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Ease configuration and add documentation for using DTD syntax for destinations.

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Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly.
This commit is contained in:
John Chilton
2016-07-20 15:58:34 -04:00
parent ed48c6c28b
commit d87957e1a2
4 changed files with 236 additions and 223 deletions
Download Patch File Download Diff File Expand all files Collapse all files
config/job_conf.xml.sample_advanced
+12 -1
View File
@@ -379,9 +379,20 @@
<!-- Make sure to setup 3 real user parameters in galaxy.ini. -->
</destination>
<destination id="dynamic" runner="dynamic">
<!-- A destination that represents a method in the dynamic runner. -->
<!-- A destination that represents a method in the dynamic runner.
foo should be a Python function defined in any file in
lib/galaxy/jobs/rules.
-->
<param id="function">foo</param>
</destination>
<destination id="dtd_destination" runner="dynamic">
<!-- DTD is a special dynamic job destination type that builds up
rules given a YAML-based DSL (see config/tool_destinations.yml.sample
for the syntax).
-->
<param id="type">dtd</param>
</destination>
<destination id="load_balance" runner="dynamic">
<param id="type">choose_one</param>
<!-- Randomly assign jobs to various static destination ids -->
lib/galaxy/jobs/rules/dynamic_tool_destination.py → lib/galaxy/jobs/dynamic_tool_destination.py
View File
lib/galaxy/jobs/mapper.py
+2
View File
@@ -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,
)
test/unit/jobs/rules/test_dynamic_tool_destination.py
+222 -222
View File
@@ -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==========================