Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser.

test/api/test_page_revisions.py

@@ -1,5 +1,5 @@
 from galaxy.exceptions import error_codes
-from functional.api.test_pages import BasePageApiTestCase
+from api.test_pages import BasePageApiTestCase
 
 
 class PageRevisionsApiTestCase( BasePageApiTestCase ):

test/base/twilltestcase.py

@@ -1074,7 +1074,7 @@ class TwillTestCase( unittest.TestCase ):
             # HACK: don't use panels because late_javascripts() messes up the twill browser and it
             # can't find form fields (and hence user can't be logged in).
             self.visit_url( "/user/login?use_panels=False" )
-            self.submit_form( 1, 'login_button', email=email, redirect=redirect, password=password )
+            self.submit_form( 'login', 'login_button', email=email, redirect=redirect, password=password )
 
     def logout( self ):
         self.visit_url( "%s/user/logout" % self.url )
@@ -1143,6 +1143,9 @@ class TwillTestCase( unittest.TestCase ):
     def last_page( self ):
         return tc.browser.get_html()
 
+    def last_url( self ):
+        return tc.browser.get_url()
+
     def load_cookies( self, file, shed_tool_id=None ):
         filename = self.get_filename( file, shed_tool_id=shed_tool_id )
         tc.load_cookies(filename)
@@ -1350,13 +1353,25 @@ class TwillTestCase( unittest.TestCase ):
     def run_ucsc_main( self, track_params, output_params ):
         """Gets Data From UCSC"""
         tool_id = "ucsc_table_direct1"
-        galaxy_url = urllib.quote_plus( "%s/tool_runner/index?" % self.url )
+        galaxy_url = "%s/tool_runner/index?" % self.url
         track_params.update( dict( GALAXY_URL=galaxy_url, hgta_compressType='none', tool_id=tool_id ) )
         self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables", params=track_params )
-        tc.fv( "mainForm", "hgta_doTopSubmit", "get output" )
-        self.submit_form( button="get output" )
-        tc.fv( 2, "hgta_doGalaxyQuery", "Send query to Galaxy" )
-        self.submit_form( button="Send query to Galaxy" )
+        log.debug( 'Last URL: %s', self.last_url() )
+        tc.fv( 'mainForm', 'checkboxGalaxy', 'on' )
+        tc.submit( 'hgta_doTopSubmit' )
+        log.debug( 'Last URL: %s', self.last_url() )
+        tc.fv( 2, "hgta_geneSeqType", "genomic" )
+        tc.submit( 'hgta_doGenePredSequence' )
+        log.debug( 'Last URL: %s', self.last_url() )
+#         log.debug( self.last_page() )
+        for index, form in enumerate( self.showforms() ):
+            log.debug( 'Form #%s: %s', index, form.name )
+            log.debug( 'Form target: %s', form.action )
+            for control_num, control in enumerate( form.controls ):
+                log.debug( '%s: %s', control.name, control.value )
+        tc.fv( 2, 'hgSeq.casing', 'upper' )
+        log.debug( tc.submit( 'hgta_doGalaxyQuery' ) )
+        log.debug( 'Last URL: %s', self.last_url() )
 
     def get_running_datasets( self ):
         self.visit_url( '/api/histories' )

