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commit/galaxy-central: greg: Fix for the execute_step() method in the SetEnvironment class.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/203623b93150/ Changeset: 203623b93150 User: greg Date: 2014-04-24 21:11:43 Summary: Fix for the execute_step() method in the SetEnvironment class. Affected #: 1 file diff -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 -r 203623b931507dcd182e2521911ab036021faf61 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -450,14 +450,20 @@ env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = self.handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) + env_var_dict = self.handle_environment_variables( app=app, + install_environment=install_environment, + tool_dependency=tool_dependency, + install_dir=install_dir, + env_var_dict=env_var_dict, + set_prior_environment_commands=cmds ) env_file_builder.append_line( **env_var_dict ) # The caller should check the status of the returned tool_dependency since return_code is not # returned by this function. return_code = env_file_builder.return_code return tool_dependency, None, None - def handle_environment_variables( self, app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): + def handle_environment_variables( self, app, install_environment, 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 @@ -539,7 +545,6 @@ set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - install_environment = recipe_manager.InstallEnvironment() command_return = install_environment.handle_command( app, tool_dependency, install_dir, command, return_output=True ) # And extract anything labeled with the name of the environment variable we're populating here. if '%s: ' % inherited_env_var_name in command_return: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix tool shed unit tests I broke with my last commit.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99056011d2db/ Changeset: 99056011d2db User: greg Date: 2014-04-24 19:45:04 Summary: Fix tool shed unit tests I broke with my last commit. Affected #: 2 files diff -r ffafb6350791453b31c841e5462314bcd04ffa88 -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 test/unit/tool_shed_unit_tests/test_fabric_util.py --- a/test/unit/tool_shed_unit_tests/test_fabric_util.py +++ b/test/unit/tool_shed_unit_tests/test_fabric_util.py @@ -1,6 +1,5 @@ from contextlib import contextmanager -from tool_shed.galaxy_install.recipe.recipe_manager import EnvFileBuilder -from tool_shed.galaxy_install.tool_dependencies import fabric_util +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder def test_env_file_builder(): @@ -10,10 +9,10 @@ mock_return = dict(value=0) def mock_file_append( text, file_path, **kwds ): - added_lines.append(text) - return mock_return["value"] + added_lines.append( text ) + return mock_return[ "value" ] - with __mock_fabric_util_method("file_append", mock_file_append): + with __mock_env_file_builder_method( env_file_builder, "file_append", mock_file_append ): env_file_builder.append_line( name="PATH", action="prepend_to", value="/usr/bin/local/R" ) assert added_lines == [ "PATH=/usr/bin/local/R:$PATH; export PATH" ] assert env_file_builder.return_code == 0 @@ -37,10 +36,10 @@ ## Poor man's mocking. Need to get a real mocking library as real Galaxy development ## dependnecy. @contextmanager -def __mock_fabric_util_method(name, mock_method): - real_method = getattr(fabric_util, name) +def __mock_env_file_builder_method( env_file_builder, name, mock_method ): + real_method = getattr( env_file_builder, name ) try: - setattr(fabric_util, name, mock_method) + setattr( env_file_builder, name, mock_method ) yield finally: - setattr(fabric_util, name, real_method) + setattr( env_file_builder, name, real_method ) diff -r ffafb6350791453b31c841e5462314bcd04ffa88 -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 test/unit/tool_shed_unit_tests/test_td_common_util.py --- a/test/unit/tool_shed_unit_tests/test_td_common_util.py +++ b/test/unit/tool_shed_unit_tests/test_td_common_util.py @@ -4,7 +4,8 @@ from tool_shed.galaxy_install.tool_dependencies import fabric_util from tool_shed.galaxy_install.tool_dependencies import td_common_util -from tool_shed.galaxy_install.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder + TEST_DEPENDENCIES_DIR = "/opt/galaxy/dependencies" TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Get tool dependency status from the install model.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ffafb6350791/ Changeset: ffafb6350791 User: davebgx Date: 2014-04-24 17:24:24 Summary: Get tool dependency status from the install model. Affected #: 1 file diff -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b -r ffafb6350791453b31c841e5462314bcd04ffa88 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -86,7 +86,7 @@ install_dir=install_dir, current_dir=current_dir, initial_download=False ) - if tool_dependency.status in [ app.model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ app.install_model.ToolDependency.installation_status.ERROR ]: # If the tool_dependency status is in an error state, return it with no additional # processing. return tool_dependency Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Update tool shed twilltestcase methods to reflect changes in the base twilltestcase's visit_url method. Fix functional tests for the tool shed. Update test tool dependencies to not actually compile EMBOSS and freebayes.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf9cd1027e2a/ Changeset: cf9cd1027e2a User: davebgx Date: 2014-04-24 17:23:03 Summary: Update tool shed twilltestcase methods to reflect changes in the base twilltestcase's visit_url method. Fix functional tests for the tool shed. Update test tool dependencies to not actually compile EMBOSS and freebayes. Affected #: 4 files diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -284,30 +284,6 @@ category = test_db_util.get_category_by_name( kwd[ 'name' ] ) return category - def create_checkbox_query_string( self, field_name, value ): - ''' - From galaxy.web.form_builder.CheckboxField: - The hidden field is necessary because if the check box is not checked on the form, it will - not be included in the request params. The hidden field ensure that this will happen. When - parsing the request, the value 'true' in the hidden field actually means it is NOT checked. - See the is_checked() method below. The prefix is necessary in each case to ensure functional - correctness when the param is inside a conditional. - - This may look strange upon initial inspection, but see the comments in the get_html() method - above for clarification. Basically, if value is not True, then it will always be a list with - 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not - checked, then value will be only the hidden field. - - The create_checkbox_query_string method emulates the described behavior with URL query parameters. - This is currently necessary because twill does not correctly parse certain forms, so the test - method has to visit the intended form target "manually". - ''' - field_value = str( value ).lower() - if value: - return '%s=%s&%s=%s' % ( field_name, field_value, field_name, field_value ) - else: - return '%s=%s' % ( field_name, field_value ) - def create_repository_dependency( self, repository=None, repository_tuples=[], @@ -547,7 +523,8 @@ def enable_email_alerts( self, repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) - self.visit_url( '/repository/browse_repositories?operation=Receive+email+alerts&id=%s' % repository_id ) + params = dict( operation='Receive email alerts', id=repository_id ) + self.visit_url( '/repository/browse_repositories' ) self.check_for_strings( strings_displayed ) def escape_html( self, string, unescape=False ): @@ -816,15 +793,19 @@ strings_not_displayed = [] self.visit_url( '/admin/roles' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - url = '/admin/roles?operation=manage+users+and+groups&id=%s' % self.security.encode_id( role.id ) + params = dict( operation='manage users and groups', id=self.security.encode_id( role.id ) ) + url = '/admin/roles' self.visit_url( url ) strings_displayed = [ common.test_user_1_email, common.test_user_2_email ] self.check_for_strings( strings_displayed, strings_not_displayed ) # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript # attached to the role selection form. Visit the action url directly with the necessary parameters. - url = '/admin/manage_users_and_groups_for_role?id=%s&in_users=%d&operation=manage+users+and+groups&role_members_edit_button=Save' % \ - ( self.security.encode_id( role.id ), user.id ) - self.visit_url( url ) + params = dict( id=self.security.encode_id( role.id ), + in_users=user.id, + operation='manage users and groups', + role_members_edit_button='Save' ) + url = '/admin/manage_users_and_groups_for_role' + self.visit_url( url, params ) strings_displayed = [ "Role '%s' has been updated" % role.name ] self.check_for_strings( strings_displayed, strings_not_displayed ) @@ -1050,8 +1031,9 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def reactivate_repository( self, installed_repository ): - url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_repository.id ) - self.visit_galaxy_url( url ) + params = dict( operation='activate or reinstall', id=self.security.encode_id( installed_repository.id ) ) + url = '/admin_toolshed/browse_repositories' + self.visit_galaxy_url( url, params ) strings_displayed = [ installed_repository.name, 'repository has been activated' ] self.check_for_strings( strings_displayed, [] ) @@ -1068,12 +1050,12 @@ self.check_for_strings( strings_displayed, strings_not_displayed=[] ) # Build the url that will simulate a filled-out form being submitted. Due to a limitation in twill, the reselect_tool_panel_section # form doesn't get parsed correctly. - repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) - tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) - url = '/admin_toolshed/reinstall_repository?id=%s&%s&%s&no_changes=%s&new_tool_panel_section_label=%s' % \ - ( encoded_repository_id, repo_dependencies, tool_dependencies, str( no_changes ), new_tool_panel_section_label ) - self.visit_galaxy_url( url ) + params = dict( id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label ) + checkbox_params = dict( install_repository_dependencies=install_repository_dependencies, + install_tool_dependencies=install_tool_dependencies ) + url = '/admin_toolshed/reinstall_repository' + self.visit_galaxy_url( url, params=params, checkbox_params=checkbox_params ) # Manually initiate the install process, as with installing a repository. See comments in the # initiate_installation_process method for details. repository_ids = self.initiate_installation_process( install_tool_dependencies, @@ -1429,8 +1411,9 @@ for tool in installed_repository.metadata[ 'tools' ]: strings = list( strings_displayed ) strings.extend( [ tool[ 'id' ], tool[ 'description' ], tool[ 'version' ], tool[ 'guid' ], tool[ 'name' ] ] ) - url = '/admin_toolshed/view_tool_metadata?repository_id=%s&tool_id=%s' % ( repository_id, urllib.quote_plus( tool[ 'id' ] ) ) - self.visit_galaxy_url( url ) + params = dict( repository_id=repository_id, tool_id=tool[ 'id' ] ) + url = '/admin_toolshed/view_tool_metadata' + self.visit_galaxy_url( url, params ) self.check_for_strings( strings, strings_not_displayed ) def verify_unchanged_repository_metadata( self, repository ): @@ -1451,9 +1434,9 @@ self.visit_galaxy_url( url ) self.check_for_strings( strings, strings_not_displayed ) - def visit_galaxy_url( self, url ): + def visit_galaxy_url( self, url, params=None, checkbox_params=None ): url = '%s%s' % ( self.galaxy_url, url ) - self.visit_url( url ) + self.visit_url( url, params=params, checkbox_params=checkbox_params ) def wait_for_repository_installation( self, repository_ids ): final_states = [ galaxy_model.ToolShedRepository.installation_status.ERROR, diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -111,8 +111,9 @@ convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) strings_displayed=[ 'Handle repository dependencies', 'convert_chars_1087', self.get_repository_tip( convert_repository ) ] # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall. - url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) - self.visit_galaxy_url( url ) + params = dict( operation='activate or reinstall', id=self.security.encode_id( installed_column_repository.id ) ) + url = '/admin_toolshed/browse_repositories' + self.visit_galaxy_url( url, params ) self.check_for_strings( strings_displayed ) strings_not_displayed = [ 'column_maker_1087' ] - self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) \ No newline at end of file diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/test_data/emboss/emboss.tar Binary file test/tool_shed/test_data/emboss/emboss.tar has changed diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/test_data/freebayes/tool_dependencies.xml --- a/test/tool_shed/test_data/freebayes/tool_dependencies.xml +++ b/test/tool_shed/test_data/freebayes/tool_dependencies.xml @@ -3,13 +3,7 @@ <package name="freebayes" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8"><install version="1.0"><actions> - <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> + <action type="shell_command">echo "Success."</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> @@ -23,17 +17,7 @@ <package name="samtools" version="0.1.18"><install version="1.0"><actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="shell_command">echo "Success."</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Fix typo in step handler.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1cb12e876c6/ Changeset: f1cb12e876c6 User: davebgx Date: 2014-04-24 17:06:59 Summary: Fix typo in step handler. Affected #: 1 file diff -r 3b6e94371b8a8e996cc8e317de8cbfe45790b94e -r f1cb12e876c659c456c0b10f577494f79211b7f4 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -592,7 +592,7 @@ install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_downloa ): + def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ): # <action type="set_environment_for_install"> # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> # <package name="numpy" version="1.7.1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add simplejson back again until 'anyjson' changes are pushed through bioblend.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b6e94371b8a/ Changeset: 3b6e94371b8a User: dannon Date: 2014-04-24 17:03:23 Summary: Add simplejson back again until 'anyjson' changes are pushed through bioblend. Affected #: 1 file diff -r de54998e192b99bd70751d692969b508463e1805 -r 3b6e94371b8a8e996cc8e317de8cbfe45790b94e eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -61,6 +61,7 @@ pytz = 2013.9 requests = 2.2.1 Routes = 1.12.3 +simplejson = 2.1.1 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 SVGFig = 1.1.6 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be twe
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de54998e192b/ Changeset: de54998e192b User: greg Date: 2014-04-24 16:46:56 Summary: Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be tweaked if desired. Affected #: 11 files diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -1,765 +1,64 @@ -# For Python 2.5 -from __future__ import with_statement - import logging import os -import Queue -import shutil -import stat -import subprocess -import sys -import tempfile -import td_common_util -import threading -import time -import shlex -from contextlib import contextmanager -from galaxy.util import DATABASE_MAX_STRING_SIZE -from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY -from galaxy.util import shrink_string_by_size -from galaxy.util import unicodify -from galaxy.util.template import fill_template from galaxy import eggs -eggs.require( 'ssh' ) -eggs.require( 'paramiko' ) eggs.require( 'Fabric' ) -from fabric import state from fabric.api import env -from fabric.api import hide from fabric.api import lcd -from fabric.api import settings -from fabric.api import prefix -from fabric.operations import _AttributeString + +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import InstallEnvironment +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import RecipeManager log = logging.getLogger( __name__ ) -INSTALLATION_LOG = 'INSTALLATION.log' -VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' - - -class AsynchronousReader( threading.Thread ): - """ - A helper class to implement asynchronous reading of a stream in a separate thread. Read lines are pushed - onto a queue to be consumed in another thread. - """ - - def __init__( self, fd, queue ): - threading.Thread.