @@ ## Utilities for sharing items and displaying shared items. ## HACK: these should probably go in the web helper object. ## +## TODO: FIXME Cannot import model here, because grids are +## used across webapps, and each webapp has it's own model. <%! from galaxy import model %> @@ -88,7 +90,7 @@ elif a_class == model.UserOpenID: class_plural = "OpenIDs" else: - class_plural = a_class.__name__ + "s" + class_plural = "items" return class_plural %></%def> --- a/templates/webapps/community/base_panels.mako Thu Jun 23 11:03:45 2011 -0400 +++ b/templates/webapps/community/base_panels.mako Thu Jun 23 15:32:07 2011 -0400 @@ -33,7 +33,6 @@ <a>Help</a><div class="submenu"><ul> - <li><a target="galaxy_main" href="${h.url_for( controller='tool', action='help' )}">How to upload, download and install tools</a></li><li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li><li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li><li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li> --- a/templates/webapps/community/repository/manage_repository.mako Thu Jun 23 11:03:45 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Jun 23 15:32:07 2011 -0400 @@ -137,6 +137,26 @@ </form></div></div> +%if trans.app.config.smtp_server: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Receive email alerts:</label> + ${alerts_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to receive email alerts when updates to this repository occur. + </div> + </div> + <div class="form-row"> + <input type="submit" name="receive_email_alerts_button" value="Save"/> + </div> + </form> + </div> + </div> +%endif <p/><div class="toolForm"><div class="toolFormTitle">User access</div> --- a/templates/webapps/community/repository/view_repository.mako Thu Jun 23 11:03:45 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Thu Jun 23 15:32:07 2011 -0400 @@ -134,8 +134,28 @@ </div></div></div> -<p/> +%if trans.user and trans.app.config.smtp_server: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Receive email alerts:</label> + ${alerts_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to receive email alerts when updates to this repository occur. + </div> + </div> + <div class="form-row"> + <input type="submit" name="receive_email_alerts_button" value="Save"/> + </div> + </form> + </div> + </div> +%endif %if repository.ratings: + <p/><div class="toolForm"><div class="toolFormTitle">Rating</div><div class="toolFormBody"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Set the HDA purged column to false upon creation. If you already upgraded to database >= 78 please do this by hand (UPDATE history_dataset_association SET purged=false WHERE purged IS NULL).
by Bitbucket 23 Jun '11

23 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/720455407d1c/ changeset: 720455407d1c user: natefoo date: 2011-06-23 17:03:45 summary: Set the HDA purged column to false upon creation. If you already upgraded to database >= 78 please do this by hand (UPDATE history_dataset_association SET purged=false WHERE purged IS NULL). affected #: 1 file (90 bytes) --- a/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py Wed Jun 22 08:36:48 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py Thu Jun 23 11:03:45 2011 -0400 @@ -33,6 +33,7 @@ c = Column( "purged", Boolean, index=True, default=False ) c.create( HistoryDatasetAssociation_table ) assert c is HistoryDatasetAssociation_table.c.purged + db_session.execute(HistoryDatasetAssociation_table.update().values(purged=False)) except Exception, e: print "Adding purged column to history_dataset_association table failed: %s" % str( e ) log.debug( "Adding purged column to history_dataset_association table failed: %s" % str( e ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Better handling of Cuffdiff outputs when set_metadata_externally=True
by Bitbucket 22 Jun '11

22 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be48d8761458/ changeset: be48d8761458 user: jgoecks date: 2011-06-22 14:36:48 summary: Better handling of Cuffdiff outputs when set_metadata_externally=True affected #: 2 files (297 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.py Tue Jun 21 16:22:14 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Wed Jun 22 08:36:48 2011 -0400 @@ -32,6 +32,9 @@ parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) + # Outputs. + parser.add_option( '', '--combined-transcripts', dest='combined_transcripts' ) + (options, args) = parser.parse_args() # output version # of tool @@ -115,6 +118,9 @@ if returncode != 0: raise Exception, stderr + # Copy outputs. + shutil.copyfile( "cc_output.combined.gtf" , options.combined_transcripts ) + # check that there are results in the output file cc_output_fname = "cc_output.stats" if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: --- a/tools/ngs_rna/cuffcompare_wrapper.xml Tue Jun 21 16:22:14 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Wed Jun 22 08:36:48 2011 -0400 @@ -26,11 +26,15 @@ --index_dir=${GALAXY_DATA_INDEX_DIR} #end if + ## Outputs. + --combined-transcripts=${transcripts_combined} + ## Inputs. ${first_input} #for $input_file in $input_files: ${input_file.additional_input} #end for + </command><inputs><param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> @@ -86,7 +90,7 @@ <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"><filter>len( input_files ) > 0</filter></data> - <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts" from_work_dir="cc_output.combined.gtf"/> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/></outputs><tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add a new select list to the upload form in the Galaxy tool shed with the following label:
by Bitbucket 21 Jun '11

21 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d4e90b847749/ changeset: d4e90b847749 user: greg date: 2011-06-21 22:22:14 summary: Add a new select list to the upload form in the Galaxy tool shed with the following label: Remove files in the repository (relative to the upload point) that are not in the uploaded archive? The selection pertains only to uploaded tar archives, not to single file uploads. If Yes is selected, files that exist in the repository (relative to the selected upload point) but that are not in the uploaded archive will be removed from the repository. Otherwise, all existing repository files will remain and the uploaded archive will be added to the repository. Fixes issue # 585. affected #: 4 files (4.4 KB) --- a/lib/galaxy/webapps/community/controllers/upload.py Tue Jun 21 10:14:24 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Jun 21 16:22:14 2011 -0400 @@ -2,7 +2,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes.checkers import * -from common import get_categories, get_repository, hg_add, hg_clone, hg_commit, hg_push, update_for_browsing +from common import get_categories, get_repository, hg_add, hg_clone, hg_commit, hg_push, hg_remove, update_for_browsing from mercurial import hg, ui log = logging.getLogger( __name__ ) @@ -29,6 +29,7 @@ repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) ) + remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = params.get( 'upload_point', None ) if upload_point is not None: @@ -144,8 +145,21 @@ # Clone the repository to a temporary location. tmp_dir, cloned_repo_dir = hg_clone( trans, repository, current_working_dir ) # Move the uploaded files to the upload_point within the cloned repository. - self.__move_to_upload_point( upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ) - # Add the files to the cloned repository. + files_to_remove = self.__move_to_upload_point( repository, + upload_point, + uploaded_file, + uploaded_file_name, + uploaded_file_filename, + cloned_repo_dir, + istar, + tar, + remove_repo_files_not_in_tar ) + if remove_repo_files_not_in_tar and files_to_remove: + # Remove files in the repository (relative to the upload point) + # that are not in the uploaded archive. + for repo_file in files_to_remove: + hg_remove( repo_file, current_working_dir, cloned_repo_dir ) + # Add the files in the uploaded archive to the cloned repository. hg_add( trans, current_working_dir, cloned_repo_dir ) # Commit the files to the cloned repository. if not commit_message: @@ -165,6 +179,8 @@ else: uncompress_str = ' ' message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) + if istar and remove_repo_files_not_in_tar: + message += " %d files were removed from the repository." % len( files_to_remove ) else: message = 'No changes to repository.' trans.response.send_redirect( web.url_for( controller='repository', @@ -199,6 +215,7 @@ repository=repository, commit_message=commit_message, uncompress_file=uncompress_file, + remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, message=message, status=status ) def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): @@ -242,7 +259,9 @@ os.close( fd ) bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) - def __move_to_upload_point( self, upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ): + def __move_to_upload_point( self, repository, upload_point, uploaded_file, uploaded_file_name, + uploaded_file_filename, cloned_repo_dir, istar, tar, remove_repo_files_not_in_tar ): + files_to_remove = [] if upload_point is not None: if istar: full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point ) ) @@ -254,6 +273,22 @@ else: full_path = os.path.abspath( os.path.join( cloned_repo_dir, uploaded_file_filename ) ) if istar: + if remove_repo_files_not_in_tar: + # Discover those files that are in the repository, but not in the uploaded archive + filenames_in_archive = [ tarinfo_obj.name for tarinfo_obj in tar.getmembers() ] + for root, dirs, files in os.walk( full_path ): + relative_dir = root.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit - should be impossible + # since we don't visit .hg dirs, but just in case... + files.remove( 'hgrc' ) + for name in files: + if name not in filenames_in_archive: + files_to_remove.append( os.path.join( relative_dir, name ) ) # Extract the uploaded tarball to the load_point within the cloned repository hierarchy tar.extractall( path=full_path ) tar.close() @@ -261,6 +296,7 @@ else: # Move the uploaded file to the load_point within the cloned repository hierarchy shutil.move( uploaded_file_name, full_path ) + return files_to_remove def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/repository/manage_repository.mako Tue Jun 21 10:14:24 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jun 21 16:22:14 2011 -0400 @@ -111,7 +111,11 @@ </div><div class="form-row"><label>Version:</label> - ${tip} + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${tip}</a> + %else: + ${tip} + %endif </div><div class="form-row"><label>Owner:</label> --- a/templates/webapps/community/repository/upload.mako Tue Jun 21 10:14:24 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Tue Jun 21 16:22:14 2011 -0400 @@ -97,7 +97,30 @@ </div></div><div class="form-row"> - <label>Message:</label> + <% + if remove_repo_files_not_in_tar: + yes_selected = 'selected' + no_selected = '' + else: + yes_selected = '' + no_selected = 'selected' + %> + <label>Remove files in the repository (relative to the upload point) that are not in the uploaded archive?</label> + <div class="form-row-input"> + <select name="remove_repo_files_not_in_tar"> + <option value="true" ${yes_selected}>Yes + <option value="false" ${no_selected}>No + </select> + </div> + <div class="toolParamHelp" style="clear: both;"> + This selection pertains only to uploaded tar archives, not to single file uploads. If <b>Yes</b> is selected, files + that exist in the repository (relative to the upload point) but that are not in the uploaded archive will be removed + from the repository. Otherwise, all existing repository files will remain and the uploaded archive files will be added + to the repository. + </div> + </div> + <div class="form-row"> + <label>Change set commit message:</label><div class="form-row-input"> %if commit_message: <textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea> @@ -118,7 +141,8 @@ </div><input type="hidden" id="upload_point" name="upload_point" value=""/><div class="toolParamHelp" style="clear: both;"> - Select a location within the repository to upload your files by clicking a check box next to the location. If a location is not selected, files will be uploaded to the repository root. + Select a location within the repository to upload your files by clicking a check box next to the location. If a location + is not selected, files will be uploaded to the repository root. </div><div style="clear: both"></div></div> --- a/templates/webapps/community/repository/view_repository.mako Tue Jun 21 10:14:24 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jun 21 16:22:14 2011 -0400 @@ -100,7 +100,11 @@ </div><div class="form-row"><label>Name:</label> - ${repository.name} + %if can_browse_contents: + <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a> + %else: + ${repository.name} + %endif </div><div class="form-row"><label>Description:</label> @@ -108,7 +112,11 @@ </div><div class="form-row"><label>Version:</label> - ${tip} + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${tip}</a> + %else: + ${tip} + %endif </div><div class="form-row"><label>Owner:</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add security checks for enabling the ability to delete files in a tool shed repository.
