galaxy-commits January 2013

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commit/galaxy-central: 2 new changesets
by Bitbucket 22 Jan '13

22 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b368163e14fe/ changeset: b368163e14fe user: inithello date: 2013-01-22 21:54:49 summary: Update functional test parameters so tests will pass. affected #: 2 files diff -r 2f3e80ded864f29b27ad3af71f4887f23293297c -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b tools/phenotype_association/dividePgSnpAlleles.xml --- a/tools/phenotype_association/dividePgSnpAlleles.xml +++ b/tools/phenotype_association/dividePgSnpAlleles.xml @@ -25,7 +25,7 @@ <tests><test><param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' /> - <param name='refcol' value='no' /> + <param name='ref' value='no' /><output name="output" file="dividePgSnp_output.txt" /></test></tests> diff -r 2f3e80ded864f29b27ad3af71f4887f23293297c -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b tools/phenotype_association/snpFreq.xml --- a/tools/phenotype_association/snpFreq.xml +++ b/tools/phenotype_association/snpFreq.xml @@ -44,6 +44,7 @@ <tests><test> + <param name="inType" value="tab" /><param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" /><param name="group1_1" value="4" /><param name="group1_2" value="5" /> https://bitbucket.org/galaxy/galaxy-central/commits/3c752f2d4d95/ changeset: 3c752f2d4d95 user: inithello date: 2013-01-22 21:55:29 summary: Make wrapper compatible with python 2.5. affected #: 1 file diff -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b -r 3c752f2d4d958f34f085f2cc707c503693b4680d tools/evolution/add_scores.py --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import with_statement import sys from galaxy import eggs 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: Handle invalid repository dependency definitions contained in tool shed repositories.
by Bitbucket 22 Jan '13

22 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f3e80ded864/ changeset: 2f3e80ded864 user: greg date: 2013-01-22 19:24:23 summary: Handle invalid repository dependency definitions contained in tool shed repositories. affected #: 2 files diff -r 0e064a23864c846483b35f893cf0a769dedf24f1 -r 2f3e80ded864f29b27ad3af71f4887f23293297c lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1888,6 +1888,7 @@ handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) elif key_rd_dicts_to_be_processed: handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies def get_repository_dependency_as_key( repository_dependency ): return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], @@ -2181,12 +2182,12 @@ for key_rd_dict in key_rd_dicts: key = key_rd_dict.keys()[ 0 ] repository_dependency = key_rd_dict[ key ] - toolshed, name, owner, changeset_revision = repository_dependency - if tool_shed_is_this_tool_shed( toolshed ): - repository = get_repository_by_name_and_owner( trans, name, owner ) + rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( rd_toolshed ): + repository = get_repository_by_name_and_owner( trans, rd_name, rd_owner ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), - changeset_revision ) + rd_changeset_revision ) if repository_metadata: # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} @@ -2196,15 +2197,20 @@ # The repository changeset_revision is no longer installable, so see if there's been an update. repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) - changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: new_key_rd_dict = {} - new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ] + new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ] # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) + else: + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ + ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) + log.debug( message ) return updated_key_rd_dicts def get_url_from_repository_tool_shed( app, repository ): """ @@ -2816,6 +2822,25 @@ new_key_rd_dict[ current_repository_key ] = repository_dependency key_rd_dicts_to_be_processed.append( new_key_rd_dict ) return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies +def prune_invalid_repository_dependencies( repository_dependencies ): + """ + Eliminate all invalid entries in the received repository_dependencies dictionary. An entry is invalid if if the value_list of the key/value pair is + empty. This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata reocrd is not found. + """ + valid_repository_dependencies = {} + description = repository_dependencies.get( 'description', None ) + root_key = repository_dependencies.get( 'root_key', None ) + if root_key is None: + return valid_repository_dependencies + for key, value in repository_dependencies.items(): + if key in [ 'description', 'root_key' ]: + continue + if value: + valid_repository_dependencies[ key ] = value + if valid_repository_dependencies: + valid_repository_dependencies[ 'description' ] = description + valid_repository_dependencies[ 'root_key' ] = root_key + return valid_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: diff -r 0e064a23864c846483b35f893cf0a769dedf24f1 -r 2f3e80ded864f29b27ad3af71f4887f23293297c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1909,6 +1909,7 @@ metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if repository_metadata: + metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, @@ -1917,6 +1918,12 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored. Make sure valid <b>toolshed</b>, ' + message += '<b>name</b>, <b>owner</b> and <b>changeset_revision</b> values are defined in the contained <b>repository_dependencies.xml</b> ' + message += 'file to correct this problem.' + status = 'error' if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -2029,6 +2036,10 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored.' + status = 'error' else: repository_metadata_id = None metadata = None @@ -2550,6 +2561,10 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored.' + status = 'error' else: repository_metadata_id = None metadata = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Exporting workflows: (a) remove spurious header and (b) add option to create workflow image. (b) inspired by Björn Grüning
