galaxy-commits November 2014

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2f7780bd1b1/ Changeset: d2f7780bd1b1 User: jmchilton Date: 2014-11-11 18:41:00+00:00 Summary: Refactor dataset matcher stuff for use outside of field generation. (i.e. for reuse in filtering datasets on the client side) Affected #: 2 files diff -r d519ad65435883112008e90ec06ebf44a91586e7 -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1796,26 +1796,52 @@ field_name = "%s%s" % ( self.name, suffix ) field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=reduction ): + name = history_dataset_collection.name + hid = str( history_dataset_collection.hid ) + hidden_text = "" # TODO + id = value_modifier( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ) ) + selected = value and history_dataset_collection in value + text = "%s:%s %s" % ( hid, hidden_text, name ) + field.add_option( text, id, selected ) + + return field + + def _get_select_dataset_field( self, history, dataset_matcher, multiple=False, suffix="" ): + field_name = "%s%s" % ( self.name, suffix ) + field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + + for hda_match, hid in self.match_datasets( history, dataset_matcher ): + if not hda_match.implicit_conversion: + hda = hda_match.hda + hda_name = hda.name + selected = dataset_matcher.selected( hda ) + if hda.visible: + hidden_text = "" + else: + hidden_text = " (hidden)" + field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) + else: + hda_name = hda_match.original_hda.name + hda = hda_match.hda # Get converted dataset + target_ext = hda_match.target_ext + selected = dataset_matcher.selected( hda ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) + + self._ensure_selection( field ) + return field + + def match_collections( self, history, dataset_matcher, reduction=True ): dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) for history_dataset_collection in history.active_dataset_collections: if dataset_collection_matcher.hdca_match( history_dataset_collection, reduction=reduction ): - name = history_dataset_collection.name - hid = str( history_dataset_collection.hid ) - hidden_text = "" # TODO - id = value_modifier( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ) ) - selected = value and history_dataset_collection in value - text = "%s:%s %s" % ( hid, hidden_text, name ) - field.add_option( text, id, selected ) + yield history_dataset_collection - return field + def match_datasets( self, history, dataset_matcher ): - def _get_select_dataset_field( self, history, dataset_matcher, multiple=False, suffix="" ): - - # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): for i, hda in enumerate( hdas ): - hda_name = hda.name if parent_hid is not None: hid = "%s.%d" % ( parent_hid, i + 1 ) else: @@ -1823,27 +1849,13 @@ hda_match = dataset_matcher.hda_match( hda ) if not hda_match: continue - if not hda_match.implicit_conversion: - selected = dataset_matcher.selected( hda ) - if hda.visible: - hidden_text = "" - else: - hidden_text = " (hidden)" - field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) - else: - hda = hda_match.hda # Get converted dataset - target_ext = hda_match.target_ext - selected = dataset_matcher.selected( hda ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) + yield (hda_match, hid) # Also collect children via association object - dataset_collector( hda.children, hid ) + for item in dataset_collector( hda.children, hid ): + yield item - field_name = "%s%s" % ( self.name, suffix ) - field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) - - dataset_collector( history.active_datasets_children_and_roles, None ) - self._ensure_selection( field ) - return field + for item in dataset_collector( history.active_datasets_children_and_roles, None ): + yield item def get_initial_value( self, trans, context, history=None ): return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history) @@ -2098,15 +2110,31 @@ return self._switch_fields( fields, default_field=default_field ) - def _get_single_collection_field( self, trans, history, value, other_values ): - field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + def match_collections( self, trans, history, dataset_matcher ): dataset_collections = trans.