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galaxy-dist commit 7d46c23bb276: Merge with 39f41821aa4eec15b04509d24715946552bb14a6
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011867 18000 # Node ID 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent 8ce82d60b2ab55966d133db136fcb2f809201c4b # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Merge with 39f41821aa4eec15b04509d24715946552bb14a6

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galaxy-dist commit 19b10fff1335: More bug fixes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290010215 18000 # Node ID 19b10fff133595cb5cd1851a7f24024c2637ad2b # Parent 918a25ed14f5427f70970b0c436159fc58fd111e More bug fixes. --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -602,7 +602,7 @@ class Forms( BaseController ): self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: for ft in trans.model.FormDefinition.supported_field_types: - self.fieldtype.add_option( ft.__name__, ft__name__ ) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) @@ -713,7 +713,7 @@ class Forms( BaseController ): form_details=form_details, field_details=field_details, form_definition=form_definition, - field_types=BaseField.form_field_types(), + field_types=trans.model.FormDefinition.supported_field_types, message=message, status=status, current_form_type=current_form[ 'type' ],

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galaxy-dist commit 264c608b48d9: Fixed inconsistency in PerM loc.sample files
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290012220 18000 # Node ID 264c608b48d9b0db2a142d820e32ec1d1fa550dd # Parent 5ec30f459e8e4a1186f666f4879e14f082f17352 Fixed inconsistency in PerM loc.sample files --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -21,8 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -# +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index

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galaxy-dist commit 5ec30f459e8e: Merge with d1baa724b393de6871df7249ebe35ecfe2054e31
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011973 18000 # Node ID 5ec30f459e8e4a1186f666f4879e14f082f17352 # Parent 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent d1baa724b393de6871df7249ebe35ecfe2054e31 Merge with d1baa724b393de6871df7249ebe35ecfe2054e31

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galaxy-dist commit d1baa724b393: Modified some test fastq files to make valid
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290011865 18000 # Node ID d1baa724b393de6871df7249ebe35ecfe2054e31 # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Modified some test fastq files to make valid --- a/test-data/bwa_wrapper_in2.fastq +++ b/test-data/bwa_wrapper_in2.fastq @@ -1,120 +1,120 @@ @seq1/1 GGACTCAGATAGTAATCC -+/1 ++ II#IIIIIII$5+.(9II @seq2/1 ATTCGACCTATCCTTGCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq3/1 GTAACAAAGTTTGGATTG -+/1 ++ IIIIIIIIIIIIIIIIII @seq4/1 AGCCGCTCGTCTTTTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq5/1 CAGTTATATGGCTTTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq6/1 AGGCGCTCGTCTTGGTAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq7/1 TGTAGGTGGTCAACCAAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq8/1 ACACCCGTCCTTTACGTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq9/1 GCCGCTATTCAGGTTGTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq10/1 ATTCTTTCTTTTCGTATC -+/1 ++ IIIIIIIIIIIIIIIIII @seq11/1 GCATTTCTACTCCTTCTC -+/1 ++ II#IIIIIII$5+.(9II @seq12/1 CGCGCTTCGATAAAAATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq13/1 ATTTCTACTCTTTCTCAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq14/1 CCCTTTTGAATGTCACGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq15/1 CCAACTTACCAAGGTGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq16/1 TCAGGGTATTAAAAGAGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq17/1 GTGATGTGCTTGCTACCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq18/1 TCAATCCCCCATGCTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq19/1 TTCCTGCGCTTAATGCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq20/1 CTTATTACCATTTCAACT -+/1 ++ IIIIIIIIIIIIIIIIII @seq21/1 CTGATACCAATAAAACCC -+/1 ++ II#IIIIIII$5+.(9II @seq22/1 AATCAAACTTACCAAGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq23/1 TGTGCTTCCCCAACTTGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq24/1 TTTCTCAATCCCCAATGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq25/1 TTGCTACTGACCGCTCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq26/1 CCGCGTGAAATTTCTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq27/1 CGCTAATCAAGTTGTTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq28/1 AAAGAGATTATTTGTCGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq29/1 CAAATTAATGCGCGCTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq30/1 ATCCCCTATGCTTGGCTT -+/1 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bwa_wrapper_in3.fastq +++ b/test-data/bwa_wrapper_in3.fastq @@ -1,74 +1,74 @@ @seq1/2 ACGCTCCTTTAAAATATC -+/2 ++ IIIII$%*$G$A31I&&B @seq2/2 CAGCTCGAGAAGCTCTTA -+/2 ++ IIIIIIIIIIIIIIIIII @seq3/2 CTACTGACCGCTCTCGTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq4/2 TAGGTGGTCAACCATTTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq5/2 TTTCTATGTGGCTTAATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq6/2 GTAGGTGGTCAACAATTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq7/2 TTTAATTGCAGGGGCTTC -+/2 ++ IIIIIIIIIIIIIIIIII @seq8/2 ATGCGCTCTATTCTCTGG -+/2 ++ IIIIIIIIIIIIIIIIII @seq9/2 TTCTGTTGGTGCTGATAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq10/2 AGGGCGTTGAGTTCGATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq11/2 ATCCCCAATGCTTGGCTT -+/2 ++ IIIII$%*$G$A31I&&B @seq12/2 GGATTGGCGTTTCCAACC -+/2 ++ IIIIIIIIIIIIIIIIII @seq13/2 CCCCAATCCTTGCCTTCC -+/2 ++ IIIAAIIIIIIIIIIIII @seq14/2 TGATATTTTGACTTTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq15/2 TTACGAAACGCGACGCCG -+/2 ++ IIIIIIIIIIIIIIIIII @seq16/2 TTATTTTTCTCCAGCCAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq17/2 AAACAATACTTTAGGCAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq18/2 CCGTTCCATAAGCAGATG -+/2 ++ IIIIIIIIIIIIIIIIII @seq19/2 GAGCGTCCTGGTGCTGAT @@ -76,45 +76,45 @@ GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII @seq20/2 ACTCCGGTTATCGCTGGC -+/2 ++ IIIIIIIIIIIIIIIIII @seq21/2 TAAGCATTTGGTTCAGGG -+/2 ++ IIIII$%*$G$A31I&&B @seq22/2 GTTACGACGCGACGCCGT -+/2 ++ IIIIIIIIIIIIIIIIII @seq23/2 TTTAATAACCCTATAGAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq24/2 CTTGGCTTCCCTAAGCAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq25/2 CGTGCTCGTTGCTGCGTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq26/2 AAGGATGTTTTCCGTTCT -+/2 ++ IIIIIIIIIIIIIIIIII @seq27/2 TGTTTGGTGCTGATATTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq28/2 TCCAGCCACTAAAGTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq29/2 GATAATGATTGGGGTATC -+/2 ++ IIIIIIIIIIIIIIIIII @seq30/2 ACCATAAGCAGATGGATA -+/2 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bowtie_in2.fastqsanger +++ b/test-data/bowtie_in2.fastqsanger @@ -1,5 +1,5 @@ @HWI-EAS91_1_30788AAXX:1:1:1513:715/1 GTTTTTTNNGCATAGATGTTTAGTTGTGGTAGTCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I