__init__( self ) - self._fd = fd - self._queue = queue - self.lines = [] - - def run( self ): - """Read lines and put them on the queue.""" - thread_lock = threading.Lock() - thread_lock.acquire() - for line in iter( self._fd.readline, '' ): - stripped_line = line.rstrip() - self.lines.append( stripped_line ) - self._queue.put( stripped_line ) - thread_lock.release() - - def installation_complete( self ): - """Make sure there is more installation and compilation logging content expected.""" - return not self.is_alive() and self._queue.empty() - - -class EnvFileBuilder( object ): - - def __init__( self, install_dir ): - self.install_dir = install_dir - self.return_code = 0 - - def append_line( self, make_executable=True, **kwd ): - env_var_dict = dict( **kwd ) - env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) - return_code = file_append( env_entry, env_file, make_executable=make_executable ) - self.return_code = self.return_code or return_code - return self.return_code - - @staticmethod - def create_or_update_env_shell_file( install_dir, env_var_dict ): - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action in [ 'prepend_to', 'set_to', 'append_to' ]: - env_var_name = env_var_dict[ 'name' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) - elif env_var_action == "source": - line = "if [ -f %s ] ; then . %s ; fi" % ( env_var_value, env_var_value ) - else: - raise Exception( "Unknown shell file action %s" % env_var_action ) - env_shell_file_path = os.path.join( install_dir, 'env.sh' ) - return line, env_shell_file_path - - -class InstallEnvironment( object ): - """Object describing the environment built up as part of the process of building and installing a package.""" - - def add_env_shell_file_paths( self, paths ): - for path in paths: - self.env_shell_file_paths.append( str( path ) ) - - def build_command( self, command, action_type='shell_command' ): - """ - Build command line for execution from simple command, but - configuring environment described by this object. - """ - env_cmds = self.environment_commands( action_type ) - return '\n'.join( env_cmds + [ command ] ) - - def __call__( self, install_dir ): - with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ): - with prefix( self.__setup_environment() ): - yield - - def environment_commands( self, action_type ): - """Build a list of commands used to construct the environment described by this object.""" - cmds = [] - for env_shell_file_path in self.env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmds.append( env_setting.strip( '\n' ) ) - else: - log.debug( 'Invalid file %s specified, ignoring %s action.' % ( str( env_shell_file_path ), str( action_type ) ) ) - return cmds - - def environment_dict( self, action_type='template_command' ): - env_vars = dict() - for env_shell_file_path in self.env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - env_string = env_setting.split( ';' )[ 0 ] - env_name, env_path = env_string.split( '=' ) - env_vars[ env_name ] = env_path - else: - log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) ) - return env_vars - - def __init__( self ): - self.env_shell_file_paths = [] - - def __setup_environment( self ): - return "&&".join( [ ". %s" % file for file in self.__valid_env_shell_file_paths() ] ) - - def __valid_env_shell_file_paths( self ): - return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ] +INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', + 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] def check_fabric_version(): version = env.version if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) -def close_file_descriptor( fd ): - """Attempt to close a file descriptor.""" - start_timer = time.time() - error = '' - while True: - try: - fd.close() - break - except IOError, e: - # Undoubtedly close() was called during a concurrent operation on the same file object. - log.debug( 'Error closing file descriptor: %s' % str( e ) ) - time.sleep( .5 ) - current_wait_time = time.time() - start_timer - if current_wait_time >= 600: - error = 'Error closing file descriptor: %s' % str( e ) - break - return error - -def enqueue_output( stdout, stdout_queue, stderr, stderr_queue ): - """ - This method places streamed stdout and stderr into a threaded IPC queue target. Received data - is printed and saved to that thread's queue. The calling thread can then retrieve the data using - thread.stdout and thread.stderr. - """ - stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) - stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) - for line in iter( stdout.readline, '' ): - output = line.rstrip() - stdout_logger.debug( output ) - stdout_queue.put( output ) - stdout_queue.put( None ) - for line in iter( stderr.readline, '' ): - output = line.rstrip() - stderr_logger.debug( output ) - stderr_queue.put( output ) - stderr_queue.put( None ) - -def file_append( text, file_path, make_executable=True ): - """ - Append a line to a file unless the line already exists in the file. This method creates the file if - it doesn't exist. If make_executable is True, the permissions on the file are set to executable by - the owner. - """ - file_dir = os.path.dirname( file_path ) - if not os.path.exists( file_dir ): - try: - os.makedirs( file_dir ) - except Exception, e: - log.exception( str( e ) ) - return 1 - if os.path.exists( file_path ): - try: - new_env_file_contents = [] - env_file_contents = file( file_path, 'r' ).readlines() - # Clean out blank lines from the env.sh file. - for line in env_file_contents: - line = line.rstrip() - if line: - new_env_file_contents.append( line ) - env_file_contents = new_env_file_contents - except Exception, e: - log.exception( str( e ) ) - return 1 - else: - env_file_handle = open( file_path, 'w' ) - env_file_handle.close() - env_file_contents = [] - if make_executable: - # Explicitly set the file's executable bits. - try: - os.chmod( file_path, int( '111', base=8 ) | os.stat( file_path )[ stat.ST_MODE ] ) - except Exception, e: - log.exception( str( e ) ) - return 1 - # Convert the received text to a list, in order to support adding one or more lines to the file. - if isinstance( text, basestring ): - text = [ text ] - for line in text: - line = line.rstrip() - if line and line not in env_file_contents: - env_file_contents.append( line ) - try: - file( file_path, 'w' ).write( '\n'.join( env_file_contents ) ) - except Exception, e: - log.exception( str( e ) ) - return 1 - return 0 - -def filter_actions_after_binary_installation( actions ): - '''Filter out actions that should not be processed if a binary download succeeded.''' - filtered_actions = [] - for action in actions: - action_type, action_dict = action - if action_type in [ 'set_environment', 'chmod', 'download_binary' ]: - filtered_actions.append( action ) - return filtered_actions - -def handle_action_shell_file_paths( env_file_builder, action_dict ): - shell_file_paths = action_dict.get( 'action_shell_file_paths', [] ) - for shell_file_path in shell_file_paths: - env_file_builder.append_line( action="source", value=shell_file_path ) - -def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): - """ - Handle a command by determining if it is "simple" or "complex" and redirecting appropriately and then - logging the results. - """ - context = app.install_model.context - command = str( cmd ) - output = handle_complex_command( command ) - log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - stdout = output.stdout - stderr = output.stderr - if len( stdout ) > DATABASE_MAX_STRING_SIZE: - print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) - stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) - if len( stderr ) > DATABASE_MAX_STRING_SIZE: - print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) - stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) - if output.return_code not in [ 0 ]: - tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR - if stderr: - tool_dependency.error_message = unicodify( stderr ) - elif stdout: - tool_dependency.error_message = unicodify( stdout ) - else: - # We have a problem if there was no stdout and no stderr. - tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ - ( str( cmd ), str( output.return_code ) ) - context.add( tool_dependency ) - context.flush() - if return_output: - return output - return output.return_code - -def handle_complex_command( command ): - """ - Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will - be captured and logged in nearly real time. This is similar to fabric.local, but allows us to - retain control over the process. This method is named "complex" because it uses queues and - threads to execute a command while capturing and displaying the output. - """ - # Launch the command as subprocess. A bufsize of 1 means line buffered. - process_handle = subprocess.Popen( str( command ), - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - bufsize=1, - close_fds=False, - shell=True, - cwd=state.env[ 