details: http://www.bx.psu.edu/hg/galaxy/rev/c0aa8af62124 changeset: 2441:c0aa8af62124 user: Greg Von Kuster greg@bx.psu.edu date: Tue Jun 09 15:03:04 2009 -0400 description: Only refresh history if necessary ( better fix than my previous commit ), add functional tests to cover behavior when deleing current history, and add better functional tests for sniffing data formats.

3 file(s) affected in this change:

lib/galaxy/web/controllers/history.py test/functional/test_history_functions.py test/functional/test_sniffing_and_metadata_settings.py

diffs (288 lines):

diff -r 6a992f466b80 -r c0aa8af62124 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Jun 09 12:08:35 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Jun 09 15:03:04 2009 -0400 @@ -79,6 +79,7 @@ @web.require_login( "work with multiple histories" ) def list( self, trans, **kwargs ): """List all available histories""" + current_history = trans.history status = message = None if 'operation' in kwargs: operation = kwargs['operation'].lower() @@ -104,12 +105,14 @@ if histories: if operation == "switch": status, message = self._list_switch( trans, histories ) + # Current history changed, refresh history frame + trans.template_context['refresh_frames'] = ['history'] elif operation == "delete": status, message = self._list_delete( trans, histories ) + if current_history in histories: + trans.template_context['refresh_frames'] = ['history'] elif operation == "undelete": status, message = self._list_undelete( trans, histories ) - # Current history may have changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] trans.sa_session.flush() # Render the list view return self.list_grid( trans, status=status, message=message, **kwargs ) diff -r 6a992f466b80 -r c0aa8af62124 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Jun 09 12:08:35 2009 -0400 +++ b/test/functional/test_history_functions.py Tue Jun 09 15:03:04 2009 -0400 @@ -47,6 +47,8 @@ latest_history.refresh() if not latest_history.deleted: raise AssertionError, "Problem deleting history id %d" % latest_history.id + # Since we deleted the current history, make sure the history frame was refreshed + self.check_history_for_string( 'Your history is empty.' ) # We'll now test deleting a list of histories # After deleting the current history, a new one should have been created global history1 @@ -60,6 +62,8 @@ self.upload_file( '2.bed', dbkey='hg18' ) ids = '%s,%s' % ( str( history1.id ), str( history2.id ) ) self.delete_history( ids ) + # Since we deleted the current history, make sure the history frame was refreshed + self.check_history_for_string( 'Your history is empty.' ) try: self.view_stored_active_histories( check_str=history1.name ) raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history1.name diff -r 6a992f466b80 -r c0aa8af62124 test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Tue Jun 09 12:08:35 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Tue Jun 09 15:03:04 2009 -0400 @@ -3,7 +3,7 @@ from base.twilltestcase import TwillTestCase