by Bitbucket 21 Jan '13

21 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e064a23864c/ changeset: 0e064a23864c user: jgoecks date: 2013-01-21 15:02:56 summary: Exporting workflows: (a) remove spurious header and (b) add option to create workflow image. (b) inspired by Björn Grüning affected #: 1 file diff -r bb3a803c207d4e1f305982bf97bcb9019810bd83 -r 0e064a23864c846483b35f893cf0a769dedf24f1 templates/workflow/export.mako --- a/templates/workflow/export.mako +++ b/templates/workflow/export.mako @@ -25,7 +25,6 @@ <h3>Export to myExperiment</h3><div class="toolForm"> - <div class="toolFormTitle">Export</div><form action="${h.url_for( action='export_to_myexp', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> @@ -46,6 +45,13 @@ <%def name="render_more(item)"> ## Add form to export to myExperiment. ${self.render_export_to_myexp(item)} + + ## Add link to render as SVG image. + <h3>Create Image</h3> + + <a href="${h.url_for( action='gen_image', id=trans.security.encode_id( item.id ) )}"> + Create image of ${get_class_display_name( item.__class__ ).lower()} in SVG format + </a></%def><%def name="center_panel()"> 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: Eliminate the tool shed's common controller.
by Bitbucket 21 Jan '13

21 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb3a803c207d/ changeset: bb3a803c207d user: greg date: 2013-01-21 14:59:31 summary: Eliminate the tool shed's common controller. affected #: 4 files diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ /dev/null @@ -1,27 +0,0 @@ -import logging -from galaxy.model.item_attrs import UsesItemRatings - -log = logging.getLogger( __name__ ) - -class ItemRatings( UsesItemRatings ): - """Overrides rate_item method since we also allow for comments""" - def rate_item( self, trans, user, item, rating, comment='' ): - """ Rate an item. Return type is <item_class>RatingAssociation. """ - item_rating = self.get_user_item_rating( trans.sa_session, user, item, webapp_model=trans.model ) - if not item_rating: - # User has not yet rated item; create rating. - item_rating_assoc_class = self._get_item_rating_assoc_class( item, webapp_model=trans.model ) - item_rating = item_rating_assoc_class() - item_rating.user = trans.user - item_rating.set_item( item ) - item_rating.rating = rating - item_rating.comment = comment - trans.sa_session.add( item_rating ) - trans.sa_session.flush() - elif item_rating.rating != rating or item_rating.comment != comment: - # User has previously rated item; update rating. - item_rating.rating = rating - item_rating.comment = comment - trans.sa_session.add( item_rating ) - trans.sa_session.flush() - return item_rating diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -13,7 +13,7 @@ import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util from galaxy.webapps.community.util import workflow_util -import common +from galaxy.webapps.community.util import common_util import galaxy.tools from galaxy import eggs @@ -518,7 +518,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ) -class RepositoryController( BaseUIController, common.ItemRatings ): +class RepositoryController( BaseUIController, common_util.ItemRatings ): install_matched_repository_grid = InstallMatchedRepositoryGrid() matched_repository_grid = MatchedRepositoryGrid() diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -6,7 +6,7 @@ from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func -import common +from galaxy.webapps.community.util import common_util from galaxy.webapps.community.util.container_util import STRSEP from repository import RepositoryGrid import galaxy.util.shed_util_common as suc @@ -260,7 +260,7 @@ .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) -class RepositoryReviewController( BaseUIController, common.ItemRatings ): +class RepositoryReviewController( BaseUIController, common_util.ItemRatings ): component_grid = ComponentGrid() repositories_reviewed_by_me_grid = RepositoriesReviewedByMeGrid() diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/util/common_util.py --- /dev/null +++ b/lib/galaxy/webapps/community/util/common_util.py @@ -0,0 +1,27 @@ +import logging +from galaxy.model.item_attrs import UsesItemRatings + +log = logging.getLogger( __name__ ) + +class ItemRatings( UsesItemRatings ): + """Overrides rate_item method since we also allow for comments""" + def rate_item( self, trans, user, item, rating, comment='' ): + """ Rate an item. Return type is <item_class>RatingAssociation. """ + item_rating = self.get_user_item_rating( trans.sa_session, user, item, webapp_model=trans.model ) + if not item_rating: + # User has not yet rated item; create rating. + item_rating_assoc_class = self._get_item_rating_assoc_class( item, webapp_model=trans.model ) + item_rating = item_rating_assoc_class() + item_rating.user = trans.user + item_rating.set_item( item ) + item_rating.rating = rating + item_rating.comment = comment + trans.sa_session.add( item_rating ) + trans.sa_session.flush() + elif item_rating.rating != rating or item_rating.comment != comment: + # User has previously rated item; update rating. + item_rating.rating = rating + item_rating.comment = comment + trans.sa_session.add( item_rating ) + trans.sa_session.flush() + return item_rating 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 missing import to update manager.