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) ) - dataset_matcher = DatasetMatcher( trans, self, value, other_values ) dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) for dataset_collection_instance in dataset_collections: if not dataset_collection_matcher.hdca_match( dataset_collection_instance ): continue + yield dataset_collection_instance + + def match_multirun_collections( self, trans, history, dataset_matcher ): + dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) + + for history_dataset_collection in history.active_dataset_collections: + if not self._history_query( trans ).can_map_over( history_dataset_collection ): + continue + + datasets_match = dataset_collection_matcher.hdca_match( history_dataset_collection ) + if datasets_match: + yield history_dataset_collection + + def _get_single_collection_field( self, trans, history, value, other_values ): + field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + dataset_matcher = DatasetMatcher( trans, self, value, other_values ) + + for dataset_collection_instance in self.match_collections( trans, history, dataset_matcher ): instance_id = dataset_collection_instance.hid instance_name = dataset_collection_instance.name selected = ( value and ( dataset_collection_instance == value ) ) @@ -2122,22 +2150,16 @@ field_name = "%s%s" % ( self.name, suffix ) field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) dataset_matcher = DatasetMatcher( trans, self, value, other_values ) - dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.active_dataset_collections: - if not self._history_query( trans ).can_map_over( history_dataset_collection ): - continue + for history_dataset_collection in self.match_multirun_collections( trans, history, dataset_matcher ): + name = history_dataset_collection.name + hid = str( history_dataset_collection.hid ) + hidden_text = "" # TODO + subcollection_type = self._history_query( trans ).collection_type_description.collection_type + id = "%s|%s" % ( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ), subcollection_type ) + text = "%s:%s %s" % ( hid, hidden_text, name ) - datasets_match = dataset_collection_matcher.hdca_match( history_dataset_collection ) - if datasets_match: - name = history_dataset_collection.name - hid = str( history_dataset_collection.hid ) - hidden_text = "" # TODO - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - id = "%s|%s" % ( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ), subcollection_type ) - text = "%s:%s %s" % ( hid, hidden_text, name ) - - field.add_option( text, id, False ) + field.add_option( text, id, False ) return field diff -r d519ad65435883112008e90ec06ebf44a91586e7 -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -53,11 +53,12 @@ return False target_ext, converted_dataset = hda.find_conversion_destination( formats ) if target_ext: + original_hda = hda if converted_dataset: hda = converted_dataset if check_security and not self.__can_access_dataset( hda.dataset ): return False - return HdaImplicitMatch( hda, target_ext ) + return HdaImplicitMatch( hda, target_ext, original_hda ) return False def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): @@ -117,7 +118,8 @@ conversion). """ - def __init__( self, hda, target_ext ): + def __init__( self, hda, target_ext, original_hda ): + self.original_hda = original_hda self.hda = hda self.target_ext = target_ext https://bitbucket.org/galaxy/galaxy-central/commits/e4c9f0b5a738/ Changeset: e4c9f0b5a738 User: jmchilton Date: 2014-11-11 18:41:00+00:00 Summary: Rework ToolDataParameter and ToolDataCollectionParameter to_dict to filter over valid matches. Doesn't do anything with them yet - passing this work off to Sam to populate the dictionaries in whatever manner makes most sense for UI consumption. Affected #: 1 file diff -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 -r e4c9f0b5a73851ab2d8644889d305aaab80208d9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2066,12 +2066,26 @@ ref = ref() return ref - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): d = super( DataToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions d['multiple'] = self.multiple + if other_values is None: + # No need to produce lists of datasets for history. + return d + + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + history = trans.history + multiple = self.multiple + for hda_match, hid in self.match_datasets( history, dataset_matcher ): + # hda_match not an hda - it is a description of the match, may + # describe match after implicit conversion. + pass + for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=multiple ): + pass return d + class DataCollectionToolParameter( BaseDataToolParameter ): """ """ @@ -2238,6 +2252,22 @@ def validate( self, value, history=None ): return True # TODO + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + d = super( DataCollectionToolParameter, self ).to_dict( trans ) + if other_values is None: + # No need to produce lists of datasets for history. + return d + + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + history = trans.history + + for hdca in self.match_collections( trans, history, dataset_matcher ): + pass + + for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): + subcollection_type = self._history_query( trans ).collection_type_description.collection_type + pass + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: Merged in anton/galaxy-central-anton (pull request #539)
