1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7b91f9d888d3/ changeset: 7b91f9d888d3 user: carlfeberhard date: 2012-12-11 23:29:35 summary: Fixes to upload functional tests (test_get_data.py); TwillTestCase: add is_history_empty which checks the length of HDA JSON instead of relying on html, add check_hda_json_key_value which checks a specific HDA's JSON for a specific value affected #: 2 files
diff -r d9e2418fb00aefd0a8f65a4686dae4e8cd6cd16d -r 7b91f9d888d33ce51e07661c77958d2a3d8d68f2 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2,6 +2,7 @@ pkg_resources.require( "twill==0.9" )
import StringIO, os, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil, subprocess +import pprint
import twill import twill.commands as tc @@ -299,10 +300,11 @@ # twill stores the regex match in a special stack variable match = twill.namespaces.get_twill_glocals()[1][ '__match__' ] json_data = from_json_string( match ) - assert check_fn( json_data ), 'failed check_fn' + assert check_fn( json_data ), 'failed check_fn: %s' %( check_fn.func_name )
except Exception, exc: log.error( exc, exc_info=True ) + log.debug( 'json_data: %s', ( '\n' + pprint.pformat( json_data ) if json_data else '(no match)' ) ) fname = self.write_temp_file( tc.browser.get_html() ) errmsg = ( "json '%s' could not be found or failed check_fn" % ( pattern ) + "\npage content written to '%s'" % ( fname ) ) @@ -310,6 +312,49 @@
self.home()
+ def is_history_empty( self ): + """ + Uses history page JSON to determine whether this history is empty + (i.e. has no undeleted datasets). + """ + def has_no_undeleted_hdas( hda_list ): + if not len( hda_list ): + return True + for hda in hda_list: + if not( hda[ 'deleted' ] or hda[ 'purged' ] ): + return False + return True + try: + self.check_history_json( r'\bhdas\s*=\s*(.*);', has_no_undeleted_hdas ) + except AssertionError, exc: + log.error( 'history is not empty' ) + raise exc + + def check_hda_json_for_key_value( self, hda_id, key, value, use_string_contains=False ): + """ + Uses history page JSON to determine whether the current history: + (1) has an hda with hda_id, + (2) that hda has a JSON var named 'key', + (3) that var 'key' == value + If use_string_contains=True, this will search for value in var 'key' + instead of testing for an entire, exact match (string only). + """ + #TODO: multi key, value + def hda_has_key_value( hda_list ): + for hda in hda_list: + # if we found the hda and there's a var in the json named key + if( ( hda[ 'id' ] == hda_id ) + and ( key in hda ) ): + var = hda[ key ] + # test for partial string containment if str and requested + if( ( type( var ) == str ) + and ( use_string_contains ) ): + return ( value in var ) + # otherwise, test for equivalence + return ( var == value ) + return False + self.check_history_json( r'\bhdas\s*=\s*(.*);', hda_has_key_value ) + def clear_history( self ): """Empties a history of all datasets""" self.visit_page( "clear_history" )
diff -r d9e2418fb00aefd0a8f65a4686dae4e8cd6cd16d -r 7b91f9d888d33ce51e07661c77958d2a3d8d68f2 test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -5,131 +5,210 @@ from base.test_db_util import *
class UploadData( TwillTestCase ): + def test_0000_setup_upload_tests( self ): - """Configuring upload tests, setting admin_user""" + """ + Configuring upload tests, setting admin_user + """ self.logout() self.login( email='test@bx.psu.edu' ) global admin_user admin_user = get_user( email='test@bx.psu.edu' ) + + def create_fresh_history( self, user ): + """ + Deletes latest history for the given user, checks for an empty history, + and returns that new, empty history + """ + # in order to remove a lot of boiler plate - and not have cascading errors + history = get_latest_history_for_user( user ) + self.delete_history( id=self.security.encode_id( history.id ) ) + self.is_history_empty() + return get_latest_history_for_user( user ) + def test_0005_upload_file( self ): - """Test uploading 1.bed, NOT setting the file format""" - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.bed, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.bed' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0006_upload_file( self ): - """Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format""" - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.bed.spaces', space_to_tab = True ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0010_upload_file( self ): - """Test uploading 4.bed.gz, manually setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 4.bed.gz, manually setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) - self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0012_upload_file( self ): - """Test uploading 4.bed.bz2, manually setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 4.bed.bz2, manually setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '4.bed.bz2', dbkey='hg17', ftype='bed' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" + self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) - self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0015_upload_file( self ): - """Test uploading 1.scf, manually setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.scf, manually setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.scf', ftype='scf' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.scf', hid=str( hda.hid ) ) - self.check_history_for_string( "Binary scf sequence file</pre>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "Binary scf sequence file", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0020_upload_file( self ): - """Test uploading 1.scf, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.scf, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.scf' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( "File Format' to 'Scf' when uploading scf files" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "misc_info", "File