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galaxy-dist commit 8ce82d60b2ab: - added the change data library sample operation functional test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011634 18000 # Node ID 8ce82d60b2ab55966d133db136fcb2f809201c4b # Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b - added the change data library sample operation functional test. - renaming dataset now checks for incorrect filename characters - fixed bugs --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1079,7 +1079,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, action='update_request_state', request_id=trans.security.encode_id( request.id ) ) ) - elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY: + elif sample_operation == trans.model.Sample.bulk_operations.SELECT_LIBRARY: # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id # and sample_operation_folder_id because the name sample_0_library_id should belong to the --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -16,6 +16,7 @@ <div class="toolForm"><form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"><thead><tr> @@ -43,9 +44,16 @@ </tbody></table><br/> + <div class="form-row"> + <div class="toolParamHelp" style="clear: both;"> + A dataset name should only contain the alphanumeric characters or underscore(_). + If a dataset name contains any other character, it would be replaced by an underscore(_). + </div> + </div><div class="form-row"><input type="submit" name="rename_datasets_button" value="Save"/><input type="submit" name="cancel_rename_datasets_button" value="Close"/></div></form> + </div> --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -24,7 +24,7 @@ def main( config_file ): cmd_list = [ 'add_user %s %s' % ( username, password ), - 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), + 'add_vhost %s' % virtual_host, 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) ] --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -430,8 +430,8 @@ class TestFormsAndRequests( TwillTestCas """Testing editing the sample information of new request1""" # logged in as regular_user1 # target data library - change it to library1 - target_library_info = dict(library=self.security.encode_id(library1.id), - folder=self.security.encode_id(library1_folder1.id) ) + target_library_info = dict(library=self.security.encode_id( library1.id ), + folder=self.security.encode_id( library1_folder1.id ) ) new_sample_value_tuples = \ [ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ), ( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ), @@ -494,6 +494,23 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_count=strings_displayed_count, strings_not_displayed=[ request1.states.COMPLETE, request1.states.REJECTED ] ) + # change the target data library back to library2 using sample operation user interface + self.change_sample_target_data_library( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + sample_ids=[ sample.id for sample in request1.samples ], + new_library_id=self.security.encode_id( library2.id ), + new_folder_id=self.security.encode_id( library2_folder1.id ), + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], + strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] ) + # check the changed target data library & folder on the request page + strings_displayed_count = [] + strings_displayed_count.append( ( library2.name, len( request1.samples ) ) ) + strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[], + strings_displayed_count=strings_displayed_count ) + # # ====== Sequencing request test methods - Admin perspective ================ # @@ -537,7 +554,7 @@ class TestFormsAndRequests( TwillTestCas request1.type.states[4].desc ] # check history of each sample for sample in request1.samples: - strings_displayed = [ 'Events for Sample "%s"' % sample.name, + strings_displayed = [ 'History of sample "%s"' % sample.name, 'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name, request1.type.states[0].name, request1.type.states[1].name ] --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -361,17 +361,29 @@ class RequestsAdmin( BaseController, Use sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) sample_datasets.append( sample_dataset ) if params.get( 'rename_datasets_button', False ): + incorrect_dataset_names = [] for sample_dataset in sample_datasets: encoded_id = trans.security.encode_id( sample_dataset.id ) selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) ) new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) ) + if not new_name: + incorrect_dataset_names.append( sample_dataset.name ) + continue + new_name = util.sanitize_for_filename( new_name ) if selected_option == 'none': sample_dataset.name = new_name else: sample_dataset.name = '%s_%s' % ( selected_option, new_name ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() - message = 'Changes saved successfully.' + if len( sample_datasets ) == len( incorrect_dataset_names ): + status = 'error' + message = 'All datasets renamed incorrectly.' + elif len( incorrect_dataset_names ): + status = 'done' + message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names ) + else: + message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, id_list=id_list, --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1638,6 +1638,23 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def change_sample_target_data_library( self, cntrller, request_id, sample_ids, new_library_id, new_folder_id, comment='', strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_id in sample_ids: + tc.fv( "1", "select_sample_%i" % sample_id, True ) + tc.fv( "1", "sample_operation", 'Select data library and folder' ) + self.refresh_form( "sample_operation", 'Select data library and folder' ) + self.check_page_for_string( "Select data library:" ) + tc.fv( "1", "sample_0_library_id", new_library_id ) + self.refresh_form( "sample_0_library_id", new_library_id ) + self.check_page_for_string( "Select folder:" ) + tc.fv( "1", "sample_0_folder_id", new_folder_id ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) def add_user_address( self, user_id, address_dict ): self.home() self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) ) --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -635,8 +635,8 @@ class Forms( BaseController ): if form_type == trans.model.FormDefinition.types.SAMPLE: for ft in trans.model.Sample.supported_field_types: if ft.__name__ == field[ 'type' ]: - self.fieldtype.add_option( ft.__name__, ft__name__, selected=True ) - if ft == 'SelectField': + self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) + if ft.__name__ == 'SelectField': self.selectbox_ui( field ) else: self.fieldtype.add_option( ft.__name__, ft.__name__ ) @@ -644,7 +644,7 @@ class Forms( BaseController ): for ft in trans.model.FormDefinition.supported_field_types: if ft.__name__ == field[ 'type' ]: self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) - if ft == 'SelectField': + if ft.__name__ == 'SelectField': self.selectbox_ui( field ) else: self.fieldtype.add_option( ft.__name__, ft.__name__ )

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galaxy-dist commit 39f41821aa4e: Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290011565 18000 # Node ID 39f41821aa4eec15b04509d24715946552bb14a6 # Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc) --- /dev/null +++ b/tool_data_table_conf.xml.oldlocstyle @@ -0,0 +1,73 @@ + +<tables> +  + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +  + <table name="bfast_indexes" comment_char="#"> + <columns>value, dbkey, formats, name, path</columns> + <file path="tool-data/bfast_indexes.loc" /> + </table> +  + <table name="blastdb" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/blastdb.loc" /> + </table> +  + <table name="blastdb_p" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> +  + <table name="bowtie_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +  + <table name="bowtie_indexes_color" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> +  + <table name="bwa_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bwa_index.loc" /> + </table> +  + <table name="indexed_maf_files"> + <columns>name, value, dbkey, species</columns> + <file path="tool-data/maf_index.loc" /> + </table> +  + <table name="ngs_sim_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/ngs_sim_fasta.loc" /> + </table> +  + <table name="lastz_seqs" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +  + <table name="perm_base_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> +  + <table name="perm_color_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> +  + <table name="srma_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/srma_index.loc" /> + </table> +  + <table name="tophat_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables>