'lcwd' ] ) - pid = process_handle.pid - # Launch the asynchronous readers of the process' stdout and stderr. - stdout_queue = Queue.Queue() - stdout_reader = AsynchronousReader( process_handle.stdout, stdout_queue ) - stdout_reader.start() - stderr_queue = Queue.Queue() - stderr_reader = AsynchronousReader( process_handle.stderr, stderr_queue ) - stderr_reader.start() - # Place streamed stdout and stderr into a threaded IPC queue target so it can - # be printed and stored for later retrieval when generating the INSTALLATION.log. - stdio_thread = threading.Thread( target=enqueue_output, - args=( process_handle.stdout, - stdout_queue, - process_handle.stderr, - stderr_queue ) ) - thread_lock = threading.Lock() - thread_lock.acquire() - stdio_thread.start() - # Check the queues for output until there is nothing more to get. - start_timer = time.time() - while not stdout_reader.installation_complete() or not stderr_reader.installation_complete(): - # Show what we received from standard output. - while not stdout_queue.empty(): - try: - line = stdout_queue.get() - except Queue.Empty: - line = None - break - if line: - print line - start_timer = time.time() - else: - break - # Show what we received from standard error. - while not stderr_queue.empty(): - try: - line = stderr_queue.get() - except Queue.Empty: - line = None - break - if line: - print line - start_timer = time.time() - else: - stderr_queue.task_done() - break - # Sleep a bit before asking the readers again. - time.sleep( .1 ) - current_wait_time = time.time() - start_timer - if stdout_queue.empty() and stderr_queue.empty() and current_wait_time > td_common_util.NO_OUTPUT_TIMEOUT: - err_msg = "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n" % \ - ( pid, td_common_util.NO_OUTPUT_TIMEOUT ) - stderr_reader.lines.append( err_msg ) - process_handle.kill() - break - thread_lock.release() - # Wait until each of the threads we've started terminate. The following calls will block each thread - # until it terminates either normally, through an unhandled exception, or until the timeout occurs. - stdio_thread.join( td_common_util.NO_OUTPUT_TIMEOUT ) - stdout_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) - stderr_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) - # Close subprocess' file descriptors. - error = close_file_descriptor( process_handle.stdout ) - error = close_file_descriptor( process_handle.stderr ) - stdout = '\n'.join( stdout_reader.lines ) - stderr = '\n'.join( stderr_reader.lines ) - # Handle error condition (deal with stdout being None, too) - output = _AttributeString( stdout.strip() if stdout else "" ) - errors = _AttributeString( stderr.strip() if stderr else "" ) - # Make sure the process has finished. - process_handle.poll() - output.return_code = process_handle.returncode - output.stderr = errors - return output - -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 its 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). - -  - <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> -  - <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' ] - # env_var_value is the text of an environment variable tag like this: <environment_variable action="prepend_to" name="LD_LIBRARY_PATH"> - # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/ - if '$ENV[' in env_var_value and ']' in env_var_value: - # Pull out the name of the environment variable to populate. - inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0] - to_replace = '$ENV[%s]' % inherited_env_var_name - # Build a command line that outputs VARIABLE_NAME: <the value of the variable>. - set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) - command = ' ; '.join( set_prior_environment_commands ) - # Run the command and capture the output. - command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) - # And extract anything labeled with the name of the environment variable we're populating here. - if '%s: ' % inherited_env_var_name in command_return: - environment_variable_value = command_return.split( '\n' ) - for line in environment_variable_value: - if line.startswith( inherited_env_var_name ): - inherited_env_var_value = line.replace( '%s: ' % inherited_env_var_name, '' ) - log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, inherited_env_var_value ) - env_var_value = env_var_value.replace( to_replace, inherited_env_var_value ) - else: - # If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on. - log.error( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name ) - env_var_value = env_var_value.replace( to_replace, '$%s' % inherited_env_var_name ) - env_var_dict[ 'value' ] = env_var_value - return env_var_dict - -def install_virtualenv( app, venv_dir ): - if not os.path.exists( venv_dir ): - with make_tmp_dir() as work_dir: - downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1] - try: - dir = td_common_util.url_download( work_dir, downloaded_filename, VIRTUALENV_URL ) - except: - log.error( "Failed to download virtualenv: td_common_util.url_download( '%s', '%s', '%s' ) threw an exception", work_dir, downloaded_filename, VIRTUALENV_URL ) - return False - full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - shutil.move( full_path_to_dir, venv_dir ) - return True - def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" install_dir = actions_dict[ 'install_dir' ] package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) filtered_actions = [] + env_file_builder = EnvFileBuilder( install_dir ) install_environment = InstallEnvironment() + recipe_manager = RecipeManager() if actions: - with make_tmp_dir() as work_dir: + with install_environment.make_tmp_dir() as work_dir: with lcd( work_dir ): - # The first action in the list of actions will be the one that defines the installation process. There - # are currently three supported processes; download_binary, download_by_url and clone via a "shell_command" - # action type. + # The first action in the list of actions will be the one that defines the initial download process. + # There are currently three supported actions; download_binary, download_by_url and clone via a + # shell_command action type. The recipe steps will be filtered at this stage in the process, with + # the filtered actions being used in the next stage below. The installation directory (i.e., dir) + # is also defined in this stage and is used in the next stage below when defining current_dir. action_type, action_dict = actions[ 0 ] - if action_type == 'download_binary': - url = action_dict[ 'url' ] - # Get the target directory for this download, if the user has specified one. Default to the root of $INSTALL_DIR. - target_directory = action_dict.get( 'target_directory', None ) - # Attempt to download a binary from the specified URL. - log.debug( 'Attempting to download from %s to %s', url, str( target_directory ) ) - downloaded_filename = None - try: - downloaded_filename = td_common_util.download_binary( url, work_dir ) - # Filter out any actions that are not download_binary, chmod, or set_environment. - filtered_actions = filter_actions_after_binary_installation( actions[ 1: ] ) - # Set actions to the same, so that the current download_binary doesn't get re-run in the - # filtered actions below. - actions = filtered_actions - except Exception, e: - log.exception( str( e ) ) - # No binary exists, or there was an error downloading the binary from the generated URL. - # Proceed with the remaining actions. - filtered_actions = actions[ 1: ] - action_type, action_dict = filtered_actions[ 0 ] - # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that - # any errors in the move step are correctly sent to the tool dependency error handler. - if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): - if target_directory: - target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) - # Make sure the target directory is not outside of $INSTALL_DIR. - if target_directory.startswith( os.path.realpath( install_dir ) ): - full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - td_common_util.move_file( current_dir=work_dir, - source=downloaded_filename, - destination=full_path_to_dir ) - if action_type == 'download_by_url': - # Eliminate the download_by_url action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - url = action_dict[ 'url' ] - is_binary = action_dict.get( 'is_binary', False ) - log.debug( 'Attempting to download via url: %s', url ) - if 'target_filename' in action_dict: - # Sometimes compressed archives extract 