by Bitbucket 19 Jan '13

19 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/34404f848979/ changeset: 34404f848979 user: greg date: 2013-01-19 23:54:48 summary: Add missing import to update manager. affected #: 1 file diff -r 7d37ffe813f2a037b560af26770ffe5924ae643f -r 34404f8489792a97096b36f012fbf775cc3b382b lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -4,6 +4,7 @@ import threading, urllib2, logging from galaxy.util import string_as_bool import galaxy.util.shed_util as shed_util +from galaxy.model.orm import and_ log = logging.getLogger( __name__ ) 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 19 Jan '13

19 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0df1612c1cb1/ changeset: 0df1612c1cb1 user: asbardellati date: 2013-01-18 17:11:04 summary: Add option for writing not aligned reads to file Reviewed-by: Nicola Soranzo <soranzo(a)crs4.it> affected #: 2 files diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -31,10 +31,29 @@ parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' ) parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) + parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' ) + parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' ) + parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' ) + (options, args) = parser.parse_args() + tmp_unaligned_file_name = None # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() + + if options.single_paired == 'paired': + if options.output_unaligned_reads_l and options.output_unaligned_reads_r: + tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) + tmp_unaligned_file_name = tmp_unaligned_file.name + tmp_unaligned_file.close() + output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name + else: + output_unaligned_reads = '' + elif options.output_unaligned_reads: + output_unaligned_reads = '--un %s' % options.output_unaligned_reads + else: + output_unaligned_reads = '' + if options.own_file: index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) ) try: @@ -71,7 +90,7 @@ index_path = options.index_path # Build bowtie command; use view and sort to create sorted bam. - cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s' + cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' # Set up reads. if options.single_paired == 'paired': @@ -104,7 +123,7 @@ opts += ' --rg %s:%s' % ( 'SM', options.rgsm ) # Final command: - cmd = cmd % ( opts, index_path, reads, options.output ) + cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output ) print cmd # Run @@ -136,6 +155,16 @@ except Exception, e: stop_err( 'Error in bowtie2:\n' + str( e ) ) + # get unaligned reads output files in place if appropriate + if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r: + try: + left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' ) + right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' ) + shutil.move( left, options.output_unaligned_reads_l ) + shutil.move( right, options.output_unaligned_reads_r ) + except Exception, e: + sys.stdout.write( 'Error producing the unaligned output files.\n' ) + # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -1,6 +1,6 @@ <tool id="bowtie2" name="Bowtie2" version="0.1"> - <description>is a short-read mapper</description> + <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement> @@ -15,6 +15,17 @@ ## Outputs. --output=$output + #if str( $singlePaired.sPaired ) == "single" + #if $output_unaligned_reads_l + --output_unaligned_reads=$output_unaligned_reads_l + #end if + #else + #if $output_unaligned_reads_l and $output_unaligned_reads_r + --output_unaligned_reads_l=$output_unaligned_reads_l + --output_unaligned_reads_r=$output_unaligned_reads_r + #end if + #end if + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile @@ -71,6 +82,7 @@ <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional> + <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option> @@ -133,7 +145,7 @@ </inputs><outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -152,6 +164,22 @@ </conditional></actions></data> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data></outputs><tests> https://bitbucket.org/galaxy/galaxy-central/commits/7d37ffe813f2/ changeset: 7d37ffe813f2 user: jgoecks date: 2013-01-19 22:35:28 summary: Merged in nsoranzo/galaxy-central (pull request #110) Add option to bowtie2 tool for writing not aligned reads to file affected #: 2 files diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -31,10 +31,29 @@ parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' ) parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) + parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' ) + parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' ) + parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' ) + (options, args) = parser.parse_args() + tmp_unaligned_file_name = None # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() + + if options.single_paired == 'paired': + if