by Bitbucket 21 Jun '11

21 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e23f05a3fb41/ changeset: e23f05a3fb41 user: greg date: 2011-06-21 16:14:24 summary: Add security checks for enabling the ability to delete files in a tool shed repository. affected #: 6 files (1.2 KB) --- a/templates/webapps/community/repository/browse_repository.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Tue Jun 21 10:14:24 2011 -0400 @@ -93,38 +93,52 @@ %if can_browse_contents: <div class="toolForm"><div class="toolFormTitle">Browse ${repository.name}</div> - <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" > - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... + %if can_push: + <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" > + <div class="form-row" > + <label>Contents:</label> + <div id="tree" > + Loading... + </div> + <div class="toolParamHelp" style="clear: both;"> + Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. + </div> + <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/></div> - <div class="toolParamHelp" style="clear: both;"> - Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. + <div class="form-row"> + <label>Message:</label> + <div class="form-row-input"> + %if commit_message: + <textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea> + %else: + <textarea name="commit_message" rows="3" cols="35"></textarea> + %endif + </div> + <div class="toolParamHelp" style="clear: both;"> + This is the commit message for the mercurial change set that will be created if you delete selected files. + </div> + <div style="clear: both"></div></div> - <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/> + <div class="form-row"> + <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/> + </div> + <div class="form-row"> + <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> + </div> + </form> + %else: + <div class="toolFormBody"> + <div class="form-row" > + <label>Contents:</label> + <div id="tree" > + Loading... + </div> + </div> + <div class="form-row"> + <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> + </div></div> - <div class="form-row"> - <label>Message:</label> - <div class="form-row-input"> - %if commit_message: - <textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea> - %else: - <textarea name="commit_message" rows="3" cols="35"></textarea> - %endif - </div> - <div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created if you delete selected files. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </form> + %endif </div><p/> %endif --- a/templates/webapps/community/repository/manage_repository.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jun 21 10:14:24 2011 -0400 @@ -11,6 +11,10 @@ can_browse_contents = not is_new can_rate = not is_new and repository.user != trans.user can_view_change_log = not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><%! @@ -74,7 +78,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/rate_repository.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Tue Jun 21 10:14:24 2011 -0400 @@ -11,6 +11,10 @@ can_rate = repository.user != trans.user can_manage = repository.user == trans.user can_view_change_log = not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><%! @@ -79,7 +83,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/view_changelog.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Tue Jun 21 10:14:24 2011 -0400 @@ -11,6 +11,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_rate = repository.user != trans.user can_upload = can_push + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><%! @@ -48,7 +52,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/view_changeset.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Tue Jun 21 10:14:24 2011 -0400 @@ -12,6 +12,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_view_change_log = not is_new can_upload = can_push + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><%! @@ -52,7 +56,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/view_repository.mako Tue Jun 21 09:38:06 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jun 21 10:14:24 2011 -0400 @@ -11,6 +11,10 @@ can_upload = can_push can_browse_contents = not is_new can_view_change_log = not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><%! @@ -74,7 +78,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add the ability to select files for deletion from the repository using the built-in file browser. Any number of selected files will be deleted. Selecting a folder will delete all of it's contents. Fixes issue # 584.
by Bitbucket 21 Jun '11

21 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dbd80b36e0ba/ changeset: dbd80b36e0ba user: greg date: 2011-06-21 15:38:06 summary: Add the ability to select files for deletion from the repository using the built-in file browser. Any number of selected files will be deleted. Selecting a folder will delete all of it's contents. Fixes issue # 584. affected #: 11 files (8.7 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jun 20 17:02:51 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Jun 21 09:38:06 2011 -0400 @@ -1,10 +1,11 @@ -import tarfile +import os, tarfile, tempfile, shutil from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.web.form_builder import SelectField from galaxy.model.item_attrs import UsesItemRatings +from mercurial import hg, ui import logging log = logging.getLogger( __name__ ) @@ -58,3 +59,55 @@ def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) +def hg_add( trans, current_working_dir, cloned_repo_dir ): + # Add files to a cloned repository. If they're already tracked, this should do nothing. + os.chdir( cloned_repo_dir ) + os.system( 'hg add > /dev/null 2>&1' ) + os.chdir( current_working_dir ) +def hg_clone( trans, repository, current_working_dir ): + # Make a clone of a repository in a temporary location. + repo_dir = repository.repo_path + tmp_dir = tempfile.mkdtemp() + tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) + if not os.path.exists( tmp_archive_dir ): + os.makedirs( tmp_archive_dir ) + cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( tmp_archive_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) + return tmp_dir, cloned_repo_dir +def hg_commit( commit_message, current_working_dir, cloned_repo_dir ): + # Commit a change set to a cloned repository. + if not commit_message: + commit_message = "No commit message" + os.chdir( cloned_repo_dir ) + os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) + os.chdir( current_working_dir ) +def hg_push( trans, repository, current_working_dir, cloned_repo_dir ): + # Push a change set from a cloned repository to a master repository. + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) + # We want these change sets to be associated with the owner of the repository, so we'll + # set the HGUSER environment variable accordingly. + os.environ[ 'HGUSER' ] = trans.user.username + cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( cloned_repo_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) +def hg_remove( file_path, current_working_dir, cloned_repo_dir ): + # Remove a file path from a cloned repository. Since mercurial doesn't track + # directories (only files), directories are automatically removed when they + # become empty. + abs_file_path = os.path.join( cloned_repo_dir, file_path ) + if os.path.exists( abs_file_path ): + cmd = 'hg remove %s > /dev/null 2>&1' % file_path + os.chdir( cloned_repo_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) +def update_for_browsing( repository, current_working_dir ): + # Make a copy of a repository's files for browsing. + repo_dir = repository.repo_path + os.chdir( repo_dir ) + os.system( 'hg update > /dev/null 2>&1' ) + os.chdir( current_working_dir ) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 20 17:02:51 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jun 21 09:38:06 2011 -0400 @@ -378,7 +378,13 @@ return config.get( "web", option ) raise Exception( "Repository %s missing allow_push entry under the [web] option in it's hgrc file." % repository.name ) def __set_allow_push( self, repository, usernames, remove_auth='' ): - # TODO: Use the mercurial api to handle this + """ + # TODO: Use the mercurial api to handle this, something like the following: + items = repo.ui.configitems( section, untrusted=False ) + push_section = repo.ui.config( 'hgrc', 'allow_push' ) + for XXX (in name you want to add): + repo.ui.updateconfig( section=extensions_section, name='XXX', value='YYY' ) + """ hgrc_file = os.path.abspath( os.path.join( repository.repo_path, ".hg", "hgrc" ) ) fh, fn = tempfile.mkstemp() for i, line in enumerate( open( hgrc_file ) ): @@ -403,6 +409,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) # Our current support for browsing a repository requires copies of the @@ -416,6 +423,56 @@ return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, + commit_message=commit_message, + message=message, + status=status ) + @web.expose + def select_files_to_delete( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + repository = get_repository( trans, id ) + _ui = ui.ui() + repo_dir = repository.repo_path + repo = hg.repository( _ui, repo_dir ) + selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) + if params.get( 'select_files_to_delete_button', False ): + if selected_files_to_delete: + selected_files_to_delete = selected_files_to_delete.split( ',' ) + current_working_dir = os.getcwd() + # Get the current repository tip. + tip = repo[ 'tip' ] + # Clone the repository to a temporary location. + tmp_dir, cloned_repo_dir = hg_clone( trans, repository, current_working_dir ) + # Delete the selected files from the repository. + cloned_repo = hg.repository( _ui, cloned_repo_dir ) + for selected_file in selected_files_to_delete: + selected_file_path = selected_file.split( 'repo_%d' % repository.id )[ 1 ].lstrip( '/' ) + hg_remove( selected_file_path, current_working_dir, cloned_repo_dir ) + # Commit the change set. + if not commit_message: + commit_message = 'Deleted selected files' + hg_commit( commit_message, current_working_dir, cloned_repo_dir ) + # Push the change set from the cloned repository to the master repository. + hg_push( trans, repository, current_working_dir, cloned_repo_dir ) + # Remove the temporary directory containing the cloned repository. + shutil.rmtree( tmp_dir ) + # Update the repository files for browsing. + update_for_browsing( repository, current_working_dir ) + # Get the new repository tip. + repo = hg.repository( _ui, repo_dir ) + if tip != repo[ 'tip' ]: + message = "The selected files were deleted from the repository." + else: + message = 'No changes to repository.' + else: + message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." + status = "error" + return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + repo=repo, + repository=repository, + commit_message=commit_message, message=message, status=status ) @web.expose --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 20 17:02:51 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Jun 21 09:38:06 2011 -0400 @@ -2,7 +2,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes.checkers import * -from common import get_categories, get_repository +from common import get_categories, get_repository, hg_add, hg_clone, hg_commit, hg_push, update_for_browsing from mercurial import hg, ui log = logging.getLogger( __name__ ) @@ -139,12 +139,39 @@ # We have a repository that is not new (it contains files). if uncompress_file and ( isgzip or isbz2 ): uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) + # Get the current repository tip. + tip = repo[ 'tip' ] # Clone the repository to a temporary location. - tmp_dir, cloned_repo_dir = self.