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galaxy-dist commit 29227c9c5992: Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1290019719 18000 # Node ID 29227c9c599292f7608e61cdd4b2be424b7a7bfc # Parent 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70 Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly. --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -965,7 +965,9 @@ class Gtf( Gff ): if len( attributes ) >= 2: try: # Imprecise: should check for a single space per the spec. - attr_name, attr_value = attributes[0].split(" ") + # strip() needed b/c Ensembl GTF files include an (illegal) + # space before attributes string. + attr_name, attr_value = attributes[0].strip().split(" ") if attr_name != 'gene_id': return False except:

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galaxy-dist commit a68c74ec8cfb: OpenID support for Galaxy.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1290006822 18000 # Node ID a68c74ec8cfbc641db4b6fe424e3f77b9f3c5d3c # Parent 56431b214df16653a966b96bf399c7646da267b8 OpenID support for Galaxy. --- a/eggs.ini +++ b/eggs.ini @@ -44,6 +44,7 @@ Paste = 1.6 PasteDeploy = 1.3.3 PasteScript = 1.7.3 pexpect = 2.4 +python_openid = 2.2.5 Routes = 1.12.3 SQLAlchemy = 0.5.6 sqlalchemy_migrate = 0.5.4 --- /dev/null +++ b/templates/user/openid_manage.mako @@ -0,0 +1,17 @@ +## Template generates a grid that enables user to select items. +<%namespace file="../grid_base.mako" import="make_grid" /> +<%namespace file="login.mako" import="render_openid_form" /> + +<%inherit file="../grid_base.mako" /> + +<%def name="grid_body( grid )"> + ${make_grid( grid )} + <h2>Associate more OpenIDs</h2> + ${render_openid_form( kwargs['referer'], True, kwargs['openid_providers'] )} +</%def> + +<%def name="center_panel()"> + <div style="margin: 1em;"> + ${grid_body( grid )} + </div> +</%def> Binary file static/images/openid-16x16.gif has changed --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1953,6 +1953,12 @@ class UserAddress( object ): html = html + '<br/>' + 'Phone: ' + self.phone return html +class UserOpenID( object ): + def __init__( self, user=None, session=None, openid=None ): + self.user = user + self.session = session + self.openid = openid + class Page( object ): def __init__( self ): self.id = None --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -15,6 +15,9 @@ %if trans.app.config.enable_api: <li><a href="${h.url_for( controller='user', action='api_keys' )}">${_('Manage your API Keys')}</a> for new histories</li> %endif + %if trans.app.config.enable_openid: + <li><a href="${h.url_for( controller='user', action='openid_manage' )}">${ ('Manage OpenIDs')}</a> linked to your account</li> + %endif %else: <li><a href="${h.url_for( controller='user', action='show_info', webapp='community' )}">${_('Manage your information')}</a></li> %endif --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py @@ -0,0 +1,48 @@ +""" +Migration script to create table for associating sessions and users with +OpenIDs. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Table to add + +UserOpenID_table = Table( "galaxy_user_openid", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "openid", TEXT, index=True, unique=True ), + ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Create galaxy_user_openid table + try: + UserOpenID_table.create() + except Exception, e: + log.debug( "Creating galaxy_user_openid table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop galaxy_user_openid table + try: + UserOpenID_table.drop() + except Exception, e: + log.debug( "Dropping galaxy_user_openid table failed: %s" % str( e ) ) --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,23 +1,77 @@ -<%inherit file="/base.mako"/> +<%! + def inherit(context): + if context.get('use_panels'): + if context.get('webapp'): + webapp = context.get('webapp') + else: + webapp = 'galaxy' + return '/webapps/%s/base_panels.mako' % webapp + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view=active_view + self.message_box_visible=False +%> +</%def> + <%namespace file="/message.mako" import="render_msg" /> -%if redirect_url: - <script type="text/javascript"> - top.location.href = '${redirect_url}'; - </script> -%endif +<%def name="center_panel()"> + ${body()} +</%def> -%if not redirect_url and message: - ${render_msg( message, status )} -%endif +<%def name="body()"> -%if not trans.user: + %if redirect_url: + <script type="text/javascript"> + top.location.href = '${redirect_url}'; + </script> + %endif + + %if context.get('use_panels'): + <div style="margin: 1em;"> + %else: + <div> + %endif + + %if message: + ${render_msg( message, status )} + %endif + + %if not trans.user: + + ${render_login_form()} + + %if trans.app.config.enable_openid: + <br/> + ${render_openid_form( referer, False, openid_providers )} + %endif + + %endif + + </div> + +</%def> + +<%def name="render_login_form( form_action=None )"> + + <% + if form_action is None: + form_action = h.url_for( controller='user', action='login', use_panels=use_panels ) + %> + %if header: ${header} %endif <div class="toolForm"><div class="toolFormTitle">Login</div> - <form name="login" id="login" action="${h.url_for( controller='user', action='login' )}" method="post" > + <form name="login" id="login" action="${form_action}" method="post" ><div class="form-row"><label>Email address:</label><input type="text" name="email" value="${email}" size="40"/> @@ -36,4 +90,32 @@ </div></form></div> -%endif + +</%def> + +<%def name="render_openid_form( referer, auto_associate, openid_providers )"> + + <div class="toolForm"> + <div class="toolFormTitle">OpenID Login</div> + <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" > + <div class="form-row"> + <label>OpenID URL:</label> + <input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="auto_associate" value="${auto_associate}" size="40"/> + </div> + <div class="form-row"> + Or, authenticate with your <select name="openid_provider"> + %for provider in openid_providers.keys(): + <option>${provider}</option> + %endfor + </select> account. + </div> + <div class="form-row"> + <input type="submit" name="login_button" value="Login"/> + </div> + </form> + </div> + +</%def> --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -321,6 +321,7 @@ class GalaxyConfig( object ): "pbs_python": lambda: "pbs" in self.config.get( "app:main", "start_job_runners" ).split(","), "threadframe": lambda: self.config.get( "app:main", "use_heartbeat" ), "guppy": lambda: self.config.get( "app:main", "use_memdump" ), + "python_openid": lambda: self.config.get( "app:main", "enable_openid" ), "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "pysam": check_pysam() }.get( egg_name, lambda: True )() --- /dev/null +++ b/templates/user/openid_associate.mako @@ -0,0 +1,75 @@ +<%! + def inherit(context): + if context.get('use_panels'): + if context.get('webapp'): + webapp = context.get('webapp') + else: + webapp = 'galaxy' + return '/webapps/%s/base_panels.mako' % webapp + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view=active_view + self.message_box_visible=False +%> +</%def> + +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="login.mako" import="render_login_form" /> +<%namespace file="register.mako" import="render_registration_form" /> + +<%def name="center_panel()"> + ${body()} +</%def> + +<%def name="body()"> + + %if context.get('use_panels'): + <div style="margin: 1em;"> + %else: + <div> + %endif + + %if message: + ${render_msg( message, status )} + %endif + + <h2>OpenID Account Association</h2> + <div> + OpenIDs must be associated with a Galaxy account before they can be used for authentication. This only needs to be done once per OpenID. You may associate your OpenID with an existing Galaxy account, or create a new one. + </div> + <br/> + + %if len( openids ) > 1: + <div> + The following OpenIDs will be associated with the account chosen or created below. + <ul> + %for openid in openids: + <li>${openid.openid}</li> + %endfor + </ul> + </div> + %else: + <div> + The OpenID <strong>${openids[0].openid}</strong> will