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d519ad654358/ Changeset: d519ad654358 User: martenson Date: 2014-11-11 17:26:45+00:00 Summary: Merged in anton/galaxy-central-anton (pull request #539) Initial tweaks to tool_conf.xml sample and one of the tools. Affected #: 2 files diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* 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: 3 new changesets
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26e1a07f9f22/ Changeset: 26e1a07f9f22 User: anton Date: 2014-10-23 16:37:58+00:00 Summary: modification to default tool_conf.xml Affected #: 1 file diff -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 -r 26e1a07f9f22035e952344e34cdfa430a7b0ef7d config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> https://bitbucket.org/galaxy/galaxy-central/commits/addd9cf18318/ Changeset: addd9cf18318 User: anton Date: 2014-10-23 16:42:15+00:00 Summary: uniq.xml edited online with Bitbucket Affected #: 1 file diff -r 26e1a07f9f22035e952344e34cdfa430a7b0ef7d -r addd9cf183181a9c2406c9956ed13b90e6c4558a tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* https://bitbucket.org/galaxy/galaxy-central/commits/d519ad654358/ Changeset: d519ad654358 User: martenson Date: 2014-11-11 17:26:45+00:00 Summary: Merged in anton/galaxy-central-anton (pull request #539) Initial tweaks to tool_conf.xml sample and one of the tools. Affected #: 2 files diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Fix field type output
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/932f4bbf2c31/ Changeset: 932f4bbf2c31 User: guerler Date: 2014-11-10 20:07:04+00:00 Summary: ToolForm: Fix field type output Affected #: 3 files diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -352,7 +352,7 @@ } // log - console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); + console.debug('tools-form::_addRow() : Auto matched field type (' + input_def.type + ').'); } // set field value diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -352,7 +352,7 @@ } // log - console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); + console.debug('tools-form::_addRow() : Auto matched field type (' + input_def.type + ').'); } // set field value diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+field_type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ 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: natefoo: Update tag latest_2014.10.06 for changeset c9759aa6e40f
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f01e2504095a/ Changeset: f01e2504095a Branch: stable User: natefoo Date: 2014-11-10 20:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset c9759aa6e40f Affected #: 1 file diff -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de -r f01e2504095a477b16970f9570eb68361f031287 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a1dca14d5b1afbf2b5bde192e3e6b6763836eff8 latest_2014.10.06 +c9759aa6e40f887dec2d27d2f244d6fd7c28e6de latest_2014.10.06 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.

1 0

commit/galaxy-central: jmchilton: Merge stable.
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c92e972a0a3/ Changeset: 1c92e972a0a3 User: jmchilton Date: 2014-11-10 16:43:09+00:00 Summary: Merge stable. Affected #: 4 files diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 latest_2014.10.06 +a1dca14d5b1afbf2b5bde192e3e6b6763836eff8 latest_2014.10.06 diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(i){var h=this.autoPair();this.trigger("autopair",h)},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" 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commit/galaxy-central: jmchilton: Bugfix renaming individual parts of pairs.
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9759aa6e40f/ Changeset: c9759aa6e40f Branch: stable User: jmchilton Date: 2014-11-10 15:07:56+00:00 Summary: Bugfix renaming individual parts of pairs. >From Carl: "Yeah - that looks fine for stable. A better fix is probably adding the pair index directly into the DOM and getting it there - I'll add that to the 'Iteration 2' card. I'll approve now if you want to do the request." Affected #: 3 files diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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"+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" 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.remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header 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h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().index()],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ 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: dannon: Branch prune.