__hg_clone( trans, repository, repo_dir, current_working_dir ) + tmp_dir, cloned_repo_dir = hg_clone( trans, repository, current_working_dir ) # Move the uploaded files to the upload_point within the cloned repository. self.__move_to_upload_point( upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ) - # Commit and push the changes from the cloned repo to the master repo. - self.__hg_push( trans, repository, file_data.filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) + # Add the files to the cloned repository. + hg_add( trans, current_working_dir, cloned_repo_dir ) + # Commit the files to the cloned repository. + if not commit_message: + commit_message = 'Uploaded' + hg_commit( commit_message, current_working_dir, cloned_repo_dir ) + # Push the changes from the cloned repository to the master repository. + hg_push( trans, repository, current_working_dir, cloned_repo_dir ) + # Remove the temporary directory containing the cloned repository. + shutil.rmtree( tmp_dir ) + # Update the repository files for browsing. + update_for_browsing( repository, current_working_dir ) + # Get the new repository tip. + repo = hg.repository( ui.ui(), repo_dir ) + if tip != repo[ 'tip' ]: + if uncompress_file: + uncompress_str = ' uncompressed and ' + else: + uncompress_str = ' ' + message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) + else: + message = 'No changes to repository.' + trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + commit_message='Deleted selected files', + message=message, + id=trans.security.encode_id( repository.id ) ) ) if ok: if files_to_commit: repo.dirstate.write() @@ -159,6 +186,7 @@ message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', + commit_message='Deleted selected files', message=message, id=trans.security.encode_id( repository.id ) ) ) else: @@ -214,55 +242,6 @@ os.close( fd ) bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) - def __hg_clone( self, trans, repository, repo_dir, current_working_dir ): - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - # Make a clone of the repository in a temporary location - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - return tmp_dir, cloned_repo_dir - def __hg_push( self, trans, repository, filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): - repo = hg.repository( ui.ui(), repo_dir ) - tip = repo[ 'tip' ] - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - # Make a copy of the updated repository files for browsing. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - shutil.rmtree( tmp_dir ) - repo = hg.repository( ui.ui(), repo_dir ) - if tip != repo[ 'tip' ]: - if uncompress_file: - uncompress_str = ' uncompressed and ' - else: - uncompress_str = ' ' - message = "The file '%s' has been successfully%suploaded to the repository." % ( filename, uncompress_str ) - else: - message = 'No changes in uploaded files.' - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) def __move_to_upload_point( self, upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ): if upload_point is not None: if istar: --- a/templates/webapps/community/repository/browse_repository.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Tue Jun 21 09:38:06 2011 -0400 @@ -93,17 +93,38 @@ %if can_browse_contents: <div class="toolForm"><div class="toolFormTitle">Browse ${repository.name}</div> - <div class="toolFormBody"> + <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" ><div class="form-row" ><label>Contents:</label><div id="tree" > Loading... </div> + <div class="toolParamHelp" style="clear: both;"> + Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. + </div> + <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/> + </div> + <div class="form-row"> + <label>Message:</label> + <div class="form-row-input"> + %if commit_message: + <textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea> + %else: + <textarea name="commit_message" rows="3" cols="35"></textarea> + %endif + </div> + <div class="toolParamHelp" style="clear: both;"> + This is the commit message for the mercurial change set that will be created if you delete selected files. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/></div><div class="form-row"><div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div></div> - </div> + </form></div><p/> %endif --- a/templates/webapps/community/repository/common.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Tue Jun 21 09:38:06 2011 -0400 @@ -35,11 +35,17 @@ // Display list of selected nodes var selNodes = dtnode.tree.getSelectedNodes(); // convert to title/key array - var selKeys = $.map(selNodes, function(node){ + var selKeys = $.map(selNodes, function(node) { return node.data.key; }); - // The following is used only in the upload form. - document.upload_form.upload_point.value = selKeys[0]; + if (document.forms["select_files_to_delete"]) { + // The following is used only ~/templates/webapps/community/repository/browse_repository.mako. + document.select_files_to_delete.selected_files_to_delete.value = selKeys.join(","); + } + // The following is used only in ~/templates/webapps/community/repository/upload.mako. + if (document.forms["upload_form"]) { + document.upload_form.upload_point.value = selKeys[0]; + } }, onActivate: function(dtnode) { var cell = $("#file_contents"); --- a/templates/webapps/community/repository/manage_repository.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jun 21 09:38:06 2011 -0400 @@ -74,7 +74,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/rate_repository.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Tue Jun 21 09:38:06 2011 -0400 @@ -79,7 +79,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/upload.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Tue Jun 21 09:38:06 2011 -0400 @@ -55,7 +55,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif </div></ul> @@ -106,7 +106,7 @@ %endif </div><div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created by this upload + This is the commit message for the mercurial change set that will be created by this upload. </div><div style="clear: both"></div></div> --- a/templates/webapps/community/repository/view_changelog.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Tue Jun 21 09:38:06 2011 -0400 @@ -48,7 +48,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/view_changeset.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Tue Jun 21 09:38:06 2011 -0400 @@ -52,7 +52,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> --- a/templates/webapps/community/repository/view_repository.mako Mon Jun 20 17:02:51 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jun 21 09:38:06 2011 -0400 @@ -74,7 +74,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Add the download/save icon to errored datasets which contain data. Fixes #207 and #583.
by Bitbucket 20 Jun '11

20 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3fb285cb031d/ changeset: 3fb285cb031d user: natefoo date: 2011-06-20 23:02:51 summary: Add the download/save icon to errored datasets which contain data. Fixes #207 and #583. affected #: 1 file (50 bytes) --- a/templates/root/history_common.mako Wed May 25 17:26:36 2011 +0100 +++ b/templates/root/history_common.mako Mon Jun 20 17:02:51 2011 -0400 @@ -1,9 +1,35 @@ <% _=n_ %> + +<%def name="render_download_links( data, dataset_id )"> + <% + from galaxy.datatypes.metadata import FileParameter + %> + %if not data.purged: + ## Check for downloadable metadata files + <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> + %if meta_files: + <div popupmenu="dataset-${dataset_id}-popup"> + <a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \ + to_ext=data.ext )}">Download Dataset</a> + <a>Additional Files</a> + %for file_type in meta_files: + <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', \ + hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a> + %endfor + </div> + <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> + %endif + <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Download" class="icon-button disk tooltip"></a> + %if meta_files: + </div> + %endif + %endif +</%def> + ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"><% dataset_id = trans.security.encode_id( data.id ) - from galaxy.datatypes.metadata import FileParameter if data.state in ['no state','',None]: data_state = "queued" @@ -126,6 +152,9 @@ </div><div><a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug tooltip"></a> + %if data.has_data(): + ${render_download_links( data, dataset_id )} + %endif <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> @@ -169,26 +198,7 @@ %endif <div> %if data.has_data(): - %if not data.purged: - ## Check for downloadable metadata files - <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> - %if meta_files: - <div popupmenu="dataset-${dataset_id}-popup"> - <a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \ - to_ext=data.ext )}">Download Dataset</a> - <a>Additional Files</a> - %for file_type in meta_files: - <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', \ - hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a> - %endfor - </div> - <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> - %endif - <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Download" class="icon-button disk tooltip"></a> - %if meta_files: - </div> - %endif - %endif + ${render_download_links( data, dataset_id )} <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 20 Jun '11

20 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/80b92e7b5d8c/ changeset: 80b92e7b5d8c user: natefoo date: 2011-06-20 19:43:19 summary: Make the ability for users to purge their own data conditional on a config variable. Due to limitations in the grid framework, the button can't be removed from the history grid, but clicking it just does the same thing as delete but adds a message explaining that the purge operation wasn't performed. affected #: 6 files (1.3 KB) --- a/lib/galaxy/config.py Fri Jun 17 16:45:25 2011 -0400 +++ b/lib/galaxy/config.py Mon Jun 20 13:43:19 2011 -0400 @@ -61,6 +61,7 @@ self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) + self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) --- a/lib/galaxy/web/controllers/dataset.py Fri Jun 17 16:45:25 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Mon Jun 20 13:43:19 2011 -0400 @@ -746,12 +746,16 @@ @web.expose def purge( self, trans, id ): + if not trans.app.config.allow_user_dataset_purge: + raise Exception( "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator." ) if self._purge( trans, id ): return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) raise Exception( "Error removing disk file" ) @web.expose def purge_async( self, trans, id ): + if not trans.app.config.allow_user_dataset_purge: + raise Exception( "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator." ) if self._purge( trans, id ): return "OK" raise Exception( "Error removing disk file" ) --- a/lib/galaxy/web/controllers/history.py Fri Jun 17 16:45:25 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Jun 20 13:43:19 2011 -0400 @@ -270,7 +270,7 @@ trans.new_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 - if purge: + if purge and trans.app.config.allow_user_dataset_purge: for hda in history.datasets: hda.purged = True trans.sa_session.add( hda ) @@ -285,8 +285,10 @@ trans.sa_session.flush() if n_deleted: part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) ) - if purge: + if purge and trans.app.config.allow_user_dataset_purge: part += " and removed %s datasets from disk" % iff( n_deleted != 1, "their", "its" ) + elif purge: + part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance" message_parts.append( "%s. " % part ) if deleted_current: message_parts.append( "Your active history was deleted, a new empty history is now active. " ) @@ -1213,4 +1215,4 @@ trans.set_history( hist ) return trans.response.send_redirect( url_for( "/" ) ) - \ No newline at end of file + --- a/lib/galaxy/web/controllers/root.py Fri Jun 17 16:45:25 2011 -0400 +++ b/lib/galaxy/web/controllers/root.py Mon Jun 20 13:43:19 2011 -0400 @@ -504,6 +504,8 @@ @web.expose def purge( self, trans, id = None, show_deleted_on_refresh = False, **kwd ): + if not trans.app.config.allow_user_dataset_purge: + return trans.show_error_message( "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator." ) hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( int( id ) ) if bool( hda.dataset.active_history_associations or hda.dataset.library_associations ): return trans.show_error_message( "Unable to purge: LDDA(s) or active HDA(s) exist" ) --- a/templates/root/history_common.mako Fri Jun 17 16:45:25 2011 -0400 +++ b/templates/root/history_common.mako Mon Jun 20 13:43:19 2011 -0400 @@ -23,7 +23,12 @@ %if data.dataset.purged or data.purged: This dataset has been deleted and removed from disk. %else: - 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 or <a href="${h.url_for( controller='dataset', action='purge', id=data.id )}" class="historyItemPurge" id="historyItemPurger-${data.id}" target="galaxy_history">here</a> to immediately remove from disk. + 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 + %if trans.app.config.allow_user_dataset_purge: + or <a href="${h.url_for( controller='dataset', action='purge', id=data.id )}" class="historyItemPurge" id="historyItemPurger-${data.id}" target="galaxy_history">here</a> to immediately remove it from disk. + %else: + it. + %endif %endif </strong></div> %endif --- a/universe_wsgi.ini.sample Fri Jun 17 16:45:25 2011 -0400 +++ b/universe_wsgi.ini.sample Mon Jun 20 13:43:19 2011 -0400 @@ -401,6 +401,11 @@ # Allow administrators to delete accounts. #allow_user_deletion = False +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + # By default, users' data will be public, but setting this to True will cause # it to be private. Does not affect existing users and data, only ones created # after this option is set. Users may still change their default back to http://bitbucket.org/galaxy/galaxy-central/changeset/e74e89a4c03a/ changeset: e74e89a4c03a user: peterjc date: 2011-05-25 18:26:36 summary: Cope with white space at start of command after processing template (see issue #159) affected #: 1 file (113 bytes) --- a/lib/galaxy/tools/__init__.py Mon Jun 20 13:43:19 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed May 25 17:26:36 2011 +0100 @@ -379,15 +379,10 @@ command = root.find("command") if command is not None and command.text is not None: self.command = command.text.lstrip() # get rid of leading whitespace - interpreter = command.get("interpreter") - if interpreter: - # TODO: path munging for cluster/dataset server relocatability - executable = self.command.split()[0] - abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) - self.command = self.command.replace(executable, abs_executable, 1) - self.command = interpreter + " " + self.command else: self.command = '' + # Must pre-pend this AFTER processing the cheetah command template + self.interpreter = command.get("interpreter", None) # Parameters used to build URL for redirection to external app redirect_url_params = root.find( "redirect_url_params" ) if redirect_url_params is not None and redirect_url_params.text is not None: @@ -1588,12 +1583,18 @@ try: # Substituting parameters into the command command_line = fill_template( self.command, context=param_dict ) - # Remove newlines from command line - command_line = command_line.replace( "\n", " " ).replace( "\r", " " ) + # Remove newlines from command line, and any leading/trailing white space + command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() except Exception, e: # Modify exception message to be more clear #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ) ) raise + if self.interpreter: + # TODO: path munging for cluster/dataset server relocatability + executable = command_line.split()[0] + abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) + command_line = command_line.replace(executable, abs_executable, 1) + command_line = self.interpreter + " " + command_line return command_line def build_dependency_shell_commands( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Escaping in tests should be more specific
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d1f2d2e5246a/ changeset: d1f2d2e5246a user: kanwei date: 2011-06-17 22:45:25 summary: Escaping in tests should be more specific affected #: 1 file (6 bytes) --- a/test/base/twilltestcase.py Fri Jun 17 16:16:28 2011 -0400 +++ b/test/base/twilltestcase.py Fri Jun 17 16:45:25 2011 -0400 @@ -242,10 +242,10 @@ self.visit_page( "history" ) for subpatt in patt.split(): try: - tc.find( escape(subpatt) ) + tc.find( subpatt ) except: fname = self.write_temp_file( tc.browser.get_html() ) - errmsg = "no match to '%s'\npage content written to '%s'" % ( escape(subpatt), fname ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( subpatt, fname ) raise AssertionError( errmsg ) self.home() def clear_history( self ): @@ -384,7 +384,7 @@ """Switches to a history in the current list of histories""" self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) if name: - self.check_history_for_string( name ) + self.check_history_for_string( escape( name ) ) self.home() def view_stored_active_histories( self, strings_displayed=[] ): self.home() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Missing migration script from the last commit.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4e3f43848b51/ changeset: 4e3f43848b51 user: natefoo date: 2011-06-17 22:16:28 summary: Missing migration script from the last commit. affected #: 1 file (0 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Library datasets can now be job inputs - needed to be able to use the deferred job runner and transfer manager with set_metadata_externally = True.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e04154ed4639/ changeset: e04154ed4639 user: natefoo date: 2011-06-17 22:06:17 summary: Library datasets can now be job inputs - needed to be able to use the deferred job runner and transfer manager with set_metadata_externally = True. affected #: 7 files (2.6 KB) --- a/lib/galaxy/jobs/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -229,7 +229,7 @@ return JOB_DELETED elif job.state == model.Job.states.ERROR: return JOB_ADMIN_DELETED - for dataset_assoc in job.input_datasets: + for dataset_assoc in job.input_datasets + job.input_library_datasets: idata = dataset_assoc.dataset if not idata: continue @@ -330,6 +330,7 @@ # Restore input / output data lists inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # Set up output dataset association for export history jobs. Because job @@ -614,6 +615,7 @@ # custom post process setup inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows param_dict = self.tool.params_from_strings( param_dict, self.app ) @@ -665,7 +667,7 @@ def get_input_fnames( self ): job = self.get_job() filenames = [] - for da in job.input_datasets: #da is JobToInputDatasetAssociation object + for da in job.input_datasets + job.input_library_datasets: #da is JobToInputDatasetAssociation object if da.dataset: filenames.append( da.dataset.file_name ) #we will need to stage in metadata file names also @@ -861,9 +863,10 @@ self.tool.handle_unvalidated_param_values( incoming, self.app ) # Restore input / output data lists inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) + out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) + out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # DBTODO New method for generating command line for a task? - out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) - out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # These can be passed on the command line if wanted as $userId $userEmail if job.history and job.history.user: # check for anonymous user! userId = '%d' % job.history.user.id --- a/lib/galaxy/jobs/deferred/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/deferred/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -98,14 +98,14 @@ job_state = self.plugins[job.plugin].check_job( job ) except Exception, e: self.__fail_job( job ) - log.error( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) ) + log.exception( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) ) continue if job_state == self.job_states.READY: try: self.plugins[job.plugin].run_job( job ) except Exception, e: self.__fail_job( job ) - log.error( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) ) + log.exception( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) ) continue elif job_state == self.job_states.INVALID: self.__fail_job( job ) @@ -160,8 +160,14 @@ self.app = app self.sa_session = app.model.context.current self.dummy = Dummy() - self.history = history - self.user = user + if not history: + self.history = Dummy() + else: + self.history = history + if not user: + self.user = Dummy() + else: + self.user = user self.model = app.model def get_galaxy_session( self ): return self.dummy --- a/lib/galaxy/jobs/deferred/data_transfer.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/deferred/data_transfer.py Fri Jun 17 16:06:17 2011 -0400 @@ -93,12 +93,18 @@ # In this case, job.params will be a dictionary that contains a key named 'result'. The value # of the result key is a dictionary that looks something like: # {'sample_dataset_id': '8', 'status': 'Not started', 'protocol': 'scp', 'name': '3.bed', - # 'file_path': '/tmp/library/3.bed', 'host': '127.0.0.1', 'sample_id': 8, 'external_service_id': 2, - # 'password': 'galaxy', 'user_name': 'gvk', 'error_msg': '', 'size': '8.0K'} - result_dict = job.params[ 'result' ] + # 'file_path': '/data/library/3.bed', 'host': '127.0.0.1', 'sample_id': 8, 'external_service_id': 2, + # 'local_path': '/tmp/kjl2Ss4', 'password': 'galaxy', 'user_name': 'gvk', 'error_msg': '', 'size': '8.0K'} + try: + tj = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params['transfer_job_id'] ) ) + result_dict = tj.params + result_dict['local_path'] = tj.path + except Exception, e: + log.error( "Updated transfer result unavailable, using old result. Error was: %s" % str( e ) ) + result_dict = job.params[ 'result' ] library_dataset_name = result_dict[ 'name' ] # Determine the data format (see the relevant TODO item in the manual_data_transfer plugin).. - extension = sniff.guess_ext( result_dict[ 'file_path' ], sniff_order=self.app.datatypes_registry.sniff_order ) + extension = sniff.guess_ext( result_dict[ 'local_path' ], sniff_order=self.app.datatypes_registry.sniff_order ) self._update_sample_dataset_status( protocol=job.params[ 'protocol' ], sample_id=int( job.params[ 'sample_id' ] ), result_dict=result_dict, @@ -132,7 +138,9 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) if self.app.config.set_metadata_externally: self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( self.app.datatypes_registry.set_external_metadata_tool, - FakeTrans( self.app ), + FakeTrans( self.app, + history=sample.history, + user=sample.request.user ), incoming = { 'input1':ldda } ) else: ldda.set_meta() --- a/lib/galaxy/jobs/transfer_manager.