details: http://www.bx.psu.edu/hg/galaxy/rev/2c6720a9130c changeset: 2436:2c6720a9130c user: Greg Von Kuster greg@bx.psu.edu date: Mon Jun 08 21:02:41 2009 -0400 description: Functional test fixes for sniffing data formats and setting metadata.
1 file(s) affected in this change:
test/functional/test_sniffing_and_metadata_settings.py
diffs (229 lines):
diff -r 3190f7d6b572 -r 2c6720a9130c test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Mon Jun 08 16:52:55 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Mon Jun 08 21:02:41 2009 -0400 @@ -1,131 +1,122 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase
class SniffingAndMetaDataSettings( TwillTestCase ): - def test_00_axt_datatype( self ): """Testing correctly sniffing axt data type upon upload""" - self.login() - self.upload_file('1.axt') - 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"') - self.delete_history_item( 1 ) + self.logout() + self.login( email='test@bx.psu.edu' ) + self.new_history( name='history1' ) + global history1 + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history1 is not None, "Problem retrieving history1 from database" + self.upload_file( '1.axt' ) + 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 ): """Testing correctly sniffing bed data type upon upload""" - self.upload_file('1.bed') - self.verify_dataset_correctness('1.bed') - self.check_history_for_string('1.bed format: <span class="bed">bed</span>, database: ? Info: uploaded file') - self.check_metadata_for_string('value="1.bed" value="?"') - self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>') - 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"') - self.delete_history_item( 1 ) + self.upload_file( '1.bed' ) + self.verify_dataset_correctness( '1.bed' ) + self.check_history_for_string( '1.bed format: <span class="bed">bed</span>, database: ? Info: uploaded file') + self.check_metadata_for_string( 'value="1.bed" value="?"' ) + self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) + 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 ): """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"') - self.delete_history_item( 1 ) + 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 ): """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"') - self.delete_history_item( 1 ) + 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 ): """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') - self.delete_history_item( 1 ) + 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 ): """Testing correctly sniffing gff data type upon upload""" - self.upload_file('5.gff') - self.verify_dataset_correctness('5.gff') - self.check_history_for_string('5.gff format: <span class="gff">gff</span>, database: ? Info: uploaded file') - 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"') - self.delete_history_item( 1 ) + self.upload_file( '5.gff' ) + self.verify_dataset_correctness( '5.gff' ) + self.check_history_for_string( '5.gff format: <span class="gff">gff</span>, database: ? Info: uploaded file' ) + 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 ): """Testing correctly sniffing gff3 data type upon upload""" - self.upload_file('5.gff3') - self.verify_dataset_correctness('5.gff3') - self.check_history_for_string('5.gff3 format: <span class="gff3">gff3</span>, database: ? Info: uploaded file') - 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"') - self.delete_history_item( 1 ) - def test_30_html_datatype( self ): - """Testing correctly sniffing html data type upon upload""" - self.upload_file('html_file.txt') - self.check_history_for_string('No data: attempted to upload an empty or inappropriate file') - self.delete_history_item( 1 ) - def test_35_interval_datatype( self ): + self.upload_file( '5.gff3' ) + self.verify_dataset_correctness( '5.gff3' ) + self.check_history_for_string( '5.gff3 format: <span class="gff3">gff3</span>, database: ? Info: uploaded file' ) + 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 ): """Testing correctly sniffing interval data type upon upload""" - self.upload_file('1.interval') - self.verify_dataset_correctness('1.interval') - self.check_history_for_string('1.interval format: <span class="interval">interval</span>, database: ? Info: uploaded file') - self.check_metadata_for_string('value="1.interval" value="?"') - self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>') - 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"') - self.delete_history_item( 1 ) - def test_40_lav_datatype( self ): + self.upload_file( '1.interval' ) + self.verify_dataset_correctness( '1.interval' ) + self.check_history_for_string( '1.interval format: <span class="interval">interval</span>, database: ? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.interval" value="?"' ) + self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) + 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 ): """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"') - self.delete_history_item( 1 ) - def test_45_maf_datatype( self ): + 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 ): """Testing correctly sniffing maf data type upon upload""" - self.upload_file('3.maf') - self.verify_dataset_correctness('3.maf') - self.check_history_for_string('3.maf format: <span class="maf">maf</span>, database: ? Info: uploaded file') - 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"') - self.delete_history_item( 1 ) - def test_50_tabular_datatype( self ): + self.upload_file( '3.maf' ) + self.verify_dataset_correctness( '3.maf' ) + self.check_history_for_string( '3.maf format: <span class="maf">maf</span>, database: ? Info: uploaded file' ) + 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 ): """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"') - self.delete_history_item( 1 ) - def test_55_wig_datatype( self ): + 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 ): """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"') - self.delete_history_item( 1 ) - def test_60_blastxml_datatype( self ): + 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>' ) - self.delete_history_item( 1 ) - def test_65_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('qualscores.qualsolid format: <span class="qualsolid">qualsolid</span>, database: ? Info: uploaded qualsolid file') - self.delete_history_item( 1 ) - def test_70_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('qualscores.qual454 format: <span class="qual454">qual454</span>, database: ? Info: uploaded qual454 file') - self.delete_history_item( 1 ) + """ + 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' ) + """ def test_9999_clean_up( self ): - self.delete_history() + self.delete_history( id=str( history1.id ) ) self.logout()