be associated with the account chosen or created. + </div> + %endif + <br/> + + <% form_action = h.url_for( use_panels=use_panels ) %> + + ${render_login_form( form_action=form_action )} + + <br/> + + ${render_registration_form( form_action=form_action )} + + </div> + +</%def> --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -22,8 +22,18 @@ ## An admin user may be creating a new user account, in which case we want to display the registration form. ## But if the current user is not an admin user, then don't display the registration form. %if trans.user_is_admin() or not trans.user: + ${render_registration_form()} +%endif + +<%def name="render_registration_form( form_action=None )"> + + <% + if form_action is None: + form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) + %> + <div class="toolForm"> - <form name="registration" id="registration" action="${h.url_for( controller='user', action='create', admin_view=admin_view )}" method="post" > + <form name="registration" id="registration" action="${form_action}" method="post" ><div class="toolFormTitle">Create account</div><div class="form-row"><label>Email address:</label> @@ -83,4 +93,5 @@ </div></form></div> -%endif + +</%def> --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -324,6 +324,10 @@ use_interactive = True # WYSIWYG editor that is very similar to a word processor. #enable_pages = False +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False + # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -68,6 +68,15 @@ UserAddress.table = Table( "user_address Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) +UserOpenID.table = Table( "galaxy_user_openid", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "openid", TEXT, index=True, unique=True ), + ) + History.table = Table( "history", metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -968,6 +977,17 @@ assign_mapper( context, UserAddress, Use order_by=desc(UserAddress.table.c.update_time)), ) ) +assign_mapper( context, UserOpenID, UserOpenID.table, + properties=dict( + session=relation( GalaxySession, + primaryjoin=( UserOpenID.table.c.session_id == GalaxySession.table.c.id ), + backref='openids', + order_by=desc( UserOpenID.table.c.update_time ) ), + user=relation( User, + primaryjoin=( UserOpenID.table.c.user_id == User.table.c.id ), + backref='openids', + order_by=desc( UserOpenID.table.c.update_time ) ) ) ) + assign_mapper( context, ValidationError, ValidationError.table ) --- a/templates/display_common.mako +++ b/templates/display_common.mako @@ -85,6 +85,8 @@ class_plural = "Forms" elif a_class == model.RequestType: class_plural = "sequencer configurations" + elif a_class == model.UserOpenID: + class_plural = "OpenIDs" else: class_plural = a_class.__name__ + "s" return class_plural --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -60,6 +60,10 @@ class UniverseApplication( object ): self.heartbeat = None self.memdump = None self.memory_usage = None + # Container for OpenID authentication routines + if self.config.enable_openid: + from galaxy.web.framework import openid_manager + self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat --- /dev/null +++ b/lib/galaxy/web/framework/openid_manager.py @@ -0,0 +1,53 @@ +""" +Mange the OpenID consumer and related data stores. +""" + +import os, pickle, logging + +from galaxy import eggs +eggs.require( 'python-openid' ) + +import openid +from openid import oidutil +from openid.store import filestore +from openid.consumer import consumer +from openid.extensions import sreg + +log = logging.getLogger( __name__ ) +def oidlog( message, level=0 ): + log.debug( message ) +oidutil.log = oidlog + +class OpenIDManager( object ): + def __init__( self, cache_path ): + self.session_path = os.path.join( cache_path, 'session' ) + self.store_path = os.path.join( cache_path, 'store' ) + for dir in self.session_path, self.store_path: + if not os.path.exists( dir ): + os.makedirs( dir ) + self.store = filestore.FileOpenIDStore( self.store_path ) + def get_session( self, trans ): + session_file = os.path.join( self.session_path, str( trans.galaxy_session.id ) ) + if not os.path.exists( session_file ): + pickle.dump( dict(), open( session_file, 'w' ) ) + return pickle.load( open( session_file ) ) + def persist_session( self, trans, oidconsumer ): + session_file = os.path.join( self.session_path, str( trans.galaxy_session.id ) ) + pickle.dump( oidconsumer.session, open( session_file, 'w' ) ) + def get_consumer( self, trans ): + return consumer.Consumer( self.get_session( trans ), self.store ) + def add_sreg( self, trans, request, required=None, optional=None ): + if required is None: + required = [] + if optional is None: + optional = [] + sreg_request = sreg.SRegRequest( required=required, optional=optional ) + request.addExtension( sreg_request ) + def get_sreg( self, info ): + return sreg.SRegResponse.fromSuccessResponse( info ) + + # so I don't have to expose all of openid.consumer.consumer + FAILURE = consumer.FAILURE + SUCCESS = consumer.SUCCESS + CANCEL = consumer.CANCEL + SETUP_NEEDED = consumer.SETUP_NEEDED --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -39,9 +39,11 @@ class Configuration( object ): # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) + self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) # Communication with a sequencer self.enable_sequencer_communication = string_as_bool( kwargs.get( 'enable_sequencer_communication', False ) ) # dataset Track files @@ -161,7 +163,17 @@ class Configuration( object ): if not os.path.isdir( path ): raise ConfigurationError("Directory does not exist: %s" % path ) # Create the directories that it makes sense to create - for path in self.file_path, self.new_file_path, self.job_working_directory, self.cluster_files_directory, self.template_cache, self.ftp_upload_dir, self.library_import_dir, self.user_library_import_dir, self.nginx_upload_store, './static/genetrack/plots', os.path.join( self.tool_data_path, 'shared', 'jars' ): + for path in self.file_path, \ + self.new_file_path, \ + self.job_working_directory, \ + self.cluster_files_directory, \ + self.template_cache, \ + self.ftp_upload_dir, \ + self.library_import_dir, \ + self.user_library_import_dir, \ + self.nginx_upload_store, \ + './static/genetrack/plots', \ + os.path.join( self.tool_data_path, 'shared', 'jars' ): if path not in [ None, False ] and not os.path.isdir( path ): try: os.makedirs( path ) --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -1,9 +1,10 @@ """ Contains the user interface in the Universe class """ +from galaxy.web.framework.helpers import time_ago, grids from galaxy.web.base.controller import * from galaxy.model.orm import * -from galaxy import util +from galaxy import util, model import logging, os, string, re, smtplib, socket from random import choice from email.MIMEText import MIMEText @@ -26,48 +27,337 @@ require_login_creation_template = requir VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" ) +OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', + 'Yahoo!' : 'http://yahoo.com', + 'AOL/AIM' : 'http://openid.aol.com', + 'Flickr' : 'http://flickr.com', + 'Launchpad' : 'http://login.launchpad.net', + } + +class UserOpenIDGrid( grids.Grid ): + use_panels = False + title = "OpenIDs linked to your account" + model_class = model.UserOpenID + template = '/user/openid_manage.mako' + default_filter = { "openid" : "All" } + default_sort_key = "-create_time" + columns = [ + grids.TextColumn( "OpenID URL", key="openid" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + ] + operations = [ + grids.GridOperation( "Delete", async_compatible=True ), + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) + class User( BaseController, UsesFormDefinitionWidgets ): + user_openid_grid = UserOpenIDGrid() @web.expose def index( self, trans, webapp='galaxy', **kwd ): return trans.fill_template( '/user/index.mako', webapp=webapp ) @web.expose + def openid_auth( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + message = 