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/transfer_manager.py Fri Jun 17 16:06:17 2011 -0400 @@ -106,6 +106,7 @@ error = dict( code=256, message='Error connecting to transfer daemon', data=str( e ) ) rval.append( dict( transfer_job_id=tj.id, state=tj.state, error=error ) ) else: + self.sa_session.refresh( tj ) rval.append( dict( transfer_job_id=tj.id, state=tj.state ) ) for tj_state in rval: if tj_state['state'] in self.app.model.TransferJob.terminal_states: --- a/lib/galaxy/model/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/model/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -95,6 +95,7 @@ self.parameters = [] self.input_datasets = [] self.output_datasets = [] + self.input_library_datasets = [] self.output_library_datasets = [] self.state = Job.states.NEW self.info = None @@ -109,6 +110,8 @@ self.input_datasets.append( JobToInputDatasetAssociation( name, dataset ) ) def add_output_dataset( self, name, dataset ): self.output_datasets.append( JobToOutputDatasetAssociation( name, dataset ) ) + def add_input_library_dataset( self, name, dataset ): + self.input_library_datasets.append( JobToInputLibraryDatasetAssociation( name, dataset ) ) def add_output_library_dataset( self, name, dataset ): self.output_library_datasets.append( JobToOutputLibraryDatasetAssociation( name, dataset ) ) def add_post_job_action(self, pja): @@ -215,6 +218,11 @@ self.name = name self.dataset = dataset +class JobToInputLibraryDatasetAssociation( object ): + def __init__( self, name, dataset ): + self.name = name + self.dataset = dataset + class JobToOutputLibraryDatasetAssociation( object ): def __init__( self, name, dataset ): self.name = name --- a/lib/galaxy/model/mapping.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/model/mapping.py Fri Jun 17 16:06:17 2011 -0400 @@ -370,6 +370,12 @@ Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), Column( "name", String(255) ) ) +JobToInputLibraryDatasetAssociation.table = Table( "job_to_input_library_dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), + Column( "name", String(255) ) ) + JobToOutputLibraryDatasetAssociation.table = Table( "job_to_output_library_dataset", metadata, Column( "id", Integer, primary_key=True ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), @@ -1376,6 +1382,9 @@ assign_mapper( context, JobToOutputDatasetAssociation, JobToOutputDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation, lazy=False ) ) ) +assign_mapper( context, JobToInputLibraryDatasetAssociation, JobToInputLibraryDatasetAssociation.table, + properties=dict( job=relation( Job ), dataset=relation( LibraryDatasetDatasetAssociation, lazy=False ) ) ) + assign_mapper( context, JobToOutputLibraryDatasetAssociation, JobToOutputLibraryDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( LibraryDatasetDatasetAssociation, lazy=False ) ) ) @@ -1410,6 +1419,7 @@ input_datasets=relation( JobToInputDatasetAssociation ), output_datasets=relation( JobToOutputDatasetAssociation ), post_job_actions=relation( PostJobActionAssociation, lazy=False ), + input_library_datasets=relation( JobToInputLibraryDatasetAssociation ), output_library_datasets=relation( JobToOutputLibraryDatasetAssociation ), external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) ) --- a/lib/galaxy/tools/actions/metadata.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/tools/actions/metadata.py Fri Jun 17 16:06:17 2011 -0400 @@ -13,6 +13,12 @@ if isinstance( value, trans.app.model.HistoryDatasetAssociation ): dataset = value dataset_name = name + type = 'hda' + break + elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ): + dataset = value + dataset_name = name + type = 'ldda' break else: raise Exception( 'The dataset to set metadata on could not be determined.' ) @@ -22,6 +28,8 @@ job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id + if trans.user: + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW try: # For backward compatibility, some tools may not have versions yet. @@ -50,7 +58,10 @@ for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) #add the dataset to job_to_input_dataset table - job.add_input_dataset( dataset_name, dataset ) + if type == 'hda': + job.add_input_dataset( dataset_name, dataset ) + elif type == 'ldda': + job.add_input_library_dataset( dataset_name, dataset ) #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset._state = dataset.states.SETTING_METADATA Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: peterjc: Support optional integer/float arguments (Fixes #403)
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/adcc600effa4/ changeset: adcc600effa4 user: peterjc date: 2010-10-22 15:30:58 summary: Support optional integer/float arguments (Fixes #403) affected #: 1 file (1.0 KB) --- a/lib/galaxy/tools/parameters/basic.py Fri Jun 17 15:31:07 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Oct 22 14:30:58 2010 +0100 @@ -36,6 +36,8 @@ self.html = "no html set" self.repeat = param.get("repeat", None) self.condition = param.get( "condition", None ) + # Optional DataToolParameters are used in tools like GMAJ and LAJ + self.optional = string_as_bool( param.get( 'optional', False ) ) self.validators = [] for elem in param.findall("validator"): self.validators.append( validation.Validator.from_element( self, elem ) ) @@ -131,7 +133,11 @@ return value def to_param_dict_string( self, value, other_values={} ): - value = str( value ) + """Called via __str__ when used in the Cheetah template""" + if value is None: + value = "" + else: + value = str( value ) if self.tool is None or self.tool.options.sanitize: if self.sanitizer: value = self.sanitizer.sanitize_param( value ) @@ -140,6 +146,8 @@ return value def validate( self, value, history=None ): + if value=="" and self.optional: + return for validator in self.validators: validator.validate( value, history ) @@ -226,9 +234,22 @@ try: return int( value ) except: + if not value and self.optional: + return "" raise ValueError( "An integer is required" ) + def to_string( self, value, app ): + """Convert a value to a string representation suitable for persisting""" + if value is None: + return "" + else: + return str( value ) def to_python( self, value, app ): - return int( value ) + try: + return int( value ) + except Exception, err: + if not value and self.optional: + return None + raise err def get_initial_value( self, trans, context ): if self.value: return int( self.value ) @@ -281,10 +302,23 @@ def from_html( self, value, trans=None, other_values={} ): try: return float( value ) - except: + except: + if not value and self.optional: + return "" raise ValueError( "A real number is required" ) + def to_string( self, value, app ): + """Convert a value to a string representation suitable for persisting""" + if value is None: + return "" + else: + return str( value ) def to_python( self, value, app ): - return float( value ) + try: + return float( value ) + except Exception, err: + if not value and self.optional: + return None + raise err def get_initial_value( self, trans, context ): try: return float( self.value ) @@ -1259,8 +1293,6 @@ formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) - # Optional DataToolParameters are used in tools like GMAJ and LAJ - self.optional = string_as_bool( elem.get( 'optional', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, # only the special case key='build' of type='data_meta' is # a valid filter Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: typo
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4a722839e77a/ changeset: 4a722839e77a user: kanwei date: 2011-06-17 21:31:07 summary: typo affected #: 1 file (1 byte) --- a/templates/workflow/list.mako Fri Jun 17 15:30:01 2011 -0400 +++ b/templates/workflow/list.mako Fri Jun 17 15:31:07 2011 -0400 @@ -121,5 +121,5 @@ <span>Configure your workflow menu</span></a></div> - </div + </div></%def> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Cleanup
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7030dfb18ef9/ changeset: 7030dfb18ef9 user: kanwei date: 2011-06-17 21:30:01 summary: Cleanup affected #: 2 files (361 bytes) --- a/templates/visualization/list.mako Fri Jun 17 15:23:28 2011 -0400 +++ b/templates/visualization/list.mako Fri Jun 17 15:30:01 2011 -0400 @@ -14,51 +14,51 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> %if message: - <% - try: - status - except: - status = "done" - %> - <p /> - <div class="${status}message"> - ${h.to_unicode( message )} - </div> + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> %endif - + ${h.to_unicode( grid )} - <br><br> - <h2>Visualizations shared with you by others</h2> + <br><br> + <h2>Visualizations shared with you by others</h2> - %if shared_by_others: - <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr class="header"> - <th>Title</th> - <th>Owner</th> - <th></th> - </tr> - %for i, association in enumerate( shared_by_others ): - <% visualization = association.visualization %> - <tr> - <td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a> - </td> - <td>${visualization.user.username}</td> - <td> - <div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a> - </div> - </td> - </tr> - %endfor - </table> - %else: + %if shared_by_others: + <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr class="header"> + <th>Title</th> + <th>Owner</th> + <th></th> + </tr> + %for i, association in enumerate( shared_by_others ): + <% visualization = association.visualization %> + <tr> + <td> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a> + </td> + <td>${visualization.user.username}</td> + <td> + <div popupmenu="shared-${i}-popup"> + <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a> + </div> + </td> + </tr> + %endfor + </table> + %else: - No visualizations have been shared with you. + No visualizations have been shared with you. - %endif + %endif </div></div> --- a/templates/workflow/list.mako Fri Jun 17 15:23:28 2011 -0400 +++ b/templates/workflow/list.mako Fri Jun 17 15:30:01 2011 -0400 @@ -15,16 +15,16 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> %if message: - <% - try: - status - except: - status = "done" - %> - <p /> - <div class="${status}message"> - ${h.to_unicode( message )} - </div> + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> %endif <h2>Your workflows</h2> @@ -43,7 +43,7 @@ </a></li></ul> - + %if workflows: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" style="width:100%;"><tr class="header"> @@ -72,7 +72,7 @@ <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( action='delete', id=trans.security.encode_id(workflow.id) )}">Delete</a></div></td> - </tr> + </tr> %endfor </table> %else: @@ -101,12 +101,12 @@ <td>${len(workflow.latest_workflow.steps)}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> + <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a></div></td> - </tr> + </tr> %endfor </table> %else: @@ -121,5 +121,5 @@ <span>Configure your workflow menu</span></a></div> - </div> + </div </%def> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Upgrade to Mako 0.4.1 and fix failing tests due to entity escaping. Improve error message for checking strings in history.