Format' to 'Scf' when uploading scf files", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0025_upload_file( self ): - """Test uploading 4.bed.zip, manually setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 4.bed.zip, manually setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '4.bed.zip', ftype='bed' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) - self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0030_upload_file( self ): - """Test uploading 4.bed.zip, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 4.bed.zip, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '4.bed.zip' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) - self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0035_upload_file( self ): - """Test uploading 1.sam NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.sam NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.sam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.sam', hid=str( hda.hid ) ) - self.check_history_for_string( "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "peek", "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0040_upload_file( self ): - """Test uploading 1.sff, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.sff, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.sff' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.sff', hid=str( hda.hid ) ) - self.check_history_for_string( 'format: <span class="sff">sff' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "misc_info", "sff", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0045_upload_file( self ): - """Test uploading 454Score.pdf, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 454Score.pdf, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '454Score.pdf' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( "1: 454Score.pdf</span>" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "name", "454Score.pdf" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0050_upload_file( self ): - """Test uploading 454Score.png, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 454Score.png, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '454Score.png' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( "454Score.png" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "name", "454Score.png" ) + + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0055_upload_file( self ): - """Test uploading lped composite datatype file, manually setting the file format""" + """ + Test uploading lped composite datatype file, manually setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + # lped data types include a ped_file and a map_file ( which is binary ) self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing @@ -138,13 +217,18 @@ # We'll test against the resulting ped file and map file for correctness self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' ) self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) - self.check_history_for_string( "rgenetics" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "metadata_base_name", "rgenetics", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0056_upload_file( self ): - """Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped)""" + """ + Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped) + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + # lped data types include a ped_file and a map_file ( which is binary ) self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing @@ -153,15 +237,25 @@ # We'll test against the resulting ped file and map file for correctness self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' ) self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) - self.check_history_for_string( "rgenetics" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "metadata_base_name", "rgenetics", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0060_upload_file( self ): - """Test uploading pbed composite datatype file, manually setting the file format""" + """ + Test uploading pbed composite datatype file, manually setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + # pbed data types include a bim_file, a bed_file and a fam_file - self.upload_file( None, ftype='pbed', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'bim_file', 'value':'tinywga.bim' }, { 'name':'bed_file', 'value':'tinywga.bed'}, { 'name':'fam_file', 'value':'tinywga.fam' } ] ) + self.upload_file( None, ftype='pbed', + metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], + composite_data = [ + { 'name':'bim_file', 'value':'tinywga.bim' }, + { 'name':'bed_file', 'value':'tinywga.bed' }, + { 'name':'fam_file', 'value':'tinywga.fam' } ]) # Get the latest hid for testing hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" @@ -169,280 +263,373 @@ self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' ) self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' ) self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' ) - self.check_history_for_string( "rgenetics" ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "metadata_base_name", "rgenetics", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0065_upload_file( self ): - """Test uploading asian_chars_1.txt, NOT setting the file format""" + """ + Test uploading asian_chars_1.txt, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( 'asian_chars_1.txt' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) ) - self.check_history_for_string( 'uploaded multi-byte char file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "misc_info", "uploaded multi-byte char file", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0070_upload_file( self ): - """Test uploading 2gen.fastq, NOT setting the file format""" + """ + Test uploading 2gen.fastq, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '2gen.fastq' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '2gen.fastq', hid=str( hda.hid ) ) - self.check_history_for_string( '2gen.fastq format: <span class="fastq">fastq</span>, database: ? Info: uploaded fastq file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fastq" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0075_upload_file( self ): - """Test uploading 1.wig, NOT setting the file format""" + """ + Test uploading 1.wig, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.wig' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.wig', hid=str( hda.hid ) ) - self.check_history_for_string( '1.wig format: <span class="wig">wig</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "wig" ) 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( id=self.security.encode_id( history.id ) ) + def test_0080_upload_file( self ): - """Test uploading 1.tabular, NOT setting the file format""" + """ + Test uploading 1.tabular, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.tabular' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.tabular', hid=str( hda.hid ) ) - self.check_history_for_string( '1.tabular format: <span class="tabular">tabular</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "tabular" ) 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( id=self.security.encode_id( history.id ) ) + def test_0085_upload_file( self ): - """Test uploading qualscores.qualsolid, NOT setting the file format""" + """ + Test uploading qualscores.qualsolid, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( 'qualscores.qualsolid' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) ) - self.check_history_for_string( '48 lines format: <span class="qualsolid">qualsolid</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qualsolid" ) self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0090_upload_file( self ): - """Test uploading qualscores.qual454, NOT setting the file format""" + """ + Test uploading qualscores.qual454, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( 'qualscores.qual454' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) ) - self.check_history_for_string( '49 lines format: <span class="qual454">qual454</span>, database: ?' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qual454" ) self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0095_upload_file( self ): - """Test uploading 3.maf, NOT setting the file format""" + """ + Test uploading 3.maf, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '3.maf' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '3.maf', hid=str( hda.hid ) ) - self.check_history_for_string( '3.maf format: <span class="maf">maf</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "maf" ) self.check_metadata_for_string( 'value="3.maf" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="interval">Convert MAF to Genomic Intervals <option value="fasta">Convert MAF to Fasta' ) self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0100_upload_file( self ): - """Test uploading 1.lav, NOT setting the file format""" + """ + Test uploading 1.lav, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.lav' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.lav', hid=str( hda.hid ) ) - self.check_history_for_string( '1.lav format: <span class="lav">lav</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "lav" ) 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( id=self.security.encode_id( history.id ) ) + def test_0105_upload_file( self ): - """Test uploading 1.interval, NOT setting the file format""" + """ + Test uploading 1.interval, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.interval' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.interval', hid=str( hda.hid ) ) - self.check_history_for_string( '1.interval format: <span class="interval">interval</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "interval" ) 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">Convert Genomic Intervals To BED' ) self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0110_upload_file( self ): - """Test uploading 5.gff3, NOT setting the file format""" + """ + Test uploading 5.gff3, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '5.gff3' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '5.gff3', hid=str( hda.hid ) ) - self.check_history_for_string( '5.gff3 format: <span class="gff3">gff3</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff3" ) self.check_metadata_for_string( 'value="5.gff3" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0115_upload_file( self ): - """Test uploading html_file.txt, NOT setting the file format""" + """ + Test uploading html_file.txt, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( 'html_file.txt' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( 'The uploaded file contains inappropriate content' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), + "misc_info", "The uploaded file contains inappropriate HTML content", use_string_contains=True ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0120_upload_file( self ): - """Test uploading 5.gff, NOT setting the file format""" - # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 5.gff, NOT setting the file format + + Test sniffer for gff. + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '5.gff' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '5.gff', hid=str( hda.hid ) ) - self.check_history_for_string( '5.gff format: <span class="gff">gff</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff" ) self.check_metadata_for_string( 'value="5.gff" value="?"' ) self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0125_upload_file( self ): - """Test uploading 1.fasta, NOT setting the file format""" + """ + Test uploading 1.fasta, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.fasta' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.fasta', hid=str( hda.hid ) ) - self.check_history_for_string( '1.fasta format: <span