details: http://www.bx.psu.edu/hg/galaxy/rev/004cd81cff72 changeset: 2444:004cd81cff72 user: Greg Von Kuster <greg(a)bx.psu.edu&gt; date: Wed Jun 10 15:46:26 2009 -0400 description: Fixes for test_get_data functional test script. 1 file(s) affected in this change: test/functional/test_get_data.py diffs (152 lines): diff -r 08194c60c290 -r 004cd81cff72 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Wed Jun 10 12:22:49 2009 -0400 +++ b/test/functional/test_get_data.py Wed Jun 10 15:46:26 2009 -0400 @@ -1,87 +1,74 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase -""" Tests are executed in order, sorted by name""" - class UploadData( TwillTestCase ): - def test_00_multi_upload( self ): - """test_get_data.test_multi_upload: Testing multiple uploads""" - self.login() - self.upload_file('1.bed') - self.verify_dataset_correctness('1.bed') - self.upload_file('2.bed', dbkey='hg17') - self.verify_dataset_correctness('2.bed') - self.upload_file('3.bed', dbkey='hg17', ftype='bed') - self.verify_dataset_correctness('3.bed') - self.upload_file('4.bed.gz', dbkey='hg17', ftype='bed') - self.verify_dataset_correctness('4.bed') - self.upload_file('1.scf', ftype='scf') - self.verify_dataset_correctness('1.scf') - self.upload_file('1.scf.zip', ftype='binseq.zip') - self.verify_dataset_correctness('1.scf.zip') + def test_000_upload_files_from_disk( self ): + """Test uploading data files from disk""" + self.logout() + self.login( email=&#39;tst(a)bx.psu.edu&#39; ) + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.upload_file( '1.bed' ) + hda1 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda1 is not None, "Problem retrieving hda1 from database" + self.verify_dataset_correctness( '1.bed', hid=str( hda1.hid ) ) + self.upload_file( '2.bed', dbkey='hg17' ) + hda2 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda2 is not None, "Problem retrieving hda2 from database" + self.verify_dataset_correctness( '2.bed', hid=str( hda2.hid ) ) + self.upload_file( '3.bed', dbkey='hg17', ftype='bed' ) + hda3 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda3 is not None, "Problem retrieving hda3 from database" + self.verify_dataset_correctness( '3.bed', hid=str( hda3.hid ) ) + self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) + hda4 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda4 is not None, "Problem retrieving hda4 from database" + self.verify_dataset_correctness( '4.bed', hid=str( hda4.hid ) ) + self.upload_file( '1.scf', ftype='scf' ) + hda5 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda5 is not None, "Problem retrieving hda5 from database" + self.verify_dataset_correctness( '1.scf', hid=str( hda5.hid ) ) + self.upload_file( '1.scf.zip', ftype='binseq.zip' ) + hda6 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda6 is not None, "Problem retrieving hda6 from database" + self.verify_dataset_correctness( '1.scf.zip', hid=str( hda6.hid ) ) + self.delete_history( id=str( history1.id ) ) + def test_005_url_paste( self ): + """Test url paste behavior""" + # Deleting the current history should have created a new history + self.check_history_for_string( 'Your history is empty' ) + history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() self.upload_url_paste( 'hello world' ) self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) - self.delete_history_item( 1 ) - self.delete_history_item( 2 ) - self.delete_history_item( 3 ) - self.delete_history_item( 4 ) - self.delete_history_item( 5 ) - self.delete_history_item( 6 ) - self.delete_history_item( 7 ) self.upload_url_paste( u'hello world' ) self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) - self.delete_history_item( 8 ) - def test_9999_clean_up( self ): - self.delete_history() - self.logout() - -class GetEncodeData( TwillTestCase ): - - def test_00_get_encode_data( self ): - """test_get_data.test_get_encode_data""" - self.login() - self.run_tool('encode_import_chromatin_and_chromosomes1', hg17=['cc.EarlyRepSeg.20051216.bed'] ) - #hg17=[ "cc.EarlyRepSeg.20051216.bed", "cc.EarlyRepSeg.20051216.gencode_partitioned.bed", "cc.LateRepSeg.20051216.bed", "cc.LateRepSeg.20051216.gencode_partitioned.bed", "cc.MidRepSeg.20051216.bed", "cc.MidRepSeg.20051216.gencode_partitioned.bed" ] ) + self.delete_history( id=str( history2.id ) ) + def test_010_upload_encode_data( self ): + """Test uploading encode data""" + # Deleting the current history should have created a new history + self.check_history_for_string( 'Your history is empty' ) + history3 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.run_tool( 'encode_import_chromatin_and_chromosomes1', hg17=['cc.EarlyRepSeg.20051216.bed'] ) self.wait() - self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.bed', hid=1) - #self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.gencode_partitioned.bed', hid=2) - #self.verify_dataset_correctness('cc.LateRepSeg.20051216.bed', hid=3) - #self.verify_dataset_correctness('cc.LateRepSeg.20051216.gencode_partitioned.bed', hid=4) - #self.verify_dataset_correctness('cc.MidRepSeg.20051216.bed', hid=5) - #self.verify_dataset_correctness('cc.MidRepSeg.20051216.gencode_partitioned.bed', hid=6) + hda7 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda7 is not None, "Problem retrieving hda7 from database" + self.verify_dataset_correctness( 'cc.EarlyRepSeg.20051216.bed', hid=str( hda7.hid ) ) self.run_tool('encode_import_gencode1', hg17=['gencode.CDS.20051206.bed']) self.wait() - self.verify_dataset_correctness('sc_3D_cds.bed', hid=2) - self.delete_history_item( 1 ) - self.delete_history_item( 2 ) - def test_9999_clean_up( self ): - self.delete_history() + hda8 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda8 is not None, "Problem retrieving hda8 from database" + self.verify_dataset_correctness( 'sc_3D_cds.bed', hid=str( hda8.hid ) ) + self.delete_history( id=str( history3.id ) ) + def test_015_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" self.logout() - -class DataSources( TwillTestCase ): - - #def test_hbvar(self): - # """Getting hybrid gene mutations from HbVar""" - # #self.load_cookies("hbvar_cookie.txt") - # self.clear_history() - # self.run_tool('hbvar') - # params = dict( - # htyp="any hybrid gene", - # ) - # self.submit_form(form=1, button="Submit Query", **params) - # params = dict( - # display_format="galaxy", - # ) - # self.submit_form(form=1, button="Go", **params) - # params = dict( - # build="hg17", - # ) - # self.submit_form(form=1, button="ok", **params); - # """ - # TODO: Currently fails when using sqlite, although successful when - # using Postgres. Upgrading our version of sqlite may fix this, but - # confirmation is required. - # """ - # self.verify_dataset_correctness('hbvar_hybrid_genes.dat') - pass