'Unspecified failure authenticating via OpenID' + status = kwd.get( 'status', 'done' ) + openid_url = kwd.get( 'openid_url', '' ) + openid_provider = kwd.get( 'openid_provider', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) + action = 'login' + if auto_associate: + action = 'openid_manage' + if not referer: + referer = url_for( '/' ) + consumer = trans.app.openid_manager.get_consumer( trans ) + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate ) + if not openid_url and openid_provider and openid_provider in OPENID_PROVIDERS: + openid_url = OPENID_PROVIDERS[openid_provider] + if openid_url: + request = None + try: + request = consumer.begin( openid_url ) + if request is None: + message = 'No OpenID services are available at %s' % openid_url + except Exception, e: + message = 'Failed to begin OpenID authentication: %s' % str( e ) + if request is not None: + trans.app.openid_manager.add_sreg( trans, request, optional=[ 'nickname', 'email' ] ) + if request.shouldSendRedirect(): + redirect_url = request.redirectURL( + trans.request.base, process_url ) + trans.app.openid_manager.persist_session( trans, consumer ) + trans.response.send_redirect( redirect_url ) + return + else: + form = request.htmlMarkup( trans.request.base, process_url, form_tag_attrs={'id':'openid_message','target':'_top'} ) + trans.app.openid_manager.persist_session( trans, consumer ) + return form + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=use_panels, + message=message, + status='error' ) ) + @web.expose + def openid_process( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) + action = 'login' + if auto_associate: + action = 'openid_manage' + if trans.app.config.bugs_email is not None: + contact = '<a href="mailto:%s">contact support</a>' % trans.app.config.bugs_email + else: + contact = 'contact support' + message = 'Verification failed for an unknown reason. Please contact support for assistance.' + status = 'error' + consumer = trans.app.openid_manager.get_consumer( trans ) + info = consumer.complete( kwd, trans.request.url ) + display_identifier = info.getDisplayIdentifier() + redirect_url = kwd.get( 'referer', url_for( '/' ) ) + if info.status == trans.app.openid_manager.FAILURE and display_identifier: + message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=True, + message=message, + status='error' ) ) + elif info.status == trans.app.openid_manager.SUCCESS: + if info.endpoint.canonicalID: + display_identifier = info.endpoint.canonicalID + user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() + if not user_openid: + user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) + elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: + user_openid.session = trans.galaxy_session + elif user_openid.user and not auto_associate: + trans.handle_user_login( user_openid.user, webapp ) + trans.log_event( "User logged in via OpenID: %s" % display_identifier ) + trans.response.send_redirect( redirect_url ) + return + if auto_associate and trans.user: + # The user is already logged in and requested association from + # the user prefs as opposed to using the OpenID form on the + # login page. + if user_openid.user and user_openid.user.id != trans.user.id: + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + status = "error" + elif user_openid.user and user_openid.user.id == trans.user.id: + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "warning" + else: + user_openid.user_id = trans.user.id + trans.sa_session.add( user_openid ) + trans.sa_session.flush() + trans.log_event( "User associated OpenID: %s" % display_identifier ) + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "done" + trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=True, + message=message, + status=status ) ) + return + trans.sa_session.add( user_openid ) + trans.sa_session.flush() + message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." + sreg_resp = trans.app.openid_manager.get_sreg( info ) + try: + username = sreg_resp.get( 'nickname', '' ) + except AttributeError: + username = '' + try: + email = sreg_resp.get( 'email', '' ) + except AttributeError: + email = '' + trans.response.send_redirect( url_for( controller='user', + action='openid_associate', + use_panels=True, + username=username, + email=email, + message=message, + status='warning' ) ) + elif info.status == trans.app.openid_manager.CANCEL: + message = "Login via OpenID was cancelled by an action at the OpenID provider's site." + status = "warning" + elif info.status == trans.app.openid_manager.SETUP_NEEDED: + if info.setup_url: + return trans.response.send_redirect( info.setup_url ) + else: + message = "Unable to log in via OpenID. Setup at the provider is required before this OpenID can be used. Please visit your provider's site to complete this step." + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=True, + message=message, + status=status ) ) + @web.expose + def openid_associate( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + email = kwd.get( 'email', '' ) + username = kwd.get( 'username', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + params = util.Params( kwd ) + admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) + openids = trans.galaxy_session.openids + if not openids: + return trans.show_error_message( 'You have not successfully completed an OpenID authentication in this session. You can do so on the <a href="%s">login</a> page.' % url_for( controller='user', action='login', use_panels=use_panels ) ) + elif admin_view: + return trans.show_error_message( 'Associating OpenIDs with accounts cannot be done by administrators.' ) + if kwd.get( 'login_button', False ): + message, status, user, success = self.__validate_login( trans, webapp, **kwd ) + if success: + for openid in openids: + openid.user = user + trans.sa_session.add( openid ) + trans.sa_session.flush() + for openid in openids: + trans.log_event( "User associated OpenID: %s" % openid.openid ) + redirect_url = referer + if not redirect_url: + redirect_url = url_for( '/' ) + trans.response.send_redirect( redirect_url ) + return + if kwd.get( 'create_user_button', False ): + password = kwd.get( 'password', '' ) + confirm = kwd.get( 'confirm', '' ) + subscribe = params.get( 'subscribe', '' ) + subscribe_checked = CheckboxField.is_checked( subscribe ) + error = '' + if not trans.app.config.allow_user_creation and not trans.user_is_admin(): + error = 'User registration is disabled. Please contact your Galaxy administrator for an account.' + else: + # Check email and password validity + error = self.__validate( trans, params, email, password, confirm, username, webapp ) + if not error: + # all the values are valid + message, status, user, success = self.__register( trans, webapp, email, password, username, subscribe_checked, kwd ) + if success: + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + for openid in openids: + openid.user = user + trans.sa_session.add( openid ) + trans.sa_session.flush() + for openid in openids: + trans.log_event( "User associated OpenID: %s" % openid.openid ) + redirect_url = referer + if not redirect_url: + redirect_url = url_for( '/' ) + trans.response.send_redirect( redirect_url ) + else: + message = error + status = 'error' + if webapp == 'galaxy': + user_info_select, user_info_form, widgets = self.