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5b9fe1d9b4fa/ changeset: 5b9fe1d9b4fa user: kanwei date: 2011-06-17 21:23:28 summary: Upgrade to Mako 0.4.1 and fix failing tests due to entity escaping. Improve error message for checking strings in history. affected #: 4 files (501 bytes) --- a/eggs.ini Fri Jun 17 15:00:22 2011 -0400 +++ b/eggs.ini Fri Jun 17 15:23:28 2011 -0400 @@ -38,7 +38,7 @@ elementtree = 1.2.6_20050316 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 -Mako = 0.2.5 +Mako = 0.4.1 nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 --- a/templates/sharing_base.mako Fri Jun 17 15:00:22 2011 -0400 +++ b/templates/sharing_base.mako Fri Jun 17 15:23:28 2011 -0400 @@ -41,13 +41,11 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> - $(document).ready( function() - { + $(document).ready( function() { // // Set up slug-editing functionality. // - var on_start = function( text_elt ) - { + var on_start = function( text_elt ) { // Replace URL with URL text. $('#item-url').hide(); $('#item-url-text').show(); @@ -58,8 +56,7 @@ }); }; - var on_finish = function( text_elt ) - { + var on_finish = function( text_elt ) { // Replace URL text with URL. $('#item-url-text').hide(); $('#item-url').show(); @@ -81,20 +78,17 @@ ${parent.stylesheets()} <style> ## Put some whitespace before each section header. - h3 - { + h3 { margin-top: 2em; } - input.action-button - { + input.action-button { margin-left: 0; } ## If page is displayed in panels, pad from edges for readability. %if context.get('use_panels'): - div#center - { - padding: 10px; - } + div#center { + padding: 10px; + } %endif </style></%def> @@ -131,8 +125,8 @@ ## Require that user have a public username before sharing or publishing an item. %if trans.get_user().username is None or trans.get_user().username is "": - To make a ${item_class_name_lc} accessible via link or publish it, you must create a public username: - <p> + <p>To make a ${item_class_name_lc} accessible via link or publish it, you must create a public username:</p> + <form action="${h.url_for( action='set_public_username', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> @@ -181,38 +175,36 @@ <p>You can: <div> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" - method="POST"> - %if not item.published: - ## Item is importable but not published. User can disable importable or publish. - <input class="action-button" type="submit" name="disable_link_access" value="Disable Access to ${item_class_name} Link"> - <div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div> - <br> - <input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST"> - <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> + <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" method="POST"> + %if not item.published: + ## Item is importable but not published. User can disable importable or publish. + <input class="action-button" type="submit" name="disable_link_access" value="Disable Access to ${item_class_name} Link"> + <div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div> + <br /> + <input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST"> + <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> - <br> - %else: ## item.published == True - ## Item is importable and published. User can unpublish or disable import and unpublish. - <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}"> - <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> - <br> - <input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish"> - <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> - %endif - + <br /> + %else: ## item.published == True + ## Item is importable and published. User can unpublish or disable import and unpublish. + <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}"> + <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + <br /> + <input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish"> + <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + %endif </form></div> %else: - This ${item_class_name_lc} is currently restricted so that only you and the users listed below can access it. You can: - <p> + <p>This ${item_class_name_lc} is currently restricted so that only you and the users listed below can access it. You can:</p> + <form action="${h.url_for( action='sharing', id=trans.security.encode_id(item.id) )}" method="POST"><input class="action-button" type="submit" name="make_accessible_via_link" value="Make ${item_class_name} Accessible via Link"><div class="toolParamHelp">Generates a web link that you can share with other people so that they can view and import the ${item_class_name_lc}.</div> - <br> + <br /><input class="action-button" type="submit" name="make_accessible_and_publish" value="Make ${item_class_name} Accessible and Publish" method="POST"><div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div></form> @@ -266,13 +258,13 @@ href="${h.url_for( action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"><span>Share with a user</span></a> - <br> + <br /> %endif </div></div> %endif - <p><br><br> + <br /><br /><a href="${h.url_for( action="list" )}">Back to ${item_class_plural_name} List</a></%def> \ No newline at end of file --- a/test/base/twilltestcase.py Fri Jun 17 15:00:22 2011 -0400 +++ b/test/base/twilltestcase.py Fri Jun 17 15:23:28 2011 -0400 @@ -8,6 +8,8 @@ import twill.commands as tc from twill.other_packages._mechanize_dist import ClientForm pkg_resources.require( "elementtree" ) +pkg_resources.require( "MarkupSafe" ) +from markupsafe import escape from elementtree import ElementTree from galaxy.web import security from galaxy.web.framework.helpers import iff @@ -239,7 +241,12 @@ else: self.visit_page( "history" ) for subpatt in patt.split(): - tc.find(subpatt) + try: + tc.find( escape(subpatt) ) + except: + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( escape(subpatt), fname ) + raise AssertionError( errmsg ) self.home() def clear_history( self ): """Empties a history of all datasets""" @@ -611,13 +618,10 @@ return hids def makeTfname(self, fname=None): - """ - safe temp name - preserve the file extension for tools that interpret it - """ + """safe temp name - preserve the file extension for tools that interpret it""" suffix = os.path.split(fname)[-1] # ignore full path - fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix) - return temp_prefix - + fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix) + return temp_prefix def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ): """Verifies that the attributes and contents of a history item meet expectations""" @@ -673,12 +677,12 @@ self.files_re_match( local_name, temp_name, attributes=attributes ) elif compare == 're_match_multiline': self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) - elif compare == 'sim_size': - delta = attributes.get('delta','100') - s1 = len(data) - s2 = os.path.getsize(local_name) - if abs(s1-s2) > int(delta): - raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) + elif compare == 'sim_size': + delta = attributes.get('delta','100') + s1 = len(data) + s2 = os.path.getsize(local_name) + if abs(s1-s2) > int(delta): + raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) elif compare == "contains": self.files_contains( local_name, temp_name, attributes=attributes ) else: @@ -749,7 +753,7 @@ errmsg += str( err ) raise AssertionError( errmsg ) finally: - os.remove( temp_name ) + os.remove( temp_name ) def is_zipped( self, filename ): if not zipfile.is_zipfile( filename ): --- a/test/functional/test_history_functions.py Fri Jun 17 15:00:22 2011 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 17 15:23:28 2011 -0400 @@ -282,9 +282,9 @@ .first() assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" # Make sure the deleted datasets are included in the cloned history - check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_2_bed.id + check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_2_bed.id self.check_history_for_string( check_str, show_deleted=True ) - check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_3_bed.id + check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_3_bed.id self.check_history_for_string( check_str, show_deleted=True ) # Test cloning only active datasets self.clone_history( self.security.encode_id( history3.id ), @@ -353,7 +353,7 @@ .first() assert history5 is not None, "Problem retrieving history5 from database" self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name=urllib.quote( 'history 5' ) ) - # Current history is hostory5 + # Current history is history5 sa_session.refresh( history5 ) # Due to the limitations of twill ( not functional with the permissions forms ), we're forced # to do this manually. At this point, we just want to restrict the access permission on history5 @@ -514,7 +514,7 @@ self.visit_page( "root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) - raise AssertionError, "history5 still shared with regular_user2 after unshaing it with that user." + raise AssertionError, "history5 still shared with regular_user2 after unsharing it with that user." except: pass self.logout() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add support for uncompressing a gz or bz2 compressed file upon upload to the galaxy tool shed. Fixes issue # 586.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a746bfc39b17/ changeset: a746bfc39b17 user: greg date: 2011-06-17 21:00:22 summary: Add support for uncompressing a gz or bz2 compressed file upon upload to the galaxy tool shed. Fixes issue # 586. affected #: 2 files (5.1 KB) --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Jun 17 14:27:47 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Jun 17 15:00:22 2011 -0400 @@ -1,6 +1,7 @@ import sys, os, shutil, logging, tarfile, tempfile from galaxy.web.base.controller import * from galaxy.model.orm import * +from galaxy.datatypes.checkers import * from common import get_categories, get_repository from mercurial import hg, ui @@ -8,6 +9,7 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +CHUNK_SIZE = 2**20 # 1Mb class UploadError( Exception ): pass @@ -26,6 +28,7 @@ repository = get_repository( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) + uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) ) uploaded_file = None upload_point = params.get( 'upload_point', None ) if upload_point is not None: @@ -59,25 +62,37 @@ uploaded_file = None elif file_data not in ( '', None ): uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = file_data.filename if uploaded_file: # Our current support for browsing repo contents requires a copy of the - # repository files in the repo root directory. To produce these copies, - # we update without passing the "-r null" flag. + # repository files in the repo root directory. To eliminate these copies, + # we update the repo, passing the "-r null" flag. os.chdir( repo_dir ) os.system( 'hg update -r null > /dev/null 2>&1' ) os.chdir( current_working_dir ) + isgzip = False + isbz2 = False + if uncompress_file: + isgzip = is_gzip( uploaded_file_name ) + if not isgzip: + isbz2 = is_bz2( uploaded_file_name ) ok = True files_to_commit = [] # Determine what we have - a single file or an archive try: - tar = tarfile.open( uploaded_file.name ) + if uncompress_file: + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) istar = True except tarfile.ReadError, e: tar = None istar = False if repository.is_new: if istar: - # We have an archive ( a tarball ) + # We have an archive ( a tarball ) in a new repository. ok, message = self.