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Add some important documentation to some tool shed methods.

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This commit is contained in:
Greg Von Kuster
2013-05-24 15:14:08 -04:00
parent 822345449f
commit 7c4c69fd3e
2 changed files with 75 additions and 6 deletions
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lib/galaxy/webapps/tool_shed/util/container_util.py
+7 -6
View File
@@ -798,12 +798,13 @@ def build_repository_containers_for_tool_shed( trans, repository, changeset_revi
label='Valid tools' )
containers_dict[ 'valid_tools' ] = valid_tools_root_folder
# Tool test results container.
if tool_test_results:
# Only create and populate this folder if there are actual tool test results to display, since the
# display of the 'Test environment' folder by itself can be misleading.
if len( tool_test_results ) > 1:
folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested )
containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder
if tool_test_results and len( tool_test_results ) > 1:
# Only create and populate this folder if there are actual tool test results to display, since the display of the 'Test environment'
# folder by itself can be misleading. We check for more than a single entry in the tool_test_results dictionary because it may have
# only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", "installation_errors", "missing_test_components"
# "skipped_tests", "not_tested" or any other entry that may be added in the future.
folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested )
containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder
# Workflows container.
if metadata:
if 'workflows' in metadata:
lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+68
View File
@@ -51,6 +51,70 @@ def handle_command( app, tool_dependency, install_dir, cmd, return_output=False
return output.return_code
def handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ):
"""
This method works with with a combination of three tool dependency definition tag sets, which are defined in the tool_dependencies.xml file in the
order discussed here. The example for this discussion is the tool_dependencies.xml file contained in the osra repository, which is available at:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/osra
The first tag set defines a complex repository dependency like this. This tag set ensures that changeset revision XXX of the repository named
package_graphicsmagick_1_3 owned by YYY in the tool shed ZZZ has been previously installed.
<tool_dependency>
<package name="graphicsmagick" version="1.3.18">
<repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" prior_installation_required="True" toolshed="ZZZ" />
</package>
...
* By the way, there is an env.sh file associated with version 1.3.18 of the graphicsmagick package which looks something like this (we'll reference
this file later in this discussion.
----
GRAPHICSMAGICK_ROOT_DIR=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick;
export GRAPHICSMAGICK_ROOT_DIR
----
The second tag set defines a specific package dependency that has been previously installed (guaranteed by the tag set discussed above) and compiled,
where the compiled dependency is needed by the tool dependency currently being installed (osra version 2.0.0 in this case) and complied in order for
it's installation and compilation to succeed. This tag set is contained within the <package name="osra" version="2.0.0"> tag set, which implies that
version 2.0.0 of the osra package requires version 1.3.18 of the graphicsmagick package in order to successfully compile. When this tag set is handled,
one of the effects is that the env.sh file associated with graphicsmagick version 1.3.18 is "sourced", which undoubtedly sets or alters certain environment
variables (e.g. PATH, PYTHONPATH, etc).
<!-- populate the environment variables from the dependent repositories -->
<action type="set_environment_for_install">
<repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" toolshed="ZZZ">
<package name="graphicsmagick" version="1.3.18" />
</repository>
</action>
The third tag set enables discovery of the same required package dependency discussed above for correctly compiling the osra version 2.0.0 package, but
in this case the package can be discovered at tool execution time. Using the $ENV[] option as shown in this example, the value of the environment
variable named GRAPHICSMAGICK_ROOT_DIR (which was set in the environment using the second tag set described above) will be used to automatically alter
the env.sh file associated with the osra version 2.0.0 tool dependency when it is installed into Galaxy. * Refer to where we discussed the env.sh file
for version 1.3.18 of the graphicsmagick package above.
<action type="set_environment">
<environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[$GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable>
<environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
<!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
<environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
</action>
The above tag will produce an env.sh file for version 2.0.0 of the osra package when it it installed into Galaxy that looks something like this. Notice
that the path to the gmagick binary is included here since it expands the defined $ENV[$GRAPHICSMAGICK_ROOT_DIR] value in the above tag set.
----
LD_LIBRARY_PATH=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick/lib/:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH
LD_LIBRARY_PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/potrace/build/lib/:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH
PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/bin:$PATH;
export PATH
OSRA_DATA_FILES=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/share;
export OSRA_DATA_FILES
----
"""
env_var_value = env_var_dict[ 'value' ]
if '$ENV[' in env_var_value and ']' in env_var_value:
# Pull out the name of the environment variable to populate.
@@ -107,6 +171,8 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
filtered_actions = actions[ 1: ]
url = action_dict[ 'url' ]
if 'target_filename' in action_dict:
# Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this
# attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction.
downloaded_filename = action_dict[ 'target_filename' ]
else:
downloaded_filename = os.path.split( url )[ -1 ]
@@ -137,6 +203,8 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
filtered_actions = actions[ 1: ]
url = action_dict[ 'url' ]
if action_dict[ 'target_filename' ]:
# Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this
# attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction.
filename = action_dict[ 'target_filename' ]
else:
filename = url.split( '/' )[ -1 ]