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72719f9c3af0/ Changeset: 72719f9c3af0 Branch: obo-owl-datatype User: dannon Date: 2014-11-10 16:16:03+00:00 Summary: Branch prune. Affected #: 0 files 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: Merged in BjoernGruening/galaxy-central-1/obo-owl-datatype (pull request #542)
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/25f0318f232f/ Changeset: 25f0318f232f User: dannon Date: 2014-11-10 16:14:49+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/obo-owl-datatype (pull request #542) Add OWL & OBO datatype. Affected #: 3 files diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -160,6 +160,8 @@ <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/></datatype> + <datatype extension="obo" type="galaxy.datatypes.text:Obo" mimetype="text/html" display_in_upload="True" /> + <datatype extension="owl" type="galaxy.datatypes.xml:Owl" mimetype="text/html" display_in_upload="True" /><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -272,6 +274,7 @@ <sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:Owl"/><sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/> @@ -294,6 +297,7 @@ <sniffer type="galaxy.datatypes.tabular:Sam"/><sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.text:Obo"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/> diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b lib/galaxy/datatypes/text.py --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -12,6 +12,7 @@ import subprocess import json import os +import re import logging log = logging.getLogger(__name__) @@ -119,3 +120,37 @@ Set the number of models in dataset. """ pass + + +class Obo( Text ): + """ + OBO file format description + http://www.geneontology.org/GO.format.obo-1_2.shtml + """ + file_ext = "obo" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Open Biomedical Ontology (OBO)" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + stanza = re.compile(r'^\[.*\]$') + with open( filename ) as handle: + first_line = handle.readline() + if not first_line.startswith('format-version:'): + return False + + for line in handle: + if stanza.match(line.strip()): + # a stanza needs to begin with an ID tag + if handle.next().startswith('id:'): + return True + return False + diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -1,6 +1,7 @@ """ XML format classes """ +import re import data import logging from galaxy.datatypes.sniff import * @@ -116,3 +117,32 @@ """ return [ 'phyloviz' ] + + +class Owl( GenericXml ): + """ + Web Ontology Language OWL format description + http://www.w3.org/TR/owl-ref/ + """ + file_ext = "owl" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Web Ontology Language OWL" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + owl_marker = re.compile(r'\<owl:') + with open( filename ) as handle: + # Check first 200 lines for the string "<owl:" + first_lines = handle.readlines(200) + for line in first_lines: + if owl_marker.search( line ): + return True + return False 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: 4 new changesets
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0be206ac31c2/ Changeset: 0be206ac31c2 Branch: obo-owl-datatype User: BjoernGruening Date: 2014-10-27 15:13:14+00:00 Summary: Add OWL & OBO datatype. Affected #: 3 files diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r 0be206ac31c2005f009e37af9d665cc9b4b955db config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -160,6 +160,8 @@ <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/></datatype> + <datatype extension="obo" type="galaxy.datatypes.text:Obo" mimetype="text/html" display_in_upload="True" /> + <datatype extension="owl" type="galaxy.datatypes.xml:Owl" mimetype="text/html" display_in_upload="True" /><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -272,6 +274,7 @@ <sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:Owl"/><sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/> @@ -294,6 +297,7 @@ <sniffer type="galaxy.datatypes.tabular:Sam"/><sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.text:Obo"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/> diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r 0be206ac31c2005f009e37af9d665cc9b4b955db lib/galaxy/datatypes/text.py --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -12,6 +12,7 @@ import subprocess import json import os +import re import logging log = logging.getLogger(__name__) @@ -119,3 +120,45 @@ Set the number of models in dataset. """ pass + + +class Obo( Text ): + """ + OBO file format description + http://www.geneontology.org/GO.format.obo-1_2.shtml + """ + file_ext = "obo" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Open Biomedical Ontology (OBO)" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + stanza = re.compile(r'^\[.