__check_archive( tar ) if ok: tar.extractall( path=repo_dir ) @@ -108,23 +123,28 @@ else: tar.close() else: - # We have a single file + # We have a single file in a new repository. + if uncompress_file and ( isgzip or isbz2 ): + uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) if upload_point is not None: - full_path = os.path.abspath( os.path.join( upload_point, file_data.filename ) ) - file_path = os.path.join( upload_point, file_data.filename ) + full_path = os.path.abspath( os.path.join( upload_point, uploaded_file_filename ) ) + file_path = os.path.join( upload_point, uploaded_file_filename ) else: - full_path = os.path.abspath( os.path.join( repo_dir, file_data.filename ) ) - file_path = os.path.join( file_data.filename ) - shutil.move( uploaded_file.name, full_path ) + full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) + file_path = os.path.join( uploaded_file_filename ) + shutil.move( uploaded_file_name, full_path ) repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: + # We have a repository that is not new (it contains files). + if uncompress_file and ( isgzip or isbz2 ): + uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) # Clone the repository to a temporary location. tmp_dir, cloned_repo_dir = self.__hg_clone( trans, repository, repo_dir, current_working_dir ) # Move the uploaded files to the upload_point within the cloned repository. - self.__move_to_upload_point( upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ) + self.__move_to_upload_point( upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ) # Commit and push the changes from the cloned repo to the master repo. - self.__hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) + self.__hg_push( trans, repository, file_data.filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() @@ -132,7 +152,11 @@ os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + if uncompress_file: + uncompress_str = ' uncompressed and ' + else: + uncompress_str = ' ' + message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', message=message, @@ -146,8 +170,50 @@ return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, commit_message=commit_message, + uncompress_file=uncompress_file, message=message, status=status ) + def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): + if isgzip: + self.__handle_gzip( repository, uploaded_file_name ) + return uploaded_file_filename.rstrip( '.gz' ) + if isbz2: + self.__handle_bz2( repository, uploaded_file_name ) + return uploaded_file_filename.rstrip( '.bz2' ) + def __handle_gzip( self, repository, uploaded_file_name ): + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) + while 1: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError, e: + os.close( fd ) + os.remove( uncompressed ) + log.exception( 'Problem uncompressing gz data "%s": %s' % ( uploaded_file_name, str( e ) ) ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + shutil.move( uncompressed, uploaded_file_name ) + def __handle_bz2( self, repository, uploaded_file_name ): + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) + while 1: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + log.exception( 'Problem uncompressing bz2 data "%s": %s' % ( uploaded_file_name, str( e ) ) ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + shutil.move( uncompressed, uploaded_file_name ) def __hg_clone( self, trans, repository, repo_dir, current_working_dir ): tmp_dir = tempfile.mkdtemp() tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) @@ -160,9 +226,9 @@ os.chdir( current_working_dir ) cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) return tmp_dir, cloned_repo_dir - def __hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + def __hg_push( self, trans, repository, filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): repo = hg.repository( ui.ui(), repo_dir ) - tip = repo.changectx( "tip" ) + tip = repo[ 'tip' ] # We want these change sets to be associated with the owner of the repository, so we'll # set the HGUSER environment variable accordingly. os.environ[ 'HGUSER' ] = trans.user.username @@ -184,19 +250,30 @@ os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) shutil.rmtree( tmp_dir ) - if tip != repo.changectx( "tip" ): - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + repo = hg.repository( ui.ui(), repo_dir ) + if tip != repo[ 'tip' ]: + if uncompress_file: + uncompress_str = ' uncompressed and ' + else: + uncompress_str = ' ' + message = "The file '%s' has been successfully%suploaded to the repository." % ( filename, uncompress_str ) else: message = 'No changes in uploaded files.' trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - def __move_to_upload_point( self, upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ): + def __move_to_upload_point( self, upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ): if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + if istar: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, uploaded_file_filename ) ) else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + full_path = os.path.abspath( os.path.join( cloned_repo_dir ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, uploaded_file_filename ) ) if istar: # Extract the uploaded tarball to the load_point within the cloned repository hierarchy tar.extractall( path=full_path ) @@ -204,7 +281,7 @@ uploaded_file.close() else: # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) + shutil.move( uploaded_file_name, full_path ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/repository/upload.mako Fri Jun 17 14:27:47 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Fri Jun 17 15:00:22 2011 -0400 @@ -72,6 +72,30 @@ </div><div style="clear: both"></div></div> + + <div class="form-row"> + <% + if uncompress_file: + yes_selected = 'selected' + no_selected = '' + else: + yes_selected = '' + no_selected = 'selected' + %> + <label>Uncompress files?</label> + <div class="form-row-input"> + <select name="uncompress_file"> + <option value="true" ${yes_selected}>Yes + <option value="false" ${no_selected}>No + </select> + </div> + <div class="toolParamHelp" style="clear: both;"> + Supported compression types are gz and bz2. If <b>Yes</b> is selected, the uploaded file will be uncompressed. However, + if the uploaded file is an archive that contains compressed files, the contained files will not be uncompressed. For + example, if the uploaded compressed file is some_file.tar.gz, some_file.tar will be uncompressed and extracted, but if + some_file.tar contains 4.bed.gz, the contained file 4.bed.gz will not be uncompressed. + </div> + </div><div class="form-row"><label>Message:</label><div class="form-row-input"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: (1) Create generic methods for copying visualizations and visualization configurations; (2) use generic visualization copying to support importing and cloning visualizations.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8a3730093edc/ changeset: 8a3730093edc user: jgoecks date: 2011-06-17 20:27:47 summary: (1) Create generic methods for copying visualizations and visualization configurations; (2) use generic visualization copying to support importing and cloning visualizations. affected #: 3 files (3.4 KB) --- a/lib/galaxy/model/__init__.py Fri Jun 17 13:16:53 2011 -0400 +++ b/lib/galaxy/model/__init__.py Fri Jun 17 14:27:47 2011 -0400 @@ -2244,20 +2244,59 @@ self.user = None class Visualization( object ): - def __init__( self ): + def __init__( self, user=None, type=None, title=None, dbkey=None, latest_revision=None ): self.id = None - self.user = None - self.type = None - self.title = None - self.latest_revision = None + self.user = user + self.type = type + self.title = title + self.dbkey = dbkey + self.latest_revision = latest_revision self.revisions = [] + if self.latest_revision: + self.revisions.append( latest_revision ) + + def copy( self, user=None, title=None ): + """ + Provide copy of visualization with only its latest revision. + """ + # NOTE: a shallow copy is done: the config is copied as is but datasets + # are not copied nor are the dataset ids changed. This means that the + # user does not have a copy of the data in his/her history and the + # user who owns the datasets may delete them, making them inaccessible + # for the current user. + # TODO: a deep copy option is needed. + + if not user: + user = self.user + if not title: + title = self.title + + copy_viz = Visualization( user=user, type=self.type, title=title, dbkey=self.dbkey ) + copy_revision = self.latest_revision.copy( visualization=copy_viz ) + copy_viz.latest_revision = copy_revision + return copy_viz class VisualizationRevision( object ): - def __init__( self ): + def __init__( self, visualization=None, title=None, dbkey=None, config=None ): self.id = None - self.visualization = None - self.title = None - self.config = None + self.visualization = visualization + self.title = title + self.dbkey = dbkey + self.config = config + + def copy( self, visualization=None ): + """ + Returns a copy of this object. + """ + if not visualization: + visualization = self.visualization + + return VisualizationRevision( + visualization=visualization, + title=self.title, + dbkey=self.dbkey, + config=self.config + ) class VisualizationUserShareAssociation( object ): def __init__( self ): --- a/lib/galaxy/web/controllers/visualization.py Fri Jun 17 13:16:53 2011 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Fri Jun 17 14:27:47 2011 -0400 @@ -92,29 +92,21 @@ @web.expose @web.require_login() def clone(self, trans, id, *args, **kwargs): - viz = self.get_visualization( trans, id, check_ownership=False ) + visualization = self.get_visualization( trans, id, check_ownership=False ) user = trans.get_user() - if viz.user == user: - owner = True - else: - if trans.sa_session.query( model.VisualizationUserShareAssociation ) \ - .filter_by( user=user, visualization=viz ).count() == 0: - error( "Visualization is not owned by or shared with current user" ) - owner = False - new_viz = model.Visualization() - new_viz.title = "Clone of '%s'" % viz.title - new_viz.dbkey = viz.dbkey - new_viz.type = viz.type - new_viz.latest_revision = viz.latest_revision - if not owner: - new_viz.title += " shared by '%s'" % viz.user.email - new_viz.user = user + if trans.sa_session.query( model.VisualizationUserShareAssociation ) \ + .filter_by( user=user, visualization=visualization ).count() == 0: + error( "Visualization is not owned by or shared with current user" ) + + cloned_visualization = visualization.copy( user=trans.user, title="Copy of '%s'" % visualization.title ) + # Persist session = trans.sa_session - session.add( new_viz ) + session.add( cloned_visualization ) session.flush() + # Display the management page - trans.set_message( 'Clone created with name "%s"' % new_viz.title ) + trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) return self.list( trans ) @web.expose @@ -205,36 +197,14 @@ elif visualization.deleted: return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) else: - # # Create imported visualization via copy. - # NOTE: a shallow copy is done: the config is copied as is but datasets - # are not copied nor are the dataset ids changed. This means that the - # user does not have a copy of the data in his/her history and the - # user who owns the datasets may delete them, making them inaccessible - # for the current user. - # TODO: - # -a deep copy is needed; - # -need to handle custom db keys. - # + # TODO: need to handle custom db keys. - imported_visualization = model.Visualization() - imported_visualization.title = visualization.title - imported_visualization.dbkey = visualization.dbkey - imported_visualization.type = visualization.type - imported_visualization.user = trans.user + imported_visualization = visualization.copy( user=trans.user, title="imported: " + visualization.title ) - # And the first visualization revision - imported_visualization_revision = model.VisualizationRevision() - imported_visualization_revision.title = visualization.title - imported_visualization_revision.config = visualization.latest_revision.config - imported_visualization_revision.dbkey = visualization.dbkey - imported_visualization_revision.visualization = imported_visualization - imported_visualization.latest_revision = imported_visualization_revision - # Persist session = trans.sa_session session.add( imported_visualization ) - session.add( imported_visualization_revision ) session.flush() # Redirect to load galaxy frames. --- a/templates/visualization/list.mako Fri Jun 17 13:16:53 2011 -0400 +++ b/templates/visualization/list.mako Fri Jun 17 14:27:47 2011 -0400 @@ -13,6 +13,19 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> + %if message: + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> + %endif + ${h.to_unicode( grid )} <br><br> @@ -35,6 +48,7 @@ <td><div popupmenu="shared-${i}-popup"><a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a></div></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Jun '11