__user_info_ui( trans, **kwd ) + else: + user_info_select = [] + user_info_form = [] + widgets = [] + return trans.fill_template( '/user/openid_associate.mako', + webapp=webapp, + email=email, + password='', + confirm='', + username=username, + header='', + use_panels=use_panels, + redirect_url='', + referer='', + refresh_frames=[], + message=message, + status=status, + active_view="user", + subscribe_checked=False, + admin_view=False, + user_info_select=user_info_select, + user_info_form=user_info_form, + widgets=widgets, + openids=openids ) + @web.expose + @web.require_login( 'manage OpenIDs' ) + def openid_disassociate( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + params = util.Params( kwd ) + ids = params.get( 'id', None ) + message = params.get( 'message', None ) + status = params.get( 'status', None ) + use_panels = params.get( 'use_panels', False ) + user_openids = [] + if not ids: + message = 'You must select at least one OpenID to disassociate from your Galaxy account.' + status = 'error' + else: + ids = util.listify( params.id ) + for id in ids: + id = trans.security.decode_id( id ) + user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).get( int( id ) ) + if not user_openid or ( trans.user.id != user_openid.user_id ): + message = 'The selected OpenID(s) are not associated with your Galaxy account.' + status = 'error' + user_openids = [] + break + user_openids.append( user_openid ) + if user_openids: + deleted_urls = [] + for user_openid in user_openids: + trans.sa_session.delete( user_openid ) + deleted_urls.append( user_openid.openid ) + trans.sa_session.flush() + for deleted_url in deleted_urls: + trans.log_event( "User disassociated OpenID: %s" % deleted_url ) + message = '%s OpenIDs were disassociated from your Galaxy account.' % len( ids ) + status = 'done' + trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + message=message, + status=status ) ) + @web.expose + @web.require_login( 'manage OpenIDs' ) + def openid_manage( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + use_panels = kwd.get( 'use_panels', False ) + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "delete": + trans.response.send_redirect( url_for( controller='user', + action='openid_disassociate', + use_panels=use_panels, + id=kwd['id'] ) ) + kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) + kwd['openid_providers'] = OPENID_PROVIDERS + return self.user_openid_grid( trans, **kwd ) + @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): referer = kwd.get( 'referer', trans.request.referer ) - use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) header = '' user = None email = kwd.get( 'email', '' ) if kwd.get( 'login_button', False ): - password = kwd.get( 'password', '' ) - referer = kwd.get( 'referer', '' ) if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: refresh_frames = [ 'masthead', 'history', 'tools' ] else: refresh_frames = [ 'masthead', 'history' ] - user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() - if not user: - message = "No such user" - status = 'error' - elif user.deleted: - message = "This account has been marked deleted, contact your Galaxy administrator to restore the account." - status = 'error' - elif user.external: - message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." - status = 'error' - elif not user.check_password( password ): - message = "Invalid password" - status = 'error' - else: - trans.handle_user_login( user, webapp ) - trans.log_event( "User logged in" ) - message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( user.email, referer, url_for( '/' ) ) - if trans.app.config.require_login: - message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + message, status, user, success = self.__validate_login( trans, webapp, **kwd ) + if success and referer: redirect_url = referer + elif success: + redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: header = require_login_creation_template % web.url_for( action='create' ) @@ -83,7 +373,37 @@ class User( BaseController, UsesFormDefi refresh_frames=refresh_frames, message=message, status=status, + openid_providers=OPENID_PROVIDERS, active_view="user" ) + def __validate_login( self, trans, webapp='galaxy', **kwd ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + email = kwd.get( 'email', '' ) + password = kwd.get( 'password', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + success = False + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + if not user: + message = "No such user" + status = 'error' + elif user.deleted: + message = "This account has been marked deleted, contact your Galaxy administrator to restore the account." + status = 'error' + elif user.external: + message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." + status = 'error' + elif not user.check_password( password ): + message = "Invalid password" + status = 'error' + else: + trans.handle_user_login( user, webapp ) + trans.log_event( "User logged in" ) + message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ + ( user.email, referer, url_for( '/' ) ) + if trans.app.config.require_login: + message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + success = True + return ( message, status, user, success ) @web.expose def logout( self, trans, webapp='galaxy' ): if webapp == 'galaxy': @@ -138,54 +458,25 @@ class User( BaseController, UsesFormDefi error = self.__validate( trans, params, email, password, confirm, username, webapp ) if not error: # all the values are valid - user = trans.app.model.User( email=email ) - user.set_password_cleartext( password ) - user.username = username - trans.sa_session.add( user ) - trans.sa_session.flush() - trans.app.security_agent.create_private_user_role( user ) - message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) - if webapp == 'galaxy': - # We set default user permissions, before we log in and set the default history permissions - trans.app.security_agent.user_set_default_permissions( user, - default_access_private=trans.app.config.new_user_dataset_access_role_default_private ) - # save user info - self.__save_user_info( trans, user, action='create', new_user=True, **kwd ) - if subscribe_checked: - # subscribe user to email list - if trans.app.config.smtp_server is None: - error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance." - else: - msg = MIMEText( 'Join Mailing list.\n' ) - to = msg[ 'To' ] = trans.app.config.mailing_join_addr - frm = msg[ 'From' ] = email - msg[ 'Subject' ] = 'Join Mailing List' - try: - s = smtplib.SMTP() - s.connect( trans.app.config.smtp_server ) - s.sendmail( frm, [ to ], msg.as_string() ) - s.close() - except: - error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed." - if not error and not admin_view: - # The handle_user_login() method has a call to the history_set_default_permissions() method - # (needed when logging in with a history), user needs to have default permissions set before logging in - trans.handle_user_login( user, webapp ) - trans.log_event( "User created a new account" ) - trans.log_event( "User logged in" ) - elif not error: - trans.response.send_redirect( web.url_for( controller='admin', - action='users', - message='Created new user account (%s)' % user.email, - status='done' ) ) - elif not admin_view: + message, status, user, success = self.__register( trans, webapp, email, password, username, subscribe_checked, kwd ) + if success and not admin_view and webapp != 'galaxy': # Must be logging into the community space webapp trans.handle_user_login( user, webapp ) - if not error: - redirect_url = referer - if error: - message=error - status='error' + redirect_url = referer + if success and not admin_view: + # The handle_user_login() method has a call to the history_set_default_permissions() method + # (needed when logging in with a history), user needs to have default permissions set before logging in + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + elif success: + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Created new user account (%s)' % user.email, + status='done' ) ) + else: + message = error + status = 'error' if webapp == 'galaxy': user_info_select, user_info_form, widgets = self.__user_info_ui( trans, **kwd ) else: @@ -209,6 +500,57 @@ class User( BaseController, UsesFormDefi refresh_frames=refresh_frames, message=message, status=status ) + def __register( self, trans, webapp, email, password, username, subscribe_checked, kwd ): + status = kwd.get( 'status', 'done' ) + admin_view = util.string_as_bool( kwd.get( 'admin_view', False ) ) + user = trans.app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() + trans.app.security_agent.create_private_user_role( user ) + error = '' + if webapp == 'galaxy': + # We set default user permissions, before we log in and set the default history permissions + trans.app.security_agent.user_set_default_permissions( user, + default_access_private=trans.app.config.new_user_dataset_access_role_default_private ) + # save user info + self.