*\]$') + with open( filename ) as handle: + first_line = handle.readline() + if not first_line.startswith('format-version:'): + return False + + for line in handle: + if stanza.match(line.strip()): + # a stanza needs to begin with an ID tag + if handle.next().startswith('id:'): + return True + return False + + + + def set_meta( self, dataset, **kwd ): + """ + Set metadata for OBO files. + """ + pass + diff -r 32929a1f9bf4b2150f99655c266223cd05d9a2bd -r 0be206ac31c2005f009e37af9d665cc9b4b955db lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -1,6 +1,7 @@ """ XML format classes """ +import re import data import logging from galaxy.datatypes.sniff import * @@ -116,3 +117,39 @@ """ return [ 'phyloviz' ] + + +class Owl( GenericXml ): + """ + Web Ontology Language OWL format description + http://www.w3.org/TR/owl-ref/ + """ + file_ext = "owl" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Web Ontology Language OWL" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + owl_marker = re.compile(r'\<owl:') + with open( filename ) as handle: + # Check first 200 lines for the string "<owl:" + first_lines = handle.readlines(200) + for line in first_lines: + if owl_marker.search( line ): + return True + return False + + def set_meta( self, dataset, **kwd ): + """ + Set metadata for OBO files. + """ + pass + https://bitbucket.org/galaxy/galaxy-central/commits/58b8aa9edad1/ Changeset: 58b8aa9edad1 Branch: obo-owl-datatype User: BjoernGruening Date: 2014-11-04 10:01:52+00:00 Summary: Remove set_meta() function. It's not used. Affected #: 1 file diff -r 0be206ac31c2005f009e37af9d665cc9b4b955db -r 58b8aa9edad12df296cde8a18b8d33c904e2e059 lib/galaxy/datatypes/text.py --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -154,11 +154,3 @@ return True return False - - - def set_meta( self, dataset, **kwd ): - """ - Set metadata for OBO files. - """ - pass - https://bitbucket.org/galaxy/galaxy-central/commits/b581932bb2ea/ Changeset: b581932bb2ea Branch: obo-owl-datatype User: BjoernGruening Date: 2014-11-04 11:01:42+00:00 Summary: Remove set_meta() function. It's not used. Affected #: 1 file diff -r 58b8aa9edad12df296cde8a18b8d33c904e2e059 -r b581932bb2ea861c50efce69fde9e508d937d739 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -146,10 +146,3 @@ if owl_marker.search( line ): return True return False - - def set_meta( self, dataset, **kwd ): - """ - Set metadata for OBO files. - """ - pass - https://bitbucket.org/galaxy/galaxy-central/commits/25f0318f232f/ Changeset: 25f0318f232f User: dannon Date: 2014-11-10 16:14:49+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/obo-owl-datatype (pull request #542) Add OWL & OBO datatype. Affected #: 3 files diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -160,6 +160,8 @@ <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/></datatype> + <datatype extension="obo" type="galaxy.datatypes.text:Obo" mimetype="text/html" display_in_upload="True" /> + <datatype extension="owl" type="galaxy.datatypes.xml:Owl" mimetype="text/html" display_in_upload="True" /><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -272,6 +274,7 @@ <sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/> + <sniffer type="galaxy.datatypes.xml:Owl"/><sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/> @@ -294,6 +297,7 @@ <sniffer type="galaxy.datatypes.tabular:Sam"/><sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.text:Obo"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/> diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b lib/galaxy/datatypes/text.py --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -12,6 +12,7 @@ import subprocess import json import os +import re import logging log = logging.getLogger(__name__) @@ -119,3 +120,37 @@ Set the number of models in dataset. """ pass + + +class Obo( Text ): + """ + OBO file format description + http://www.geneontology.org/GO.format.obo-1_2.shtml + """ + file_ext = "obo" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Open Biomedical Ontology (OBO)" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + stanza = re.compile(r'^\[.*\]$') + with open( filename ) as handle: + first_line = handle.readline() + if not first_line.startswith('format-version:'): + return False + + for line in handle: + if stanza.match(line.strip()): + # a stanza needs to begin with an ID tag + if handle.next().startswith('id:'): + return True + return False + diff -r a3ebaac5d31258a02bc7f037721f898c2c1e80e3 -r 25f0318f232ff783972c1e3e26fa853c0b9f085b lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -1,6 +1,7 @@ """ XML format classes """ +import re import data import logging from galaxy.datatypes.sniff import * @@ -116,3 +117,32 @@ """ return [ 'phyloviz' ] + + +class Owl( GenericXml ): + """ + Web Ontology Language OWL format description + http://www.w3.org/TR/owl-ref/ + """ + file_ext = "owl" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "Web Ontology Language OWL" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + owl_marker = re.compile(r'\<owl:') + with open( filename ) as handle: + # Check first 200 lines for the string "<owl:" + first_lines = handle.readlines(200) + for line in first_lines: + if owl_marker.search( line ): + return True + return False 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 November 2014