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 ] - dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) - if is_binary: - log_file = os.path.join( install_dir, INSTALLATION_LOG ) - if os.path.exists( log_file ): - logfile = open( log_file, 'ab' ) - else: - logfile = open( log_file, 'wb' ) - logfile.write( 'Successfully downloaded from url: %s\n' % action_dict[ 'url' ] ) - logfile.close() - log.debug( 'Successfully downloaded from url: %s' % action_dict[ 'url' ] ) - elif action_type == 'shell_command': - # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - # Eliminate the shell_command clone action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) - if return_code: - return tool_dependency - dir = package_name - elif action_type == 'download_file': - # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> - # Download a single file to the working directory. - 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. - filename = action_dict[ 'target_filename' ] - else: - filename = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, filename, url ) - dir = os.path.curdir - elif action_type == 'setup_r_environment': - # setup an R environment - # <action type="setup_r_environment"> - # <repository name="package_r_3_0_1" owner="bgruening"> - # <package name="R" version="3.0.1" /> - # </repository> - #  - # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing R environment. Please check your specified R installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_r_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - tarball_names = [] - for url in action_dict[ 'r_packages' ]: - filename = url.split( '/' )[ -1 ] - tarball_names.append( filename ) - td_common_util.url_download( work_dir, filename, url, extract=False ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - for tarball_name in tarball_names: - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; - Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % \ - ( str( tarball_name ) ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - # R libraries are installed to $INSTALL_DIR (install_dir), we now set the R_LIBS path to that directory - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in R environment (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - env_file_builder.append_line( name="R_LIBS", action="prepend_to", value=install_dir ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'setup_ruby_environment': - # setup an Ruby environment - # <action type="setup_ruby_environment"> - # <repository name="package_ruby_2_0" owner="bgruening"> - # <package name="ruby" version="2.0" /> - # </repository> - #  - # <package>protk</package> - # <package>protk=1.2.4</package> - # <package>http://url-to-some-gem-file.de/protk.gem</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing Ruby environment, make sure your specified Ruby installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_ruby_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - ruby_package_tups = action_dict.get( 'ruby_package_tups', [] ) - for ruby_package_tup in ruby_package_tups: - gem, gem_version = ruby_package_tup - if os.path.isfile( gem ): - # we assume a local shipped gem file - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install --local %s''' % ( gem ) - elif gem.find( '://' ) != -1: - # We assume a URL to a gem file. - url = gem - gem_name = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, gem_name, url, extract=False ) - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install --local %s ''' % ( gem_name ) - else: - # gem file from rubygems.org with or without version number - if gem_version: - # Specific ruby gem version was requested. - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - cmd = r'''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install %s --version "=%s"''' % ( gem, gem_version) - else: - # no version number given - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install %s''' % ( gem ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in ruby dependencies (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - env_file_builder.append_line( name="GEM_PATH", action="prepend_to", value=install_dir ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join(install_dir, 'bin') ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'setup_perl_environment': - # setup an Perl environment - # <action type="setup_perl_environment"> - # <repository name="package_perl_5_18" owner="bgruening"> - # <package name="perl" version="5.18.1" /> - # </repository> - #  - # <package>XML::Parser</package> - # <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing Rerl environment, make sure your specified Rerl installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_perl_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - perl_packages = action_dict.get( 'perl_packages', [] ) - for perl_package in perl_packages: - # If set to a true value then MakeMaker's prompt function will always - # return the default without waiting for user input. - cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; ''' - if perl_package.find( '://' ) != -1: - # We assume a URL to a gem file. - url = perl_package - perl_package_name = url.split( '/' )[ -1 ] - dir = td_common_util.url_download( work_dir, perl_package_name, url, extract=True ) - # Search for Build.PL or Makefile.PL (ExtUtils::MakeMaker vs. Module::Build). - tmp_work_dir = os.path.join( work_dir, dir ) - if os.path.exists( os.path.join( tmp_work_dir, 'Makefile.PL' ) ): - cmd += '''perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install''' - elif os.path.exists( os.path.join( tmp_work_dir, 'Build.PL' ) ): - cmd += '''perl Build.PL --install_base $INSTALL_DIR && perl Build && perl Build install''' - else: - log.debug( 'No Makefile.PL or Build.PL file found in %s. Skipping installation of %s.' % \ - ( url, perl_package_name ) ) - return tool_dependency - with lcd( tmp_work_dir ): - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - else: - # perl package from CPAN without version number. - # cpanm should be installed with the parent perl distribution, otherwise this will not work. - cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( perl_package ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in perl dependencies (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - # Recursively add dependent PERL5LIB and PATH to env.sh & anything else needed. - env_file_builder.append_line( name="PERL5LIB", action="prepend_to", value=os.path.join( install_dir, 'lib', 'perl5' ) ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'bin' ) ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency + if action_type in INSTALL_ACTIONS: + # Some of the parameters passed here are needed only by a subset of the step handler classes, + # but to allow for a standard method signature we'll pass them along. We don't check the + # tool_dependency status in this stage because it should not have been changed based on a + # download. + tool_dependency, filtered_actions, dir = \ + recipe_manager.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_type=action_type, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=None, + initial_download=True ) else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> @@ -767,207 +66,33 @@ # </action> filtered_actions = [ a for a in actions ] dir = install_dir - full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - if not os.path.exists( full_path_to_dir ): - os.makedirs( full_path_to_dir ) - # The package has been down-loaded, so we can now perform all of the actions defined for building it. + # We're in stage 2 of the installation process. The package has been down-loaded, so we can + # now perform all of the actions defined for building it. for action_tup in filtered_actions: current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) with lcd( current_dir ): action_type, action_dict = action_tup - if action_type == 'make_directory': - if os.path.isabs( action_dict[ 'full_path' ] ): - full_path = action_dict[ 'full_path' ] - else: - full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) - td_common_util.make_directory( full_path=full_path ) - elif action_type == 'move_directory_files': - td_common_util.move_directory_files( current_dir=current_dir, - source_dir=os.path.join( action_dict[ 'source_directory' ] ), - destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) - elif action_type == 'move_file': - td_common_util.move_file( current_dir=current_dir, - source=os.path.join( action_dict[ 