17 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/55af252cd550/ changeset: 55af252cd550 user: jgoecks date: 2011-06-17 19:16:34 summary: Enable importing of visualizations via a shallow copy: only a viz's config is copied, not its datasets. affected #: 2 files (1.1 KB) --- a/lib/galaxy/web/controllers/visualization.py Fri Jun 17 12:16:53 2011 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Fri Jun 17 13:16:34 2011 -0400 @@ -87,7 +87,7 @@ @web.require_login( "use Galaxy visualizations", use_panels=True ) def index( self, trans, *args, **kwargs ): """ Lists user's saved visualizations. """ - return self.list( trans, args, kwargs ) + return self.list( trans, *args, **kwargs ) @web.expose @web.require_login() @@ -202,20 +202,39 @@ visualization = self.get_visualization( trans, id, check_ownership=False ) if visualization.importable == False: return trans.show_error_message( "The owner of this visualization has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) - elif visualization.user == trans.user: - return trans.show_error_message( "You can't import this visualization because you own it.<br>You can %s" % referer_message, use_panels=True ) elif visualization.deleted: return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) else: - # Create imported visualization via copy. TODO: Visualizations use datasets -- do we need to check to ensure that - # datasets can be imported/viewed and/or copy datasets to user? + # + # Create imported visualization via copy. + # NOTE: a shallow copy is done: the config is copied as is but datasets + # are not copied nor are the dataset ids changed. This means that the + # user does not have a copy of the data in his/her history and the + # user who owns the datasets may delete them, making them inaccessible + # for the current user. + # TODO: + # -a deep copy is needed; + # -need to handle custom db keys. + # + imported_visualization = model.Visualization() - imported_visualization.title = "imported: " + visualization.title - imported_visualization.latest_revision = visualization.latest_revision + imported_visualization.title = visualization.title + imported_visualization.dbkey = visualization.dbkey + imported_visualization.type = visualization.type imported_visualization.user = trans.user - # Save new visualization. + + # And the first visualization revision + imported_visualization_revision = model.VisualizationRevision() + imported_visualization_revision.title = visualization.title + imported_visualization_revision.config = visualization.latest_revision.config + imported_visualization_revision.dbkey = visualization.dbkey + imported_visualization_revision.visualization = imported_visualization + imported_visualization.latest_revision = imported_visualization_revision + + # Persist session = trans.sa_session session.add( imported_visualization ) + session.add( imported_visualization_revision ) session.flush() # Redirect to load galaxy frames. --- a/templates/visualization/display.mako Fri Jun 17 12:16:53 2011 -0400 +++ b/templates/visualization/display.mako Fri Jun 17 13:16:34 2011 -0400 @@ -49,7 +49,12 @@ </%def><%def name="render_item_links( visualization )"> - + <a + href="${h.url_for( controller='/visualization', action='imp', id=trans.security.encode_id( visualization.id ) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import visualization">Import visualization</a></%def><%def name="render_item( visualization, config )"> http://bitbucket.org/galaxy/galaxy-central/changeset/dc33340cad7d/ changeset: dc33340cad7d user: jgoecks date: 2011-06-17 19:16:53 summary: Merge. affected #: 1 file (8 bytes) --- a/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:16:34 2011 -0400 +++ b/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:16:53 2011 -0400 @@ -26,7 +26,7 @@ def set_meta( self, dataset, overwrite = True, **kwd ): - Tabular.set_meta( self, dataset, overwrite=overwrite, skip=1, max_data_lines=None, **kwd ) + Tabular.set_meta( self, dataset, overwrite=overwrite, max_data_lines=None, **kwd ) # these two if statements work around a potential bug in metadata.py if dataset.metadata.labels is None or dataset.metadata.labels == dataset.metadata.spec['labels'].no_value: self._set_column_labels_metadata( dataset ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fixed displayed line count
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/acbd9488ba36/ changeset: acbd9488ba36 user: richard_burhans date: 2011-06-17 19:13:01 summary: fixed displayed line count affected #: 1 file (8 bytes) --- a/lib/galaxy/datatypes/wsf.py Fri Jun 17 12:16:53 2011 -0400 +++ b/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:13:01 2011 -0400 @@ -26,7 +26,7 @@ def set_meta( self, dataset, overwrite = True, **kwd ): - Tabular.set_meta( self, dataset, overwrite=overwrite, skip=1, max_data_lines=None, **kwd ) + Tabular.set_meta( self, dataset, overwrite=overwrite, max_data_lines=None, **kwd ) # these two if statements work around a potential bug in metadata.py if dataset.metadata.labels is None or dataset.metadata.labels == dataset.metadata.spec['labels'].no_value: self._set_column_labels_metadata( dataset ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: updated error handling for genome diversity select snps tool
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7feab5786a19/ changeset: 7feab5786a19 user: richard_burhans date: 2011-06-17 18:16:53 summary: updated error handling for genome diversity select snps tool affected #: 2 files (3.1 KB) --- a/tools/genome_diversity/genome_diversity.py Fri Jun 17 10:53:41 2011 -0400 +++ b/tools/genome_diversity/genome_diversity.py Fri Jun 17 12:16:53 2011 -0400 @@ -1,5 +1,6 @@ #!/usr/bin/env python2.5 +import sys import cdblib def _openfile( filename=None, mode='r' ): @@ -21,7 +22,7 @@ return None -class SnpFile: +class SnpFile( object ): def __init__( self, filename=None, seq_col=1, pos_col=2, ref_seq_col=7, ref_pos_col=8 ): self.filename = filename self.fh = _openfile( filename ) @@ -63,7 +64,7 @@ return None, None -class IndexedFile: +class IndexedFile( object ): def __init__( self, data_file=None, index_file=None ): self.data_file = data_file @@ -176,3 +177,90 @@ else: return None + + +class LocationFile( object ): + def __init__(self, filename): + self.build_map(filename) + + def build_map(self, filename): + self.map = {} + self.open_file(filename) + for line in self.read_lines(): + elems = line.split('\t', 1) + if len(elems) == 2: + self.map[ elems[0].strip() ] = elems[1].strip() + self.close_file() + + def read_lines(self): + for line in self.fh: + if not line.startswith('#'): + line = line.rstrip('\r\n') + yield line + + def open_file(self, filename): + self.filename = filename + try: + self.fh = open(filename, 'r') + except IOError, err: + print >> sys.stderr, "Error opening location file '%s': %s" % (filename, str(err)) + sys.exit(1) + + def close_file(self): + self.fh.close() + + def loc_file( self, key ): + if key in self.map: + return self.map[key] + else: + print >> sys.stderr, "'%s' does not appear in location file '%s'" % (key, self.filename) + sys.exit(1) + +class ChrLens( object ): + def __init__( self, location_file, species ): + self.chrlen_loc = LocationFile( location_file ) + self.chrlen_filename = self.chrlen_loc.loc_file( species ) + self.build_map() + + def build_map(self): + self.map = {} + self.open_file(self.chrlen_filename) + for line in self.read_lines(): + elems = line.split('\t', 1) + if len(elems) == 2: + chrom = elems[0].strip() + chrom_len_text = elems[1].strip() + try: + chrom_len = int( chrom_len_text ) + except ValueError: + print >> sys.stderr, "Bad length '%s' for chromosome '%s' in '%s'" % (chrom_len_text, chrom, self.chrlen_filename) + self.map[ chrom ] = chrom_len + self.close_file() + + def read_lines(self): + for line in self.fh: + if not line.startswith('#'): + line = line.rstrip('\r\n') + yield line + + def open_file(self, filename): + self.filename = filename + try: + self.fh = open(filename, 'r') + except IOError, err: + print >> sys.stderr, "Error opening chromosome length file '%s': %s" % (filename, str(err)) + sys.exit(1) + + def close_file(self): + self.fh.close() + + def length( self, key ): + if key in self.map: + return self.map[key] + else: + return None + + def __iter__( self ): + for chrom in self.map: + yield chrom + --- a/tools/genome_diversity/select_snps.py Fri Jun 17 10:53:41 2011 -0400 +++ b/tools/genome_diversity/select_snps.py Fri Jun 17 12:16:53 2011 -0400 @@ -1,16 +1,9 @@ #!/usr/bin/env python -""" -basic version -need to add - o indexing - o better error handing -""" - import sys -import string import math from optparse import OptionParser +import genome_diversity as gd def main_function(parse_arguments=None): if parse_arguments is None: @@ -37,32 +30,19 @@ @main_function(parse_arguments) def main(options, arguments): - ref_chrom_idx = int( options.ref_chrom_col ) - 1 - ref_pos_idx = int( options.ref_pos_col ) - 1 - chrlens_fh = open( options.chrlens_loc, 'r' ) - for line in chrlens_fh: - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - elems = line.split( '\t' ) - if len(elems) >= 2 and elems[0] == options.species: - chrom_info_file = elems[1] + ref_chrom_idx = to_int( options.ref_chrom_col ) -1 + ref_pos_idx = to_int( options.ref_pos_col ) -1 - chrom_info = open( chrom_info_file, 'r' ) + if (ref_chrom_idx < 1) or (ref_pos_idx < 1) or (ref_chrom_idx == ref_pos_idx): + print >> sys.stderr, "Cannot locate reference genome sequence (ref) or reference genome position (rPos) column for this dataset." + sys.exit(1) + + chrlens = gd.ChrLens( options.chrlens_loc, options.species ) + total_len = 0 - for i, line in enumerate( chrom_info ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - elems = line.split() - if len(elems) == 2: - chrom = elems[0] - try: - chrom_len = int(elems[1]) - except ValueError: - sys.stderr.write( "bad chrom len in line %d column 2: %s\n" % ( i, elems[1] ) ) - sys.exit(1) - total_len += chrom_len; - chrom_info.close() + for chrom in chrlens: + total_len += chrlens.length(chrom) total_requested = int( options.num_snps ) lines, data, comments = get_snp_lines_data_and_comments( options.input, ref_chrom_idx, ref_pos_idx ) @@ -70,6 +50,13 @@ out_data = fix_selection_and_order_like_input(data, selected, total_requested) write_selected_snps( options.output, out_data, lines, comments ) +def to_int( value ): + try: + int_value = int( value ) + except ValueError: + int_value = 0 + return int_value + def get_snp_lines_data_and_comments( filename, chrom_idx, pos_idx ): fh = open( filename, 'r' ) if (chrom_idx >= pos_idx): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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