__save_user_info( trans, user, action='create', new_user=True, **kwd ) + if subscribe_checked: + # subscribe user to email list + if trans.app.config.smtp_server is None: + error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance." + else: + msg = MIMEText( 'Join Mailing list.\n' ) + to = msg[ 'To' ] = trans.app.config.mailing_join_addr + frm = msg[ 'From' ] = email + msg[ 'Subject' ] = 'Join Mailing List' + try: + s = smtplib.SMTP() + s.connect( trans.app.config.smtp_server ) + s.sendmail( frm, [ to ], msg.as_string() ) + s.close() + except: + error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed." + if not error and not admin_view: + # The handle_user_login() method has a call to the history_set_default_permissions() method + # (needed when logging in with a history), user needs to have default permissions set before logging in + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + elif not error: + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Created new user account (%s)' % user.email, + status='done' ) ) + if error: + message = error + status = 'error' + success = False + else: + message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) + success = True + return ( message, status, user, success ) def __save_user_info(self, trans, user, action, new_user=True, **kwd): ''' This method saves the user information for new users as well as editing user --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -29,12 +29,19 @@ ## <%def name="center_panel()"> - ${make_grid( grid )} + ${self.grid_body( grid )} </%def> ## Render the grid's basic elements. Each of these elements can be subclassed. <%def name="body()"> - ${make_grid( grid )} + ${self.grid_body( grid )} +</%def> + +## Because body() is special and always exists even if not explicitly defined, +## it's not possible to override body() in the topmost template in the chain. +## Because of this, override grid_body() instead. +<%def name="grid_body( grid )"> + ${self.make_grid( grid )} </%def><%def name="title()">${grid.title}</%def>

1 0

galaxy-dist commit 7bded9108bd8: More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290007512 18000 # Node ID 7bded9108bd8297ea609e9ec06bbe516b5f0b83a # Parent a68c74ec8cfbc641db4b6fe424e3f77b9f3c5d3c More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model. --- a/templates/admin/requests/edit_request_type.mako +++ b/templates/admin/requests/edit_request_type.mako @@ -28,7 +28,7 @@ </div><div class="form-row"><label> - Sequencing Request Form definition: + Sequencing request form definition: </label><select name="form_id"> %for form in forms: @@ -42,7 +42,7 @@ </div><div class="form-row"><label> - Sample Form definition: + Sample form definition: </label><select name="form_id"> %for form in forms: --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -18,12 +18,6 @@ class BaseField(object): return ' disabled="disabled"' else: return '' - @staticmethod - def form_field_types(): - return ['TextField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField', 'WorkflowField'] - @staticmethod - def sample_field_types(): - return ['TextField', 'SelectField', 'CheckboxField', 'WorkflowField'] class TextField(BaseField): """ @@ -559,8 +553,8 @@ class AddressField(BaseField): self.select_address.add_option( 'Add a new address', 'new' ) return self.select_address.get_html( disabled=disabled ) + address_html -class WorkflowField(BaseField): - def __init__(self, name, user=None, value=None, params=None): +class WorkflowField( BaseField ): + def __init__( self, name, user=None, value=None, params=None ): self.name = name self.user = user self.value = value @@ -580,7 +574,7 @@ class WorkflowField(BaseField): else: self.select_workflow.add_option( a.name, str( a.id ) ) return self.select_workflow.get_html( disabled=disabled ) - + def get_suite(): """Get unittest suite for this module""" import doctest, sys @@ -592,11 +586,11 @@ def build_select_field( trans, objs, lab selected_value='none', refresh_on_change=False, multiple=False, display=None, size=None ): """ Build a SelectField given a set of objects. The received params are: - - objs: the set of object used to populate the option list + - objs: the set of objects used to populate the option list - label_attr: the attribute of each obj (e.g., name, email, etc ) whose value is used to populate each option label. If the string 'self' is passed as label_attr, each obj in objs is assumed to be a string, so the obj itself is used - select_field_name: the name of the SelectField - - initial_value: the vlaue of the first option in the SelectField - allows for an option telling the user to select something + - initial_value: the value of the first option in the SelectField - allows for an option telling the user to select something - selected_value: the value of the currently selected option - refresh_on_change: True if the SelectField should perform a refresh_on_change """ --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -38,7 +38,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Sequencing Request form definition</label> + <label>Sequencing request form definition</label> ${request_type.request_form.name} </div><div class="form-row"> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1495,12 +1495,11 @@ class MetadataFile( object ): class FormDefinition( object ): # The following form_builder classes are supported by the FormDefinition class. - # AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField supported_field_types = [ AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField ] types = Bunch( REQUEST = 'Sequencing Request Form', SAMPLE = 'Sequencing Sample Form', LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) + USER_INFO = 'User Information' ) def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc @@ -1792,6 +1791,8 @@ class RequestTypePermissions( object ): self.role = role class Sample( object ): + # The following form_builder classes are supported by the Sample class. + supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField ] bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) api_collection_visible_keys = ( 'id', 'name' ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -588,12 +588,8 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - events_list = [] - for event in request.events: - events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) return trans.fill_template( '/requests/common/view_request_history.mako', cntrller=cntrller, - events_list=events_list, request=request ) @web.expose @web.require_login( "edit email notification settings" ) @@ -777,7 +773,7 @@ class RequestsCommon( BaseController, Us search_box=search_box ) @web.expose @web.require_login( "sample events" ) - def sample_events( self, trans, cntrller, **kwd ): + def view_sample_history( self, trans, cntrller, **kwd ): params = util.Params( kwd ) status = params.get( 'status', 'done' ) message = util.restore_text( params.get( 'message', '' ) ) @@ -786,15 +782,8 @@ class RequestsCommon( BaseController, Us sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, cntrller, sample_id ) - events_list = [] - for event in sample.events: - events_list.append( ( event.state.name, - event.state.desc, - time_ago( event.update_time ), - event.comment ) ) - return trans.fill_template( '/requests/common/sample_events.mako', + return trans.fill_template( '/requests/common/view_sample_history.mako', cntrller=cntrller, - events_list=events_list, sample=sample ) @web.expose @web.require_login( "add sample" ) @@ -1054,9 +1043,9 @@ class RequestsCommon( BaseController, Us # selected sets of samples. If samples are selected, the sample_operation param # will have a value other than 'none', and the samples param will be a list of # encoded sample