options.output_unaligned_reads_l and options.output_unaligned_reads_r: + tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) + tmp_unaligned_file_name = tmp_unaligned_file.name + tmp_unaligned_file.close() + output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name + else: + output_unaligned_reads = '' + elif options.output_unaligned_reads: + output_unaligned_reads = '--un %s' % options.output_unaligned_reads + else: + output_unaligned_reads = '' + if options.own_file: index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) ) try: @@ -71,7 +90,7 @@ index_path = options.index_path # Build bowtie command; use view and sort to create sorted bam. - cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s' + cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' # Set up reads. if options.single_paired == 'paired': @@ -104,7 +123,7 @@ opts += ' --rg %s:%s' % ( 'SM', options.rgsm ) # Final command: - cmd = cmd % ( opts, index_path, reads, options.output ) + cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output ) print cmd # Run @@ -136,6 +155,16 @@ except Exception, e: stop_err( 'Error in bowtie2:\n' + str( e ) ) + # get unaligned reads output files in place if appropriate + if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r: + try: + left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' ) + right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' ) + shutil.move( left, options.output_unaligned_reads_l ) + shutil.move( right, options.output_unaligned_reads_r ) + except Exception, e: + sys.stdout.write( 'Error producing the unaligned output files.\n' ) + # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -1,6 +1,6 @@ <tool id="bowtie2" name="Bowtie2" version="0.1"> - <description>is a short-read mapper</description> + <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement> @@ -15,6 +15,17 @@ ## Outputs. --output=$output + #if str( $singlePaired.sPaired ) == "single" + #if $output_unaligned_reads_l + --output_unaligned_reads=$output_unaligned_reads_l + #end if + #else + #if $output_unaligned_reads_l and $output_unaligned_reads_r + --output_unaligned_reads_l=$output_unaligned_reads_l + --output_unaligned_reads_r=$output_unaligned_reads_r + #end if + #end if + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile @@ -71,6 +82,7 @@ <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional> + <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option> @@ -133,7 +145,7 @@ </inputs><outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -152,6 +164,22 @@ </conditional></actions></data> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data></outputs><tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: api/history_contents, index: handle hda_dict building exceptions by appending an error-state hda_dict (instead of 'fail-on-first'); history panel: handle bootstrapped and ajax hda api exceptions more gracefully, show hda api exceptions as hdas in the error state.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/50c65739cd1a/ changeset: 50c65739cd1a user: carlfeberhard date: 2013-01-18 22:32:05 summary: api/history_contents, index: handle hda_dict building exceptions by appending an error-state hda_dict (instead of 'fail-on-first'); history panel: handle bootstrapped and ajax hda api exceptions more gracefully, show hda api exceptions as hdas in the error state. affected #: 4 files diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -60,8 +60,20 @@ # but we(I?) need an hda collection with full data somewhere ids = ids.split( ',' ) for hda in history.datasets: - if trans.security.encode_id( hda.id ) in ids: - rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + #TODO: curr. ordered by history, change to order from ids list + encoded_hda_id = trans.security.encode_id( hda.id ) + if encoded_hda_id in ids: + #TODO: share code with show + try: + rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + + except Exception, exc: + # don't fail entire list if hda err's, record and move on + # (making sure http recvr knows it's err'd) + trans.response.status = 500 + log.error( "Error in history API at listing contents " + + "with history %s, hda %s: %s", history_id, encoded_hda_id, str( exc ) ) + rval.append( self._exception_as_hda_dict( trans, encoded_hda_id, exc ) ) else: # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history @@ -69,12 +81,14 @@ rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: - rval = "Error in history API at listing contents" + # for errors that are not specific to one hda (history lookup or summary list) + rval = "Error in history API at listing contents: " + str( e ) log.error( rval + ": %s, %s" % ( type( e ), str( e ) ) ) trans.response.status = 500 return rval + #TODO: move to model or Mixin def _summary_hda_dict( self, trans, history_id, hda ): """ Returns a dictionary based on the HDA in .. _summary form:: @@ -94,6 +108,26 @@ 'url' : url_for( 