diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced index cf9cab73d80..b3a1cf5c449 100644 --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -379,9 +379,20 @@ - + foo + + + dtd + choose_one diff --git a/lib/galaxy/jobs/rules/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py similarity index 100% rename from lib/galaxy/jobs/rules/dynamic_tool_destination.py rename to lib/galaxy/jobs/dynamic_tool_destination.py diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py index 5ccdaa51a29..ba2866b6fec 100644 --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -5,6 +5,7 @@ import sys import galaxy.jobs.rules from galaxy.jobs import stock_rules +from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination from .rule_helper import RuleHelper log = logging.getLogger( __name__ ) @@ -33,6 +34,7 @@ STOCK_RULES = dict( choose_one=stock_rules.choose_one, burst=stock_rules.burst, docker_dispatch=stock_rules.docker_dispatch, + dtd=map_tool_to_destination, ) diff --git a/test/unit/jobs/rules/test_dynamic_tool_destination.py b/test/unit/jobs/rules/test_dynamic_tool_destination.py index 34686a8517e..8cbbefce773 100644 --- a/test/unit/jobs/rules/test_dynamic_tool_destination.py +++ b/test/unit/jobs/rules/test_dynamic_tool_destination.py @@ -5,9 +5,9 @@ sys.path.append("") import unittest import mockGalaxy as mg import ymltests as yt -import galaxy.jobs.rules.dynamic_tool_destination as dt +import galaxy.jobs.dynamic_tool_destination as dt -from galaxy.jobs.rules.dynamic_tool_destination import map_tool_to_destination +from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination from testfixtures import log_capture from galaxy.jobs.mapper import JobMappingException @@ -99,11 +99,11 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertRaises(JobMappingException, map_tool_to_destination, runJob, theApp, vanillaTool, "user@email.com", True, broken_default_dest_path) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB') ) @log_capture() @@ -112,16 +112,16 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, priority_path) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1') ) @log_capture() @@ -130,14 +130,14 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, priority_path) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0') ) @log_capture() @@ -146,16 +146,16 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, priority_path) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1') ) @log_capture() @@ -166,18 +166,18 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'Destination1_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1_high'.") ) @log_capture() @@ -188,14 +188,14 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'waffles_default_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'waffles_default'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'waffles_default_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'waffles_default'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'waffles_default_high'.") ) @log_capture() @@ -206,12 +206,12 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'Destination6_med' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6_med'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6_med'.") ) @log_capture() @@ -222,12 +222,12 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'waffles_default_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'waffles_default'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'waffles_default_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'waffles_default'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'waffles_default_high'.") ) @log_capture() @@ -238,14 +238,14 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'waffles_default_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'waffles_default'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'waffles_default_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'waffles_default'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'waffles_default_high'.") ) @log_capture() @@ -256,16 +256,16 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'Destination4_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.") ) @log_capture() @@ -276,16 +276,16 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( priority_job, 'Destination4_high' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.") ) @log_capture() @@ -294,7 +294,7 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( job, 'Destination1' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_no_verbose' with 'Destination1'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_no_verbose' with 'Destination1'.") ) @log_capture() @@ -303,7 +303,7 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( job, 'special_cluster' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'special_cluster'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'special_cluster'."), ) @log_capture() @@ -312,7 +312,7 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEquals( job, 'lame_cluster' ) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.") ) @@ -326,11 +326,11 @@ class TestDynamicToolDestination(unittest.TestCase): def test_bad_nice(self, l): dt.parse_yaml(path=yt.ivYMLTest11, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running config validation..."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "nice_value goes from -20 to 20; rule 1 in 'spades' has a nice_value of '-21'. Setting nice_value to 0."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() @@ -341,337 +341,337 @@ class TestDynamicToolDestination(unittest.TestCase): def test_no_tool_name(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest3, test=True), yt.iv3dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_rule_type(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest4, test=True), yt.ivDict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_rule_lower_bound(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest51, test=True), yt.ivDict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_rule_upper_bound(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest52, test=True), yt.ivDict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_rule_arg(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest53, test=True), yt.ivDict53) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_bad_rule_type(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest6, test=True), yt.ivDict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_err_msg(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest91, test=True), yt.iv91dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_no_default_dest(self, l): dt.parse_yaml(path=yt.ivYMLTest7, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_invalid_category(self, l): dt.parse_yaml(path=yt.ivYMLTest8, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_arguments_no_err_msg(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest12, test=True), yt.iv12dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_arguments_no_args(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest131, test=True), yt.iv131dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_arguments_no_arg(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest132, test=True), yt.iv132dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_multiple_jobs(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest133, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'.") ) @log_capture() def