class="fasta">fasta</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fasta" ) self.check_metadata_for_string( 'value="1.fasta" value="?" Change data type selected value="fasta" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0130_upload_file( self ): - """Test uploading 1.customtrack, NOT setting the file format""" + """ + Test uploading 1.customtrack, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.customtrack' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.customtrack', hid=str( hda.hid ) ) - self.check_history_for_string( '1.customtrack format: <span class="customtrack">customtrack</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "customtrack" ) self.check_metadata_for_string( 'value="1.customtrack" value="?" Change data type selected value="customtrack" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0135_upload_file( self ): - """Test uploading shrimp_cs_test1.csfasta, NOT setting the file format""" + """ + Test uploading shrimp_cs_test1.csfasta, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( 'shrimp_cs_test1.csfasta' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) ) - self.check_history_for_string( '2,500 sequences format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "csfasta" ) self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="?" Change data type value="csfasta" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0145_upload_file( self ): - """Test uploading 1.axt, NOT setting the file format""" + """ + Test uploading 1.axt, NOT setting the file format + """ # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.axt' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.axt', hid=str( hda.hid ) ) - self.check_history_for_string( '1.axt format: <span class="axt">axt</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "axt" ) self.check_metadata_for_string( 'value="1.axt" value="?" Change data type selected value="axt" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0150_upload_file( self ): - """Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.bam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ), attributes={ 'ftype' : 'bam' } ) - self.check_history_for_string( '<span class="bam">bam</span>' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" ) # Make sure the Bam index was created assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0155_upload_file( self ): - """Test uploading 3unsorted.bam, which is an unsorted Bam file, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 3unsorted.bam, which is an unsorted Bam file, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '3unsorted.bam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" # Since 3unsorted.bam is not sorted, we cannot verify dataset correctness since the uploaded # dataset will be sorted. However, the check below to see if the index was created is # sufficient. - self.check_history_for_string( '<span class="bam">bam</span>' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" ) # Make sure the Bam index was created assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3unsorted.bam" + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0160_url_paste( self ): - """Test url paste behavior""" + """ + Test url paste behavior + """ # Logged in as admin_user - # Deleting the current history should have created a new history - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + history = self.create_fresh_history( admin_user ) + self.upload_url_paste( 'hello world' ) - self.check_history_for_string( 'Pasted Entry' ) - self.check_history_for_string( 'hello world' ) + self.check_history_for_exact_string( 'Pasted Entry' ) + self.check_history_for_exact_string( 'hello world' ) self.upload_url_paste( u'hello world' ) - self.check_history_for_string( 'Pasted Entry' ) - self.check_history_for_string( 'hello world' ) + self.check_history_for_exact_string( 'Pasted Entry' ) + self.check_history_for_exact_string( 'hello world' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0165_upload_file( self ): - """Test uploading 1.pileup, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.pileup, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.pileup' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) ) - self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: ? Info: uploaded file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "pileup" ) self.check_metadata_for_string( 'value="1.pileup" value="?" Change data type selected value="pileup" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0170_upload_file( self ): - """Test uploading 1.bigbed, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.bigbed, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.bigbed' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bigbed', hid=str( hda.hid ) ) - self.check_history_for_string( '1.bigbed</span> database: ? Info: uploaded bigbed file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigbed" ) self.check_metadata_for_string( 'value="1.bigbed" value="?" Change data type selected value="bigbed" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0175_upload_file( self ): - """Test uploading 1.bigwig, NOT setting the file format""" - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) + """ + Test uploading 1.bigwig, NOT setting the file format + """ + history = self.create_fresh_history( admin_user ) + self.upload_file( '1.bigwig' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bigwig', hid=str( hda.hid ) ) - self.check_history_for_string( '1.bigwig</span> database: ? Info: uploaded bigwig file' ) + self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigwig" ) self.check_metadata_for_string( 'value="1.bigwig" value="?" Change data type selected value="bigwig" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_9999_clean_up( self ): self.logout()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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