ids. There are currently only 2 multi-select operations; - # 'Change state' and 'Select data library and folder'. If sample_operation is - # 'none, then the samples param will be a list of sample objects. - if sample_operation == 'Change state': + # model.Sample.bulk_operations.CHANGE_STATE and model.sample.bulk_operations.SELECT_LIBRARY. + # If sample_operation is 'none, then the samples param will be a list of sample objects. + if sample_operation == trans.model.Sample.bulk_operations.CHANGE_STATE: sample_state_id = params.get( 'sample_state_id', None ) if sample_state_id in [ None, 'none' ]: message = "Select a new state from the <b>Change current state</b> list before clicking the <b>Save</b> button." @@ -1090,7 +1079,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, action='update_request_state', request_id=trans.security.encode_id( request.id ) ) ) - elif sample_operation == 'Select data library and folder': + elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY: # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id # and sample_operation_folder_id because the name sample_0_library_id should belong to the --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -64,12 +64,12 @@ class FormsGrid( grids.Grid ): ] class Forms( BaseController ): - # Empty form field + # Empty TextField empty_field = { 'label': '', 'helptext': '', 'visible': True, 'required': False, - 'type': BaseField.form_field_types()[0], + 'type': model.TextField.__name__, 'selectlist': [], 'layout': 'none', 'default': '' } @@ -597,12 +597,12 @@ class Forms( BaseController ): self.selectbox_options = [] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - if form_type == trans.app.model.FormDefinition.types.SAMPLE: - for ft in BaseField.sample_field_types(): - self.fieldtype.add_option(ft, ft) + if form_type == trans.model.FormDefinition.types.SAMPLE: + for ft in trans.model.Sample.supported_field_types: + self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in BaseField.form_field_types(): - self.fieldtype.add_option(ft, ft) + for ft in trans.model.Request.supported_field_types: + self.fieldtype.add_option( ft.__name__, ft__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) @@ -632,22 +632,22 @@ class Forms( BaseController ): field[ 'selectlist' ] = ['', ''] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - if form_type == trans.app.model.FormDefinition.types.SAMPLE: - for ft in BaseField.sample_field_types(): - if ft == field['type']: - self.fieldtype.add_option(ft, ft, selected=True) + if form_type == trans.model.FormDefinition.types.SAMPLE: + for ft in trans.model.Sample.supported_field_types: + if ft.__name__ == field[ 'type' ]: + self.fieldtype.add_option( ft.__name__, ft__name__, selected=True ) if ft == 'SelectField': - self.selectbox_ui(field) + self.selectbox_ui( field ) else: - self.fieldtype.add_option(ft, ft) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in BaseField.form_field_types(): - if ft == field['type']: - self.fieldtype.add_option(ft, ft, selected=True) + for ft in trans.model.Request.supported_field_types: + if ft.__name__ == field[ 'type' ]: + self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) if ft == 'SelectField': - self.selectbox_ui(field) + self.selectbox_ui( field ) else: - self.fieldtype.add_option(ft, ft) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) # required/optional if field['required'] == 'required': self.required = SelectField('field_required_'+str(self.index), display='radio') --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -39,7 +39,7 @@ <div style="clear: both"></div></div> %endfor - <div class="toolFormTitle">Possible sample states</div> + <div class="toolFormTitle">Sample states</div> %if len(rt_states_widgets): %for index, info in enumerate(rt_states_widgets): ${render_state( index, info[0], info[1] )} --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -160,7 +160,7 @@ %if is_unsubmitted: <td>Unsubmitted</td> %else: - <td valign="top"><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> + <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> %endif %else: <td></td> @@ -334,7 +334,7 @@ %if is_unsubmitted: <td>Unsubmitted</td> %else: - <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> + <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1536,7 +1536,7 @@ class TwillTestCase( unittest.TestCase ) self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def view_sample_history( self, cntrller, sample_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): - self.visit_url( "%s/requests_common/sample_events?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) + self.visit_url( "%s/requests_common/view_sample_history?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[], strings_displayed=[], strings_displayed_after_submit=[] ): --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -8,7 +8,6 @@ is_unsubmitted = request.is_unsubmitted can_add_samples = is_unsubmitted can_reject = is_admin and is_submitted - can_select_datasets = is_admin and ( is_complete or is_submitted ) can_submit_request = request.samples and is_unsubmitted %> @@ -24,9 +23,6 @@ %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif - %if can_select_datasets: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> - %endif </div></ul> --- /dev/null +++ b/templates/requests/common/view_sample_history.mako @@ -0,0 +1,38 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% from galaxy.web.framework.helpers import time_ago %> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<h3>History of sample "${sample.name}"</h3> + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Description</th> + <th>Last Updated</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for event in sample.events: + <tr> + <td><b>${event.state.name}</b></td> + <td>${event.state.desc}</td> + <td>${time_ago( event.update_time )}</td> + <td>${event.comment}</td> + </tr> + %endfor + </tbody> + </table> +</div> --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -44,8 +44,6 @@ class Configuration( object ): # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) - # Communication with a sequencer - self.enable_sequencer_communication = string_as_bool( kwargs.get( 'enable_sequencer_communication', False ) ) # dataset Track files self.track_store_path = kwargs.get( "track_store_path", "${extra_files_path}/tracks") self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) --- a/templates/requests/common/view_request_history.mako +++ b/templates/requests/common/view_request_history.mako @@ -2,6 +2,8 @@ <%namespace file="/message.mako" import="render_msg" /><% + from galaxy.web.framework.helpers import time_ago + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() is_complete = request.is_complete is_submitted = request.is_submitted @@ -41,16 +43,16 @@ <thead><tr><th>State</th> - <th>Last Update</th> + <th>Last Updated</th><th>Comments</th></tr></thead><tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> + %for event in request.events: + <tr> + <td><b>${event.state}</b></td> + <td>${time_ago( event.update_time )}</td> + <td>${event.comment}</td></tr> %endfor </tbody> --- a/templates/requests/common/sample_events.mako +++ /dev/null @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="title()">Events for Sample ${sample.name}</%def> - -<h2>Events for Sample "${sample.name}"</h2> -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> -</ul> -<h3>Sequencing Request "${sample.request.name}"</h3> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="form-row"> - <div class="toolParamHelp" style="clear: both;"> - <b>Possible states: </b> - <% states = " > ".join([ ss.name for ss in sample.request.type.states ]) %> - ${states} - </div> - </div> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Description</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, desc, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${desc}</a></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div>

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