1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3bdd01eda31d/
Changeset: 3bdd01eda31d
User: greg
Date: 2014-05-17 16:10:23
Summary: I meant to make this file a .sample file.
Affected #: 3 files
diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
--- a/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<user>
- <email>admin(a)test.org</email>
- <password>testuser</password>
- <username>admin</username>
-</user>
diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
--- /dev/null
+++ b/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<!--
+If you are planning to use the export / import repository capsule process for development in your
+local Tool Shed, make sure to change the following to be the account you'll use for development.
+When you export your developed repositories for importing into another Tool Shed, this account
+must be available in that Tool Shed..
+-->
+<user>
+ <email>admin(a)test.org</email>
+ <password>testuser</password>
+ <username>admin</username>
+</user>
diff -r 2e6e51179f7177b743bd970095be7e261ae62700 -r 3bdd01eda31d3f9b195b11982b31c58bc37254e8 run_tool_shed.sh
--- a/run_tool_shed.sh
+++ b/run_tool_shed.sh
@@ -15,6 +15,7 @@
tool_sheds_conf.xml.sample
openid_conf.xml.sample
universe_wsgi.ini.sample
+ lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
tool-data/shared/ncbi/builds.txt.sample
tool-data/shared/ensembl/builds.txt.sample
tool-data/shared/ucsc/builds.txt.sample
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9fbe27547931/
Changeset: 9fbe27547931
User: dan
Date: 2014-05-16 21:13:29
Summary: Fix for checking dataset access permissions when reruning a tool by job_id.
Affected #: 1 file
diff -r 1b06ee57191c56cd50c0248239f876f4c5311831 -r 9fbe2754793109a1680239131b5507614d431870 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -118,6 +118,11 @@
job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
except:
error( "Invalid value for 'job_id' parameter" )
+ if not trans.user_is_admin():
+ for data_assoc in job.output_datasets:
+ #only allow rerunning if user is allowed access to the dataset.
+ if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data_assoc.dataset.dataset ):
+ error( "You are not allowed to rerun this job" )
param_error_text = "Failed to get parameters for job id %d " % job_id
else:
if not id:
@@ -130,7 +135,6 @@
id = trans.security.decode_id( id )
except:
error( "Invalid value for 'id' parameter" )
-
# Get the dataset object
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id )
#only allow rerunning if user is allowed access to the dataset.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1b06ee57191c/
Changeset: 1b06ee57191c
User: jmchilton
Date: 2014-05-16 17:24:54
Summary: A bit more LWR client logging.
Affected #: 1 file
diff -r 2f592b5f1883520d62fc6ceab6a1657edd188294 -r 1b06ee57191c56cd50c0248239f876f4c5311831 lib/galaxy/jobs/runners/lwr_client/client.py
--- a/lib/galaxy/jobs/runners/lwr_client/client.py
+++ b/lib/galaxy/jobs/runners/lwr_client/client.py
@@ -313,7 +313,9 @@
# before queueing.
setup_params = _setup_params_from_job_config(job_config)
launch_params["setup_params"] = setup_params
- return self.client_manager.exchange.publish("setup", launch_params)
+ response = self.client_manager.exchange.publish("setup", launch_params)
+ log.info("Job published to setup message queue.")
+ return response
def clean(self):
del self.client_manager.status_cache[self.job_id]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2f592b5f1883/
Changeset: 2f592b5f1883
User: jmchilton
Date: 2014-05-16 17:14:52
Summary: Update LWR client and behavior through LWR changeset 8ea7265.
LWR now informed of job submission failures in MQ mode so jobs shouldn't sit in queued state forever if job fails to queue remotely. Also small fixes and more logging.
Affected #: 4 files
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr.py
--- a/lib/galaxy/jobs/runners/lwr.py
+++ b/lib/galaxy/jobs/runners/lwr.py
@@ -28,6 +28,7 @@
NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "LWR misconfiguration - LWR client configured to set metadata remotely, but remote LWR isn't properly configured with a galaxy_home directory."
NO_REMOTE_DATATYPES_CONFIG = "LWR client is configured to use remote datatypes configuration when setting metadata externally, but LWR is not configured with this information. Defaulting to datatypes_conf.xml."
+GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server."
# Is there a good way to infer some default for this? Can only use
# url_for from web threads. https://gist.github.com/jmchilton/9098762
@@ -266,7 +267,7 @@
if failed:
job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True)
except Exception:
- message = "Failed to communicate with remote job server."
+ message = GENERIC_REMOTE_ERROR
job_wrapper.fail( message, exception=True )
log.exception("failure finishing job %d" % job_wrapper.job_id)
return
@@ -284,7 +285,7 @@
Seperated out so we can use the worker threads for it.