'source' ] ), - destination=os.path.join( action_dict[ 'destination' ] ), - rename_to=action_dict[ 'rename_to' ] ) - elif action_type == 'set_environment': - # Currently the only action supported in this category is "environment_variable". - # Build a command line from the prior_installation_required, in case an environment variable is referenced - # in the set_environment action. - cmds = install_environment.environment_commands( 'set_environment' ) - env_var_dicts = action_dict[ 'environment_variable' ] - env_file_builder = EnvFileBuilder( install_dir ) - for env_var_dict in env_var_dicts: - # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) - env_file_builder.append_line( **env_var_dict ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'set_environment_for_install': - # Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files, - # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> - # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. - install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) - elif action_type == 'setup_virtualenv': - # TODO: maybe should be configurable - venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) - if not install_virtualenv( app, venv_src_directory ): - log.error( 'Unable to install virtualenv' ) - return tool_dependency - requirements = action_dict[ 'requirements' ] - if os.path.exists( os.path.join( dir, requirements ) ): - # requirements specified as path to a file - requirements_path = requirements - else: - # requirements specified directly in XML, create a file with these for pip. - requirements_path = os.path.join( install_dir, "requirements.txt" ) - with open( requirements_path, "w" ) as f: - f.write( requirements ) - venv_directory = os.path.join( install_dir, "venv" ) - # TODO: Consider making --no-site-packages optional. - setup_command = "python %s/virtualenv.py --no-site-packages '%s'" % (venv_src_directory, venv_directory) - # POSIXLY_CORRECT forces shell commands . and source to have the same - # and well defined behavior in bash/zsh. - activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) - install_command = "python '%s' install -r '%s'" % ( os.path.join( venv_directory, "bin", "pip" ), requirements_path ) - full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) - return_code = handle_command( app, tool_dependency, install_dir, full_setup_command ) - if return_code: - return tool_dependency - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - site_packages_command = r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % os.path.join( venv_directory, "bin", "python" ) - output = handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - return tool_dependency - if not os.path.exists( output.stdout ): - log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'shell_command': - with settings( warn_only=True ): - cmd = install_environment.build_command( action_dict[ 'command' ] ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'template_command': - env_vars = dict() - env_vars = install_environment.environment_dict() - env_vars.update( td_common_util.get_env_var_values( install_dir ) ) - language = action_dict[ 'language' ] - with settings( warn_only=True, **env_vars ): - if language == 'cheetah': - # We need to import fabric.api.env so that we can access all collected environment variables. - cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'make_install': - # make; make install; allow providing make options - with settings( warn_only=True ): - make_opts = action_dict.get( 'make_opts', '' ) - cmd = install_environment.build_command( 'make %s && make install' % make_opts ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'autoconf': - # Handle configure, make and make install allow providing configuration options - with settings( warn_only=True ): - configure_opts = action_dict.get( 'configure_opts', '' ) - if 'prefix=' in configure_opts: - pre_cmd = './configure %s && make && make install' % configure_opts - else: - pre_cmd = './configure --prefix=$INSTALL_DIR %s && make && make install' % configure_opts - cmd = install_environment.build_command( td_common_util.evaluate_template( pre_cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'download_file': - # Download a single file to the current working directory. - url = action_dict[ 'url' ] - if 'target_filename' in action_dict: - filename = action_dict[ 'target_filename' ] - else: - filename = url.split( '/' )[ -1 ] - extract = action_dict.get( 'extract', False ) - td_common_util.url_download( current_dir, filename, url, extract=extract ) - elif action_type == 'change_directory': - target_directory = os.path.realpath( os.path.normpath( os.path.join( current_dir, action_dict[ 'directory' ] ) ) ) - if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory within the current working directory. - dir = target_directory - elif target_directory.startswith( os.path.realpath( work_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory above the current working directory, but within the defined work_dir. - dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' ) - else: - log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory ) - elif action_type == 'chmod': - for target_file, mode in action_dict[ 'change_modes' ]: - if os.path.exists( target_file ): - os.chmod( target_file, mode ) - else: - log.error( 'Invalid file %s specified, ignoring %s action.', target_file, action_type ) - elif action_type == 'download_binary': - url = action_dict[ 'url' ] - target_directory = action_dict.get( 'target_directory', None ) - try: - downloaded_filename = td_common_util.download_binary( url, work_dir ) - except Exception, e: - log.exception( str( e ) ) - # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that - # any errors in the move step are correctly sent to the tool dependency error handler. - if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): - if target_directory: - target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) - # Make sure the target directory is not outside of $INSTALL_DIR. - if target_directory.startswith( os.path.realpath( install_dir ) ): - full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - td_common_util.move_file( current_dir=work_dir, - source=downloaded_filename, - destination=full_path_to_dir ) + tool_dependency, tmp_filtered_actions, tmp_dir = \ + recipe_manager.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_type=action_type, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=current_dir, + initial_download=False ) + if tool_dependency.status in [ app.model.ToolDependency.installation_status.ERROR ]: + # If the tool_dependency status is in an error state, return it with no additional + # processing. + return tool_dependency + # Make sure to handle the special case where the value of dir is reset (this happens when + # the action_type is change_directiory). In all other action types, dir will be returned as + # None. + if tmp_dir is not None: + dir = tmp_dir return tool_dependency - -def log_results( command, fabric_AttributeString, file_path ): - """Write attributes of fabric.operations._AttributeString to a specified log file.""" - if os.path.exists( file_path ): - logfile = open( file_path, 'ab' ) - else: - logfile = open( file_path, 'wb' ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDOUT\n' % command ) - logfile.write( str( fabric_AttributeString.stdout ) ) - logfile.write( "\n#############################################\n" ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDERR\n' % command ) - logfile.write( str( fabric_AttributeString.stderr ) ) - logfile.write( "\n#############################################\n" ) - logfile.close() - -@contextmanager -def make_tmp_dir(): - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-mtd" ) - yield work_dir - if os.path.exists( work_dir ): - try: - shutil.rmtree( work_dir ) - except Exception, e: - log.exception( str( e ) ) - -def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): - """General Galaxy environment configuration. This method is not currently used.""" - env.user = galaxy_user - env.install_dir = tool_dependency_dir - env.host_string = host - env.shell = shell - env.use_sudo = False - return env diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -5,9 +5,10 @@ import subprocess import sys import tempfile -from string import Template import fabric_util import td_common_util +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import RecipeManager import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util from tool_shed.util