[2] | 1 | import galaxy.model |
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| 2 | from galaxy.model.orm import * |
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| 3 | from galaxy.model.mapping import context as sa_session |
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| 4 | from base.twilltestcase import TwillTestCase |
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| 5 | |
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| 6 | """ A sample analysis""" |
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| 7 | |
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| 8 | class AnalysisDNAseHSSFlankedGenes( TwillTestCase ): |
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| 9 | def test_get_DNAseHSS_flanked_genes( self ): |
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| 10 | self.logout() |
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| 11 | self.login( email='test@bx.psu.edu' ) |
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| 12 | admin_user = sa_session.query( galaxy.model.User ) \ |
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| 13 | .filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ) \ |
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| 14 | .one() |
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| 15 | self.new_history( name='DNAseHSS_flanked_genes' ) |
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| 16 | history1 = sa_session.query( galaxy.model.History ) \ |
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| 17 | .filter( and_( galaxy.model.History.table.c.deleted==False, |
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| 18 | galaxy.model.History.table.c.user_id==admin_user.id ) ) \ |
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| 19 | .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ |
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| 20 | .first() |
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| 21 | track_params = dict( |
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| 22 | db="hg17", |
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| 23 | hgta_group="regulation", |
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| 24 | hgta_table="dukeDnaseCd4Sites", |
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| 25 | hgta_track="dukeDnaseCd4Sites", |
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| 26 | hgta_regionType="range", |
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| 27 | position="chr22", |
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| 28 | hgta_outputType="bed", |
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| 29 | sendToGalaxy="1" |
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| 30 | ) |
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| 31 | output_params = dict( |
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| 32 | fbQual="whole", |
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| 33 | ) |
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| 34 | # Test 1 |
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| 35 | self.run_ucsc_main( track_params, output_params ) |
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| 36 | self.wait() |
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| 37 | self.verify_dataset_correctness('DNAseHSS.dat') |
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| 38 | latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ |
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| 39 | .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ |
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| 40 | .first() |
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| 41 | # Due to twill not being able to handle the permissions forms, we'll eliminate |
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| 42 | # DefaultHistoryPermissions prior to uploading a dataset so that the permission |
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| 43 | # form will not be displayed on ted edit attributes page. |
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| 44 | for dp in latest_hda.dataset.actions: |
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| 45 | sa_session.delete( dp ) |
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| 46 | sa_session.flush() |
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| 47 | sa_session.refresh( latest_hda.dataset ) |
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| 48 | self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" ) |
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| 49 | self.check_metadata_for_string( "DNAse HS" ) |
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| 50 | track_params = dict( |
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| 51 | db="hg17", |
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| 52 | hgta_group="genes", |
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| 53 | hgta_table="knownGene", |
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| 54 | hgta_track="knownGene", |
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| 55 | hgta_regionType="range", |
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| 56 | position="chr22", |
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| 57 | hgta_outputType="bed", |
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| 58 | sendToGalaxy="1" |
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| 59 | ) |
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| 60 | output_params = dict( |
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| 61 | fbQual="whole", |
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| 62 | ) |
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| 63 | # Test 2 |
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| 64 | self.run_ucsc_main( track_params, output_params ) |
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| 65 | self.wait() |
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| 66 | self.verify_dataset_correctness('hg17chr22KnownGenes.dat') |
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| 67 | latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ |
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| 68 | .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ |
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| 69 | .first() |
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| 70 | for dp in latest_hda.dataset.actions: |
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| 71 | sa_session.delete( dp ) |
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| 72 | sa_session.flush() |
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| 73 | sa_session.refresh( latest_hda.dataset ) |
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| 74 | self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" ) |
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| 75 | self.check_metadata_for_string( "Genes" ) |
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| 76 | # Test 3 |
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| 77 | self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" ) |
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| 78 | self.wait() |
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| 79 | self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' ) |
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| 80 | latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ |
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| 81 | .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ |
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| 82 | .first() |
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| 83 | for dp in latest_hda.dataset.actions: |
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| 84 | sa_session.delete( dp ) |
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| 85 | sa_session.flush() |
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| 86 | sa_session.refresh( latest_hda.dataset ) |
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| 87 | self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" ) |
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| 88 | self.check_metadata_for_string( "Flanks" ) |
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| 89 | # Test 4 |
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| 90 | self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none" ) |
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| 91 | self.wait() |
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| 92 | # We cannot verify this dataset, because this tool spits out data in a non-deterministic order |
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| 93 | #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) |
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| 94 | # Test 5 |
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| 95 | self.run_tool( 'Filter1', input="4", cond="c17==1000" ) |
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| 96 | self.wait() |
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| 97 | self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' ) |
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| 98 | self.delete_history( self.security.encode_id( history1.id ) ) |
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| 99 | self.logout() |
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