'history_content', history_id=history_id, id=encoded_id, ), } + #TODO: move to model or Mixin + def _exception_as_hda_dict( self, trans, hda_id, exception ): + """ + Returns a dictionary for an HDA that raised an exception when it's + dictionary was being built. + { + 'id' : < the encoded dataset id >, + 'type' : < name of the dataset >, + 'url' : < api url to retrieve this datasets full data >, + } + """ + return { + 'id' : hda_id, + 'state' : trans.app.model.Dataset.states.ERROR, + 'visible' : True, + 'misc_info' : str( exception ), + 'misc_blurb': 'Failed to retrieve dataset information.', + 'error' : str( exception ) + } + @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -445,7 +445,7 @@ if( !this.model.get( 'purged' ) ){ parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); } - parent.append( ( _l( 'An error occurred running this job' ) + ': ' + parent.append( ( _l( 'An error occurred with this dataset' ) + ': ' + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers.concat([ this._render_downloadButton ]) diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -55,9 +55,17 @@ this.hdas = new HDACollection(); // if we've got hdas passed in the constructor, load them and set up updates if needed - if( initialHdas && initialHdas.length ){ - this.hdas.reset( initialHdas ); - this.checkForUpdates(); + if( initialHdas ){ + if( _.isArray( initialHdas ) ){ + this.hdas.reset( initialHdas ); + this.checkForUpdates(); + + // handle errors in initialHdas + //TODO: errors from the api shouldn't be plain strings... + //TODO: remove when mappers and hda_dict are unified (or move to alt history) + } else if( _.isString( initialHdas ) && ( initialHdas.match( /error/i ) ) ){ + alert( _l( 'Error loading bootstrapped history' ) + ':\n' + initialHdas ); + } } // events @@ -163,7 +171,7 @@ // send the changed ids (if any) to dataset collection to have them fetch their own model changes if( changedIds.length ){ - history.updateHdas( changedIds ); + history.fetchHdaUpdates( changedIds ); } // set up to keep pulling if this history in run/queue state @@ -193,16 +201,37 @@ * If it's not in the collection, addHdas will be used to create it. * @param {String[]} hdaIds an array of the encoded ids of the hdas to get from the server. */ - updateHdas : function( hdaIds ){ + fetchHdaUpdates : function( hdaIds ){ //TODO:?? move to collection? still need proper url var history = this; jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), + /** + * @inner + */ error : function( xhr, status, error ){ - var msg = 'ERROR updating hdas from api history contents:'; - history.log( msg, hdaIds, xhr, status, error ); - alert( msg + hdaIds.join(',') ); + if( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ){ return; } + + var errorJson = JSON.parse( xhr.responseText ); + if( _.isArray( errorJson ) ){ + + // just for debugging/reporting purposes + var grouped = _.groupBy( errorJson, function( hdaData ){ + if( _.has( hdaData, 'error' ) ){ return 'errored'; } + return 'ok'; + }); + history.log( 'fetched, errored datasets:', grouped.errored ); + + // the server already formats the error'd hdas in proper hda-model form + // so we're good to send these on + history.updateHdas( errorJson ); + + } else { + var msg = _l( 'ERROR updating hdas from api history contents' ) + ': '; + history.log( msg, hdaIds, xhr, status, error, errorJSON ); + alert( msg + hdaIds.join(',') ); + } }, /** when the proper models for the requested ids are returned, @@ -210,30 +239,41 @@ * @inner */ success : function( hdaDataList, status, xhr ){ - history.log( history + '.updateHdas, success:', hdaDataList, status, xhr ); - //TODO: compile new models to be added in one go - var hdasToAdd = []; - - _.each( hdaDataList, function( hdaData, index ){ - var existingModel = history.hdas.get( hdaData.id ); - // if this model exists already, update it - if( existingModel ){ - history.log( 'found existing model in list for id ' + hdaData.id + ', updating...:' ); - existingModel.set( hdaData ); - - // if this model is new and isn't in the hda collection, cache it to be created - } else { - history.log( 'NO existing model for id ' + hdaData.id + ', creating...:' ); - hdasToAdd.push( hdaData ); - } - }); - if( hdasToAdd.length ){ - history.addHdas( hdasToAdd ); - } + history.log( history + '.fetchHdaUpdates, success:', status, xhr ); + history.updateHdas( hdaDataList ); } }); }, + /** Update the models in the hdas collection from the data given. + * If a model exists in the collection, set will be used with the new data. + * If it's not in the collection, addHdas will be used to create it. + * @param {Object[]} hdaDataList an array of the model data used to update. + */ + updateHdas : function( hdaDataList ){ + var history = this, + // models/views that need to be created + hdasToAdd = []; + history.log( history + '.updateHdas:', hdaDataList ); + + _.each( hdaDataList, function( hdaData, index ){ + var existingModel = history.hdas.get( hdaData.id ); + // if this model exists already, update it + if( existingModel ){ + history.log( 'found existing model in list for id ' + hdaData.id + ', updating...:' ); + existingModel.set( hdaData ); + + // if this model is new and isn't in the hda collection, cache it to be created + } else { + history.log( 'NO existing model for id ' + hdaData.id + ', creating...:' ); + hdasToAdd.push( hdaData ); + } + }); + if( hdasToAdd.length ){ + history.addHdas( hdasToAdd ); + } + }, + /** Add multiple hda models to the hdas collection from an array of hda data. */ addHdas : function( hdaDataList ){ diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -191,13 +191,19 @@ ##TODO: api/web controllers should use common code, and this section should call that code <%def name="get_history( id )"><% - return trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) + history_json = trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) + #assert isinstance( history, dict ), ( + # 'Bootstrapped history was expecting a dictionary: %s' %( str( history ) ) ) + return history_json %></%def><%def name="get_current_user()"><% - return trans.webapp.api_controllers[ 'users' ].show( trans, 'current' ) + user_json = trans.webapp.api_controllers[ 'users' ].show( trans, 'current' ) + #assert isinstance( hdaDataList, list ), ( + # 'Bootstrapped current user was expecting a dictionary: %s' %( str( user ) ) ) + return user_json %></%def> @@ -207,10 +213,10 @@ if not hdas: return '[]' # rather just use the history.id (wo the datasets), but... - return trans.webapp.api_controllers[ 'history_contents' ].index( - #trans, trans.security.encode_id( history_id ), + hda_json = trans.webapp.api_controllers[ 'history_contents' ].index( trans, trans.security.encode_id( history_id ), ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) + return hda_json %></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Filter request params to only those necessary when redirecting to monitor installing tool shed repositories.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/34e42ae79232/ changeset: 34e42ae79232 user: greg date: 2013-01-18 21:46:22 summary: Filter request params to only those necessary when redirecting to monitor installing tool shed repositories. affected #: 1 file diff -r b238d26ca9269aec91e26370348b89ee14c3d1ae -r 34e42ae792320b1ee2471f11f341ac55445f52e0 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -977,9 +977,10 @@ return trans.show_error_message( 'Invalid repository specified.' ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: + tool_shed_repository_ids = [ repository_id ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', - **kwd ) ) + tool_shed_repository_ids=tool_shed_repository_ids ) ) if repository.can_install and operation == 'install': # Send a request to the tool shed to install the repository. url = suc.url_join( tool_shed_url, 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: Handle long urls when installing and reinstalling tool shed repositories.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b238d26ca926/ changeset: b238d26ca926 user: greg date: 2013-01-18 21:11:39 summary: Handle long urls when installing and reinstalling tool shed repositories. affected #: 2 files diff -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 -r b238d26ca9269aec91e26370348b89ee14c3d1ae lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -350,7 +350,7 @@ # Keep the one-to-one mapping between items in 3 lists. created_or_updated_tool_shed_repositories.append( tool_shed_repository ) tool_panel_section_keys.append( tool_panel_section_key ) - filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) + filtered_repo_info_dicts.append( repo_info_dict ) # Build repository dependency relationships even if the user chose to not install repository dependencies. suc.build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message diff -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 -r b238d26ca9269aec91e26370348b89ee14c3d1ae lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -798,24 +798,6 @@ status=status ) ) @web.expose @web.require_admin - def initiate_repository_installation( self, trans, shed_repository_ids, encoded_kwd, reinstalling=False ): - tsr_ids = util.listify( shed_repository_ids ) - tool_shed_repositories = [] - for tsr_id in tsr_ids: - tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) - tool_shed_repositories.append( tsr ) - clause_list = [] - for tsr_id in tsr_ids: - clause_list.append( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( tsr_id ) ) - query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) - return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', - encoded_kwd=encoded_kwd, - query=query, - tool_shed_repositories=tool_shed_repositories, - initiate_repository_installation_ids=shed_repository_ids, - reinstalling=reinstalling ) - @web.expose - @web.require_admin def