import encoding_util @@ -94,7 +95,7 @@ package_name, package_version, required_repository ) - env_file_builder = fabric_util.EnvFileBuilder( tool_dependency.installation_directory( app ) ) + env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( app ) ) env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: @@ -497,19 +498,24 @@ elif package_elem.tag == 'readme': # Nothing to be done. continue - #elif package_elem.tag == 'proprietary_fabfile': + #elif package_elem.tag == 'custom_fabfile': # # TODO: This is not yet supported or functionally correct... - # # Handle tool dependency installation where the repository includes one or more proprietary fabric scripts. + # # Handle tool dependency installation where the repository includes one or more custom fabric scripts. # if not fabric_version_checked: # check_fabric_version() # fabric_version_checked = True # fabfile_name = package_elem.get( 'name', None ) - # proprietary_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) - # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path + # custom_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) + # print 'Installing tool dependencies via fabric script ', custom_fabfile_path return tool_dependency -def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ): - """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" +def install_via_fabric( app, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None, + actions_elem=None, action_elem=None, **kwd ): + """ + Parse a tool_dependency.xml file's <actions> tag set to gather information for installation using the + fabric_util.install_and_build_package() method. The use of fabric is being eliminated, so some of these + functions may need to be renamed at some point. + """ sa_session = app.install_model.context if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -517,278 +523,30 @@ if package_name: actions_dict[ 'package_name' ] = package_name actions = [] - all_env_shell_file_paths = [] - env_var_dicts = [] + is_binary_download = False if actions_elem is not None: elems = actions_elem if elems.get( 'os' ) is not None and elems.get( 'architecture' ) is not None: is_binary_download = True - else: - is_binary_download = False elif action_elem is not None: # We were provided with a single <action> element to perform certain actions after a platform-specific tarball was downloaded. elems = [ action_elem ] else: elems = [] + recipe_manager = RecipeManager() for action_elem in elems: # Make sure to skip all comments, since they are now included in the XML tree. if action_elem.tag != 'action': continue action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) - if action_type == 'download_binary': - platform_info_dict = tool_dependency_util.get_platform_info_dict() - platform_info_dict[ 'name' ] = tool_dependency.name - platform_info_dict[ 'version' ] = tool_dependency.version - url_template_elems = action_elem.findall( 'url_template' ) - # Check if there are multiple url_template elements, each with attrib entries for a specific platform. - if len( url_template_elems ) > 1: - # <base_url os="darwin" extract="false">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</base_url> - # This method returns the url_elem that best matches the current platform as received from os.uname(). - # Currently checked attributes are os and architecture. - # These correspond to the values sysname and processor from the Python documentation for os.uname(). - url_template_elem = tool_dependency_util.get_download_url_for_platform( url_template_elems, platform_info_dict ) - else: - url_template_elem = url_template_elems[ 0 ] - action_dict[ 'url' ] = Template( url_template_elem.text ).safe_substitute( platform_info_dict ) - action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None ) - elif action_type == 'shell_command': - # <action type="shell_command">make</action> - action_elem_text = td_common_util.evaluate_template( action_elem.text, install_dir ) - if action_elem_text: - action_dict[ 'command' ] = action_elem_text - else: - continue - elif action_type == 'template_command': - # Default to Cheetah as it's the first template language supported. - language = action_elem.get( 'language', 'cheetah' ).lower() - if language == 'cheetah': - # Cheetah template syntax. - # <action type="template_command" language="cheetah"> - # #if env.PATH: - # make - # #end if - # </action> - action_elem_text = action_elem.text.strip() - if action_elem_text: - action_dict[ 'language' ] = language - action_dict[ 'command' ] = action_elem_text - else: - continue - else: - log.debug( "Unsupported template language '%s'. Not proceeding." % str( language ) ) - raise Exception( "Unsupported template language '%s' in tool dependency definition." % str( language ) ) - elif action_type == 'download_by_url': - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - if is_binary_download: - action_dict[ 'is_binary' ] = True - if action_elem.text: - action_dict[ 'url' ] = action_elem.text - target_filename = action_elem.get( 'target_filename', None ) - if target_filename: - action_dict[ 'target_filename' ] = target_filename - else: - continue - elif action_type == 'download_file': - # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> - if action_elem.text: - action_dict[ 'url' ] = action_elem.text - target_filename = action_elem.get( 'target_filename', None ) - if target_filename: - action_dict[ 'target_filename' ] = target_filename - action_dict[ 'extract' ] = asbool( action_elem.get( 'extract', False ) ) - else: - continue - elif action_type == 'make_directory': - # <action type="make_directory">$INSTALL_DIR/lib/python</action> - if action_elem.text: - action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) - else: - continue - elif action_type == 'change_directory': - # <action type="change_directory">PHYLIP-3.6b</action> - if action_elem.text: - action_dict[ 'directory' ] = action_elem.text - else: - continue - elif action_type == 'move_directory_files': - # <action type="move_directory_files"> - # <source_directory>bin</source_directory> - # <destination_directory>$INSTALL_DIR/bin</destination_directory> - # </action> - for move_elem in action_elem: - move_elem_text = td_common_util.evaluate_template( move_elem.text, install_dir ) - if move_elem_text: - action_dict[ move_elem.tag ] = move_elem_text - elif action_type == 'move_file': - # <action type="move_file" rename_to="new_file_name"> - # <source>misc/some_file</source> - # <destination>$INSTALL_DIR/bin</destination> - # </action> - action_dict[ 'source' ] = td_common_util.evaluate_template( action_elem.find( 'source' ).text, install_dir ) - action_dict[ 'destination' ] = td_common_util.evaluate_template( action_elem.find( 'destination' ).text, install_dir ) - action_dict[ 'rename_to' ] = action_elem.get( 'rename_to' ) - elif action_type == 'set_environment': - # <action type="set_environment"> - # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - for env_elem in action_elem: - if env_elem.tag == 'environment_variable': - env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) - if env_var_dict: - env_var_dicts.append( env_var_dict ) - if env_var_dicts: - # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'. - action_dict[ 'environment_variable' ] = env_var_dicts - else: - continue - elif action_type == 'set_environment_for_install': - # <action type="set_environment_for_install"> - # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> - # <package name="numpy" version="1.7.1" /> - # </repository> - # </action> - # This action type allows for defining an environment that will properly compile a tool dependency. Currently, tag set definitions like - # that above are supported, but in the future other approaches to setting environment variables or other environment attributes can be - # supported. The above tag set will result in the installed and compiled numpy version 1.7.1 binary to be used when compiling the current - # tool dependency package. See the package_matplotlib_1_2 repository in the test tool shed for a real-world example. - for env_elem in action_elem: - if env_elem.tag == 'repository': - env_shell_file_paths = td_common_util.get_env_shell_file_paths( app, env_elem ) - if env_shell_file_paths: - all_env_shell_file_paths.extend( env_shell_file_paths ) - if all_env_shell_file_paths: - action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths - else: - continue - elif action_type == 'setup_virtualenv': - # <action type="setup_virtualenv" /> - ## Install requirements from file requirements.txt