class SniffingAndMetaDataSettings( TwillTestCase ): - def test_00_axt_datatype( self ): + def test_000_axt_datatype( self ): """Testing correctly sniffing axt data type upon upload""" self.logout() self.login( email='test@bx.psu.edu' ) @@ -15,7 +15,12 @@ self.verify_dataset_correctness( '1.axt' ) self.check_history_for_string( '1.axt format: <span class="axt">axt</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.axt" value="?" Change data type selected value="axt" selected="yes"' ) - def test_05_bed_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving axt hda from the database" + if not latest_hda.name == '1.axt' and not latest_hda.extension == 'axt': + raise AssertionError, "axt data type was not correctly sniffed." + def test_005_bed_datatype( self ): """Testing correctly sniffing bed data type upon upload""" self.upload_file( '1.bed' ) self.verify_dataset_correctness( '1.bed' ) @@ -25,24 +30,64 @@ self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED <option value="gff">BED to GFF' ) self.check_metadata_for_string( 'Change data type selected value="bed" selected="yes"' ) - def test_10_customtrack_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving bed hda from the database" + if not latest_hda.name == '1.bed' and not latest_hda.extension == 'bed': + raise AssertionError, "bed data type was not correctly sniffed." + def test_010_blastxml_datatype( self ): + """Testing correctly sniffing blastxml data type upon upload""" + self.upload_file( 'megablast_xml_parser_test1.gz' ) + self.check_history_for_string( 'NCBI Blast XML data format: <span class="blastxml">blastxml</span>' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving blastxml hda from the database" + if not latest_hda.name == 'megablast_xml_parser_test1' and not latest_hda.extension == 'blastxml': + raise AssertionError, "blastxml data type was not correctly sniffed." + def test_015_csfasta_datatype( self ): + """Testing correctly sniffing csfasta data type upon upload""" + self.upload_file( 'shrimp_cs_test1.csfasta' ) + self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta' ) + self.check_history_for_string( '162.6 Kb, format: <span class="csfasta">csfasta</span>, <td>&gt;2_14_26_F3,-1282216.0</td>' ) + self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="?" Change data type value="csfasta" selected="yes"' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving csfasta hda from the database" + if not latest_hda.name == 'shrimp_cs_test1.csfasta' and not latest_hda.extension == 'csfasta': + raise AssertionError, "csfasta data type was not correctly sniffed." + def test_020_customtrack_datatype( self ): """Testing correctly sniffing customtrack data type upon upload""" self.upload_file( '1.customtrack' ) self.verify_dataset_correctness( '1.customtrack' ) self.check_history_for_string( '1.customtrack format: <span class="customtrack">customtrack</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.customtrack" value="?" Change data type selected value="customtrack" selected="yes"' ) - def test_15_fasta_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving customtrack hda from the database" + if not latest_hda.name == '1.customtrack' and not latest_hda.extension == 'customtrack': + raise AssertionError, "customtrack data type was not correctly sniffed." + def test_025_fasta_datatype( self ): """Testing correctly sniffing fasta data type upon upload""" self.upload_file( '1.fasta' ) self.verify_dataset_correctness( '1.fasta' ) self.check_history_for_string( '1.fasta format: <span class="fasta">fasta</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.fasta" value="?" Change data type selected value="fasta" selected="yes"' ) - def test_18_fastqsolexa_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving fasta hda from the database" + if not latest_hda.name == '1.fasta' and not latest_hda.extension == 'fasta': + raise AssertionError, "fasta data type was not correctly sniffed." + def test_030_fastqsolexa_datatype( self ): """Testing correctly sniffing fastqsolexa ( the Solexa variant ) data type upon upload""" self.upload_file( '1.fastqsolexa' ) self.verify_dataset_correctness( '1.fastqsolexa' ) self.check_history_for_string( '1.fastqsolexa format: <span class="fastqsolexa">fastqsolexa</span>, database: ? Info: uploaded fastqsolexa file' ) - def test_20_gff_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving fastqsolexa hda from the database" + if not latest_hda.name == '1.fastqsolexa' and not latest_hda.extension == 'fastqsolexa': + raise AssertionError, "fastqsolexa data type was not correctly sniffed." + def test_035_gff_datatype( self ): """Testing correctly sniffing gff data type upon upload""" self.upload_file( '5.gff' ) self.verify_dataset_correctness( '5.gff' ) @@ -50,7 +95,12 @@ self.check_metadata_for_string( 'value="5.gff" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) - def test_25_gff3_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving gff hda from the database" + if not latest_hda.name == '5.gff' and not latest_hda.extension == 'gff': + raise AssertionError, "gff data type was not correctly sniffed." + def test_040_gff3_datatype( self ): """Testing correctly sniffing gff3 data type upon upload""" self.upload_file( '5.gff3' ) self.verify_dataset_correctness( '5.gff3' ) @@ -58,7 +108,21 @@ self.check_metadata_for_string( 'value="5.gff3" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) - def test_30_interval_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving gff3 hda from the database" + if not latest_hda.name == '5.gff3' and not latest_hda.extension == 'gff3': + raise AssertionError, "gff3 data type was not correctly sniffed." + def test_045_html_datatype( self ): + """Testing correctly sniffing html data type upon upload""" + self.upload_file( 'html_file.txt' ) + self.check_history_for_string( 'An error occurred running this job: No data: you attempted to upload an inappropriate file.' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving html hda from the database" + if not latest_hda.name == 'html_file.txt' and not latest_hda.extension == 'data': + raise AssertionError, "html data type was not correctly sniffed." + def test_050_interval_datatype( self ): """Testing correctly sniffing interval data type upon upload""" self.upload_file( '1.interval' ) self.verify_dataset_correctness( '1.interval' ) @@ -68,14 +132,24 @@ self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED' ) self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) - def test_35_lav_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving interval hda from the database" + if not latest_hda.name == '1.interval' and not latest_hda.extension == 'interval': + raise AssertionError, "interval data type was not correctly sniffed." + def test_055_lav_datatype( self ): """Testing correctly sniffing lav data type upon upload""" self.upload_file( '1.lav' ) self.verify_dataset_correctness( '1.lav' ) self.check_history_for_string( '1.lav format: <span class="lav">lav</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.lav" value="?"' ) self.check_metadata_for_string( 'Change data type selected value="lav" selected="yes"' ) - def test_40_maf_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving lav hda from the database" + if not latest_hda.name == '1.lav' and not latest_hda.extension == 'lav': + raise AssertionError, "lav data type was not correctly sniffed." + def test_060_maf_datatype( self ): """Testing correctly sniffing maf data type upon upload""" self.upload_file( '3.maf' ) self.verify_dataset_correctness( '3.maf' ) @@ -83,40 +157,57 @@ self.check_metadata_for_string( 'value="3.maf" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="interval">MAF to Genomic Intervals <option value="fasta">MAF to Fasta' ) self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) - def test_45_tabular_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving maf hda from the database" + if not latest_hda.name == '3.maf' and not latest_hda.extension == 'maf': + raise AssertionError, "maf data type was not correctly sniffed." + def test_065_qual454_datatype( self ): + """Testing correctly sniffing qual454 data type upon upload""" + self.upload_file( 'qualscores.qual454' ) + self.verify_dataset_correctness( 'qualscores.qual454' ) + self.check_history_for_string( '5.6 Kb, format: <span class="qual454">qual454</span>, database: ?' ) + self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving qual454 hda from the database" + if not latest_hda.name == 'qualscores.qual454' and not latest_hda.extension == 'qual454': + raise AssertionError, "qual454 data type was not correctly sniffed." + def test_070_qualsolid_datatype( self ): + """Testing correctly sniffing qualsolid data type upon upload""" + self.upload_file( 'qualscores.qualsolid' ) + self.verify_dataset_correctness('qualscores.qualsolid' ) + self.check_history_for_string('2.5 Kb, format: <span class="qualsolid">qualsolid</span>, database: ? Info: uploaded file' ) + self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving qualsolid hda from the database" + if not latest_hda.name == 'qualscores.qualsolid' and not latest_hda.extension == 'qualsolid': + raise AssertionError, "qualsolid data type was not correctly sniffed." + def test_075_tabular_datatype( self ): """Testing correctly sniffing tabular data type upon upload""" self.upload_file( '1.tabular' ) self.verify_dataset_correctness( '1.tabular' ) self.check_history_for_string( '1.tabular format: <span class="tabular">tabular</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.tabular" value="?"' ) self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' ) - def test_50_wig_datatype( self ): + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving tabular hda from the database" + if not latest_hda.name == '1.tabular' and not latest_hda.extension == 'tabular': + raise AssertionError, "tabular data type was not correctly sniffed." + def test_080_wig_datatype( self ): """Testing correctly sniffing wig data type upon upload""" self.upload_file( '1.wig' ) self.verify_dataset_correctness( '1.wig' ) self.check_history_for_string( '1.wig format: <span class="wig">wig</span>, database: ? Info: uploaded file' ) self.check_metadata_for_string( 'value="1.wig" value="?"' ) self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' ) - def test_55_blastxml_datatype( self ): - """Testing correctly sniffing blastxml data type upon upload""" - self.upload_file( 'megablast_xml_parser_test1.gz' ) - self.check_history_for_string( 'NCBI Blast XML data' ) - self.check_history_for_string( 'format: <span class="blastxml">blastxml</span>' ) - """ - TODO: It is currently not even possible to set the following format on upload. They - should be included in the File Format select list on the upload form if they are to - be tested here... - def test_60_qualsolid_datatype( self ): - Testing correctly sniffing qualsolid data type upon upload - self.upload_file( 'qualscores.qualsolid' ) - self.verify_dataset_correctness('qualscores.qualsolid' ) - self.check_history_for_string('2.5 Kb, format: <span class="fasta">fasta</span>, database: ? Info: uploaded file' ) - def test_65_qual454_datatype( self ): - Testing correctly sniffing qual454 data type upon upload - self.upload_file( 'qualscores.qual454' ) - self.verify_dataset_correctness( 'qualscores.qual454' ) - self.check_history_for_string( '5.6 Kb, format: <span class="qual454">qual454</span>, database: ? Info: uploaded qual454 file' ) - """ + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert latest_hda is not None, "Problem retrieving wig hda from the database" + if not latest_hda.name == '1.wig' and not latest_hda.extension == 'wig': + raise AssertionError, "wig data type was not correctly sniffed." def test_9999_clean_up( self ): self.delete_history( id=str( history1.id ) ) self.logout()