initiate_tool_dependency_installation( self, trans, tool_dependencies ): """Install specified dependencies for repository tools.""" # Get the tool_shed_repository from one of the tool_dependencies. @@ -1303,7 +1285,7 @@ else: tool_panel_section_key = None tool_section = None - tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + encoded_repository_ids = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] # Create a one-to-one mapping of tool shed repository id and tool panel section key. All tools contained in the repositories # being installed will be loaded into the same section in the tool panel. for tsr in created_or_updated_tool_shed_repositories: @@ -1319,15 +1301,24 @@ status=status, tool_path=tool_path, tool_panel_section_keys=tool_panel_section_keys, - tool_shed_repository_ids=tsrids_list, + tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) - tsrids_str = ','.join( tsrids_list ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='initiate_repository_installation', - shed_repository_ids=tsrids_str, - encoded_kwd=encoded_kwd, - reinstalling=False ) ) + tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] + tool_shed_repositories = [] + for tsr_id in tsr_ids: + tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( tsr_id ) + tool_shed_repositories.append( tsr ) + clause_list = [] + for tsr_id in tsr_ids: + clause_list.append( trans.model.ToolShedRepository.table.c.id == tsr_id ) + query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) + return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', + encoded_kwd=encoded_kwd, + query=query, + tool_shed_repositories=tool_shed_repositories, + initiate_repository_installation_ids=encoded_repository_ids, + reinstalling=False ) else: kwd[ 'message' ] = message kwd[ 'status' ] = status @@ -1516,11 +1507,21 @@ tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='initiate_repository_installation', - shed_repository_ids=encoded_repository_ids, - encoded_kwd=encoded_kwd, - reinstalling=True ) ) + tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] + tool_shed_repositories = [] + for tsr_id in tsr_ids: + tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( tsr_id ) + tool_shed_repositories.append( tsr ) + clause_list = [] + for tsr_id in tsr_ids: + clause_list.append( trans.model.ToolShedRepository.table.c.id == tsr_id ) + query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) + return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', + encoded_kwd=encoded_kwd, + query=query, + tool_shed_repositories=tool_shed_repositories, + initiate_repository_installation_ids=encoded_repository_ids, + reinstalling=True ) @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching 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: dannon: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/03d2ce228f7e/ changeset: 03d2ce228f7e user: dannon date: 2013-01-18 20:38:51 summary: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission. affected #: 1 file diff -r 98f724202d9d3cea035d7de04d89465bcf3092b1 -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -76,22 +76,24 @@ } }); //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("change paste keyup input propertychange", function(){ + $("#id_secret, #id_key_id").bind("paste input propertychange", function(){ secret_el = $("#id_secret"); key_el = $("#id_key_id"); if (secret_el.val().length === 40 && key_el.val().length === 20){ //Submit these to get_account_info, unhide fields, and update as appropriate - $.getJSON(ACCOUNT_URL, - {key_id: key_el.val(),secret:secret_el.val()}, - function(result){ + $.ajax({type: "POST", + url: ACCOUNT_URL, + dataType: 'json', + data: {key_id: key_el.val(),secret:secret_el.val()}, + success: function(result){ cloudlaunch_clusters = result.clusters; var kplist = $("#id_keypair"); var clusterlist = $("#id_existing_instance"); kplist.find('option').remove(); clusterlist.find('option').remove(); //Update fields with appropriate elements + clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); if (_.size(result.clusters) > 0){ - clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); _.each(result.clusters, function(cluster, index){ clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); }); @@ -104,7 +106,8 @@ kplist.append($('<option/>').val(keypair).text(keypair)); }); $('#hidden_options').show('fast'); - }); + } + }); } }); $('#loading_indicator').ajaxStart(function(){ @@ -130,7 +133,7 @@ //Dig up zone info for selected cluster, set hidden input. //This is not necessary to present to the user though the interface may prove useful. var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); - if( ei_val.value !== "New Cluster"){ + if( ei_val && (ei_val.value !== "New Cluster")){ var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); zdata.value = cluster.zone; 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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galaxy-commits January 2013