"""
self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) )
- job_state.job_wrapper.fail( job_state.fail_message )
+ job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) )
def check_pid( self, pid ):
try:
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/client.py
--- a/lib/galaxy/jobs/runners/lwr_client/client.py
+++ b/lib/galaxy/jobs/runners/lwr_client/client.py
@@ -300,7 +300,7 @@
launch_params = dict(command_line=command_line, job_id=self.job_id)
submit_params_dict = submit_params(self.destination_params)
if submit_params_dict:
- launch_params['params'] = submit_params_dict
+ launch_params['submit_params'] = submit_params_dict
if dependencies_description:
launch_params['dependencies_description'] = dependencies_description.to_dict()
if env:
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/manager.py
--- a/lib/galaxy/jobs/runners/lwr_client/manager.py
+++ b/lib/galaxy/jobs/runners/lwr_client/manager.py
@@ -97,6 +97,7 @@
try:
if "job_id" in body:
self.status_cache[body["job_id"]] = body
+ log.debug("Handling asynchronous status update from remote LWR.")
callback(body)
except Exception:
log.exception("Failure processing job status update message.")
@@ -104,6 +105,7 @@
def run():
self.exchange.consume("status_update", callback_wrapper, check=self)
+ log.debug("Leaving LWR client status update thread, no additional LWR updates will be processed.")
thread = threading.Thread(
name="lwr_client_%s_status_update_callback" % self.manager_name,
diff -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad -r 2f592b5f1883520d62fc6ceab6a1657edd188294 lib/galaxy/jobs/runners/lwr_client/util.py
--- a/lib/galaxy/jobs/runners/lwr_client/util.py
+++ b/lib/galaxy/jobs/runners/lwr_client/util.py
@@ -62,6 +62,7 @@
contents.append(name)
return contents
+
def parse_amqp_connect_ssl_params(params):
ssl = None
rval = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/26b9fe985ee7/
Changeset: 26b9fe985ee7
User: greg
Date: 2014-05-16 15:48:50
Summary: Fix query filters for various Tool Shed "latest revision" grids by making sure revisions have actually been tested by the install and test framework, and not sure prepared the framework's preparation scripts.
Affected #: 1 file
diff -r 7e95105c466051432e5c47ff977826a19758b867 -r 26b9fe985ee718ddf25ee2e9e9d5096e8b315fad lib/tool_shed/grids/repository_grids.py
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -1940,8 +1940,8 @@
of type repository_suite_definition and tool_dependency_definition.
"""
repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository )
- if repository_metadata \
- and repository_metadata.tool_test_results is not None \
+ if repository_metadata is not None \
+ and has_been_tested( repository_metadata ) \
and not repository_metadata.missing_test_components \
and not repository_metadata.tools_functionally_correct \
and not repository_metadata.test_install_error:
@@ -1957,7 +1957,9 @@
tool_dependency_definition.
"""
repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository )
- if repository_metadata and repository_metadata.missing_test_components:
+ if repository_metadata is not None \
+ and has_been_tested( repository_metadata ) \
+ and repository_metadata.missing_test_components:
return repository_metadata.changeset_revision
return None
@@ -1968,9 +1970,10 @@
and tool_dependency_definition.
"""
repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository )
- if repository_metadata is not None and \
- not repository_metadata.missing_test_components and \
- repository_metadata.tools_functionally_correct:
+ if repository_metadata is not None \
+ and has_been_tested( repository_metadata ) \
+ and not repository_metadata.missing_test_components \
+ and repository_metadata.tools_functionally_correct:
return repository_metadata.changeset_revision
return None
@@ -1993,7 +1996,9 @@
"""
repository_metadata = get_latest_downloadable_repository_metadata_if_it_has_test_install_errors( trans, repository )
# Filter further by eliminating repositories that are missing test components.
- if repository_metadata is not None and not repository_metadata.missing_test_components:
+ if repository_metadata is not None \
+ and has_been_tested( repository_metadata ) \
+ and not repository_metadata.missing_test_components:
return repository_metadata.changeset_revision
return None
@@ -2067,7 +2072,9 @@
well as types repository_suite_definition and tool_dependency_definition.
"""
repository_metadata = get_latest_downloadable_repository_metadata( trans, repository )
- if repository_metadata is not None and repository_metadata.test_install_error:
+ if repository_metadata is not None \
+ and has_been_tested( repository_metadata ) \
+ and repository_metadata.test_install_error:
return repository_metadata
return None
@@ -2104,3 +2111,25 @@
if metadata is not None and 'invalid_tools' in metadata:
return repository_metadata
return None
+
+def has_been_tested( repository_metadata ):
+ """
+ Return True if the received repository_metadata record'd tool_test_results column was populated by
+ the Tool Shed's install and test framework.
+ """
+ tool_test_results = repository_metadata.tool_test_results
+ if tool_test_results is None:
+ return False
+ # The install and test framework's preparation scripts will populate the tool_test_results column
+ # with something like this:
+ # [{"test_environment":
+ # {"time_tested": "2014-05-15 16:15:18",
+ # "tool_shed_database_version": 22,
+ # "tool_shed_mercurial_version": "2.2.3",
+ # "tool_shed_revision": "13459:9a1415f8108f"}
+ # }]
+ tool_test_results = listify( tool_test_results )
+ for test_results_dict in tool_test_results:
+ if len( test_results_dict ) > 1:
+ return True
+ return False
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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