test_return_rule_for_multiple_jobs(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest133, test=True), yt.iv133dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_no_destination(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest134, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'.") ) @log_capture() def test_return_rule_for_no_destination(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest134, test=True), yt.iv134dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_rule_for_reversed_bounds(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest135, test=True), yt.iv135dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_missing_tool_fields(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest136, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!") ) @log_capture() def test_return_rule_for_missing_tool_fields(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest136, test=True), yt.iv136dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_blank_tool(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest137, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!") ) @log_capture() def test_return_rule_for_blank_tool(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest137, test=True), yt.iv137dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_malformed_users(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest138, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!") ) @log_capture() def test_return_rule_for_malformed_users(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest138, test=True), yt.iv138dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_no_users(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!") ) @log_capture() def test_return_rule_for_no_users(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest139, test=True), yt.iv139dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_malformed_user_email(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!") ) @log_capture() def test_return_rule_for_malformed_user_email(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest140, test=True), yt.iv140dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_empty_users(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!") ) @log_capture() def test_return_rule_for_empty_users(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest141, test=True), yt.iv141dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_bad_num_input_datasets_bounds(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest142, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'smalt'.") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'smalt'.") ) @log_capture() def test_return_rule_for_bad_num_input_datasets_bound(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest142, test=True), yt.iv142dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_return_bool_for_worse_num_input_datasets_bounds(self, l): self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest143, test=True, return_bool=True)) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!") + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!") ) @log_capture() def test_return_rule_for_worse_num_input_datasets_bound(self, l): self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest143, test=True), yt.iv143dict) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_priority_default_destination_without_med_priority_destination(self, l): dt.parse_yaml(path=yt.ivYMLTest144, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No default 'med' priority destination!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default 'med' priority destination!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_priority_default_destination_with_invalid_priority_destination(self, l): dt.parse_yaml(path=yt.ivYMLTest145, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Invalid default priority destination 'mine' found in config!"), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default priority destination 'mine' found in config!"), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_tool_without_med_priority_destination(self, l): dt.parse_yaml(path=yt.ivYMLTest146, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "No 'med' priority destination for rule 1 in 'smalt'. Ignoring..."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No 'med' priority destination for rule 1 in 'smalt'. Ignoring..."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_tool_with_invalid_priority_destination(self, l): dt.parse_yaml(path=yt.ivYMLTest147, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "Invalid priority destination 'mine' for rule 1 in 'smalt'. Ignoring..."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority destination 'mine' for rule 1 in 'smalt'. Ignoring..."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) @log_capture() def test_users_with_invalid_priority(self, l): dt.parse_yaml(path=yt.ivYMLTest148, test=True) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', "User 'user@email.com', priority is not valid! Must be either low, med, or high."), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "User 'user@email.com', priority is not valid! Must be either low, med, or high."), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.') ) # ================================Valid yaml files============================== @@ -689,20 +689,20 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertTrue(dt.parse_yaml(yt.vYMLTest7, test=True, return_bool=True)) self.assertEqual(dt.parse_yaml(yt.vYMLTest7, test=True), yt.vdictTest7_yml) l.check( - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), - ('galaxy.jobs.rules.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'), + ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'), ) # ================================Testing str_to_bytes==========================