test/functional/test_DNAse_flanked_genes.py

@@ -1,102 +0,0 @@
-import galaxy.model
-from galaxy.model.orm import *
-import database_contexts
-from base.twilltestcase import TwillTestCase
-
-""" A sample analysis"""
-
-
-class AnalysisDNAseHSSFlankedGenes( TwillTestCase ):
-
-    def test_get_DNAseHSS_flanked_genes( self ):
-        sa_session = database_contexts.galaxy_context
-        self.logout()
-        self.login( email='test@bx.psu.edu' )
-        admin_user = sa_session.query( galaxy.model.User ) \
-                               .filter( galaxy.model.User.table.c.email == 'test@bx.psu.edu' ) \
-                               .one()
-        self.new_history( name='DNAseHSS_flanked_genes' )
-        history1 = sa_session.query( galaxy.model.History ) \
-                             .filter( and_( galaxy.model.History.table.c.deleted == False,
-                                            galaxy.model.History.table.c.user_id == admin_user.id ) ) \
-                             .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
-                             .first()
-        track_params = dict(
-            db="hg17",
-            hgta_group="regulation",
-            hgta_table="dukeDnaseCd4Sites",
-            hgta_track="dukeDnaseCd4Sites",
-            hgta_regionType="range",
-            position="chr22",
-            hgta_outputType="bed",
-            sendToGalaxy="1"
-        )
-        output_params = dict(
-            fbQual="whole",
-        )
-        # Test 1
-        self.run_ucsc_main( track_params, output_params )
-        self.wait()
-        self.verify_dataset_correctness('DNAseHSS.dat')
-        latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
-                               .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
-                               .first()
-        # Due to twill not being able to handle the permissions forms, we'll eliminate
-        # DefaultHistoryPermissions prior to uploading a dataset so that the permission
-        # form will not be displayed on ted edit attributes page.
-        for dp in latest_hda.dataset.actions:
-            sa_session.delete( dp )
-            sa_session.flush()
-        sa_session.refresh( latest_hda.dataset )
-        self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" )
-        self.check_metadata_for_string( "DNAse HS" )
-        track_params = dict(
-            db="hg17",
-            hgta_group="genes",
-            hgta_table="knownGene",
-            hgta_track="knownGene",
-            hgta_regionType="range",
-            position="chr22",
-            hgta_outputType="bed",
-            sendToGalaxy="1"
-        )
-        output_params = dict(
-            fbQual="whole",
-        )
-        # Test 2
-        self.run_ucsc_main( track_params, output_params )
-        self.wait()
-        self.verify_dataset_correctness('hg17chr22KnownGenes.dat')
-        latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
-                               .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
-                               .first()
-        for dp in latest_hda.dataset.actions:
-            sa_session.delete( dp )
-            sa_session.flush()
-        sa_session.refresh( latest_hda.dataset )
-        self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" )
-        self.check_metadata_for_string( "Genes" )
-        # Test 3
-        self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" )
-        self.wait()
-        self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' )
-        latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
-                               .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
-                               .first()
-        for dp in latest_hda.dataset.actions:
-            sa_session.delete( dp )
-            sa_session.flush()
-        sa_session.refresh( latest_hda.dataset )
-        self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" )
-        self.check_metadata_for_string( "Flanks" )
-        # Test 4
-        self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none"  )
-        self.wait()
-        # We cannot verify this dataset, because this tool spits out data in a non-deterministic order
-        #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' )
-        # Test 5
-        self.run_tool( 'Filter1', input="4", cond="c17==1000"  )
-        self.wait()
-        self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' )
-        self.delete_history( self.security.encode_id( history1.id ) )
-        self.logout()

test/functional/test_ucsc_table_browser.py

@@ -0,0 +1,35 @@
+from base import test_db_util
+from base.twilltestcase import TwillTestCase
+
+""" A sample analysis"""
+
+
+class UCSCMain( TwillTestCase ):
+
+    def test_0000_create_users( self ):
+        self.logout()
+        self.login( email='test@bx.psu.edu' )
+        admin_user = test_db_util.get_user( 'test@bx.psu.edu' )
+        assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database'
+    
+    def test_0005_get_mm10_5HTT_sequence( self ):
+        self.logout()
+        self.login( email='test@bx.psu.edu' )
+        admin_user = test_db_util.get_user( 'test@bx.psu.edu' )
+        self.new_history( name='UCSC_Main' )
+        track_params = dict(
+            db="mm10",
+            hgta_group="genes",
+            hgta_table="knownGene",
+            hgta_track="knownGene",
+            hgta_regionType="range",
+            position="chr5:34761740-34912521",
+            hgta_outputType="sequence",
+            sendToGalaxy="1"
+        )
+        output_params = dict(
+            fbQual="whole",
+        )
+        self.run_ucsc_main( track_params, output_params )
+        self.wait()
+        self.verify_dataset_correctness( 'GRCm38mm10_chr5_34761740-34912521.fa' )