of downloaded bundle - or - - # <action type="setup_virtualenv">tools/requirements.txt</action> - ## Install requirements from specified file from downloaded bundle -or - - # <action type="setup_virtualenv">pyyaml==3.2.0 - # lxml==2.3.0</action> - ## Manually specify contents of requirements.txt file to create dynamically. - action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) - elif action_type == 'autoconf': - # Handle configure, make and make install allow providing configuration options - if action_elem.text: - configure_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) - action_dict[ 'configure_opts' ] = configure_opts - elif action_type == 'setup_r_environment': - # setup an R environment. - # <action type="setup_r_environment"> - # <repository name="package_r_3_0_1" owner="bgruening"> - # <package name="R" version="3.0.1" /> - # </repository> - #  - # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - r_packages = list() - for env_elem in action_elem: - if env_elem.tag == 'package': - r_packages.append( env_elem.text.strip() ) - if r_packages: - action_dict[ 'r_packages' ] = r_packages - else: - continue - elif action_type == 'setup_ruby_environment': - # setup a Ruby environment. - # <action type="setup_ruby_environment"> - # <repository name="package_ruby_2_0" owner="bgruening"> - # <package name="ruby" version="2.0" /> - # </repository> - #  - # <package>protk</package> - # <package>protk=1.2.4</package> - # <package>http://url-to-some-gem-file.de/protk.gem</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - ruby_package_tups = [] - for env_elem in action_elem: - if env_elem.tag == 'package': - #A valid gem definition can be: - # protk=1.2.4 - # protk - # ftp://ftp.gruening.de/protk.gem - gem_token = env_elem.text.strip().split( '=' ) - if len( gem_token ) == 2: - # version string - gem_name = gem_token[ 0 ] - gem_version = gem_token[ 1 ] - ruby_package_tups.append( ( gem_name, gem_version ) ) - else: - # gem name for rubygems.org without version number - gem = env_elem.text.strip() - ruby_package_tups.append( ( gem, None ) ) - if ruby_package_tups: - action_dict[ 'ruby_package_tups' ] = ruby_package_tups - else: - continue - elif action_type == 'setup_perl_environment': - # setup a Perl environment. - # <action type="setup_perl_environment"> - # <repository name="package_perl_5_18" owner="bgruening"> - # <package name="perl" version="5.18.1" /> - # </repository> - #  - # <package>XML::Parser</package> - # <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - perl_packages = [] - for env_elem in action_elem: - if env_elem.tag == 'package': - # A valid package definition can be: - # XML::Parser - # http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz - # Unfortunately CPAN does not support versioning, so if you want real reproducibility you need to specify - # the tarball path and the right order of different tarballs manually. - perl_packages.append( env_elem.text.strip() ) - if perl_packages: - action_dict[ 'perl_packages' ] = perl_packages - else: - continue - elif action_type == 'make_install': - # make; make install; allow providing make options - if action_elem.text: - make_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) - action_dict[ 'make_opts' ] = make_opts - elif action_type == 'chmod': - # Change the read, write, and execute bits on a file. - # <action type="chmod"> - # <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file> - # </action> - file_elems = action_elem.findall( 'file' ) - chmod_actions = [] - # A unix octal mode is the sum of the following values: - # Owner: - # 400 Read 200 Write 100 Execute - # Group: - # 040 Read 020 Write 010 Execute - # World: - # 004 Read 002 Write 001 Execute - for file_elem in file_elems: - # So by the above table, owner read/write/execute and group read permission would be 740. - # Python's os.chmod uses base 10 modes, convert received unix-style octal modes to base 10. - received_mode = int( file_elem.get( 'mode', 600 ), base=8 ) - # For added security, ensure that the setuid and setgid bits are not set. - mode = received_mode & ~( stat.S_ISUID | stat.S_ISGID ) - file = td_common_util.evaluate_template( file_elem.text, install_dir ) - chmod_tuple = ( file, mode ) - chmod_actions.append( chmod_tuple ) - action_dict[ 'change_modes' ] = chmod_actions - else: - log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) - raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) + action_dict = recipe_manager.prepare_step( app=app, + tool_dependency=tool_dependency, + action_type=action_type, + action_elem=action_elem, + action_dict=action_dict, + install_dir=install_dir, + is_binary_download=is_binary_download ) action_tuple = ( action_type, action_dict ) if action_type == 'set_environment': if action_tuple not in actions: @@ -797,15 +555,15 @@ actions.append( action_tuple ) if actions: actions_dict[ 'actions' ] = actions - if proprietary_fabfile_path: + if custom_fabfile_path is not None: # TODO: this is not yet supported or functional, but when it is handle it using the fabric api. - # run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=package_name ) + # execute_custom_fabric_script( app, elem, custom_fabfile_path, install_dir, package_name=package_name ) raise Exception( 'Tool dependency installation using proprietary fabric scripts is not yet supported.' ) else: tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency -def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): +def execute_custom_fabric_script( app, elem, custom_fabfile_path, install_dir, package_name=None, **kwd ): """ TODO: Handle this using the fabric api. Parse a tool_dependency.xml file's fabfile <method> tag set to build the method parameters and execute the method. @@ -834,10 +592,10 @@ else: params_str = params_str.rstrip( ',' ) try: - cmd = 'fab -f %s %s:%s' % ( proprietary_fabfile_path, method_name, params_str ) + cmd = 'fab -f %s %s:%s' % ( custom_fabfile_path, method_name, params_str ) returncode, message = run_subprocess( app, cmd ) except Exception, e: - return "Exception executing fabric script %s: %s. " % ( str( proprietary_fabfile_path ), str( e ) ) + return "Exception executing fabric script %s: %s. " % ( str( custom_fabfile_path ), str( e ) ) if returncode: return message handle_environment_settings( app, tool_dependency, install_dir, cmd ) @@ -913,7 +671,7 @@ set_status=True ) if env_var_version == '1.0': # Create this tool dependency's env.sh file. - env_file_builder = fabric_util.EnvFileBuilder( install_dir ) + env_file_builder = EnvFileBuilder( install_dir ) return_code = env_file_builder.append_line( make_executable=True, **env_var_dict ) if return_code: error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -0,0 +1,449 @@ +import logging +import os +import Queue +import shutil +import stat +import subprocess +import tempfile +import threading +import time + +from contextlib import contextmanager + +# TODO: eliminate the use of fabric here. +from galaxy import eggs +eggs.require( 'Fabric' ) + +from fabric.operations import _AttributeString +from fabric import state +from fabric.api import prefix + +from galaxy.util import DATABASE_MAX_STRING_SIZE +from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY +from galaxy.util import shrink_string_by_size +from galaxy.util import unicodify + +from tool_shed.galaxy_install.tool_dependencies import td_common_util +from tool_shed.galaxy_install.tool_dependencies.recipe import step_handler + +log = logging.getLogger( __name__ ) + + +class AsynchronousReader( threading.Thread ): + """ + A helper class to implement asynchronous reading of a stream in a separate thread. Read lines are pushed + onto a queue to be consumed in another thread. + """ + + def __init__( self, fd, queue ): + threading.Thread.__init__( self ) + self._fd = fd + self._queue = queue + self.lines = [] + + def run( self ): + """Read lines and put them on the queue.""" + thread_lock = threading.Lock() + thread_lock.acquire() + for line in iter( self._fd.readline, '' ): + stripped_line = line.rstrip() + self.lines.append( stripped_line ) + self._queue.put( stripped_line ) + thread_lock.release() + + def installation_complete( self ): + """Make sure there is more installation and compilation logging content expected.""" + return not self.is_alive() and self._queue.empty() + + +class EnvFileBuilder( object ): + + def __init__( self, install_dir ): + self.install_dir = install_dir + self.return_code = 0 + + def append_line( self, make_executable=True, **kwd ): + env_var_dict = dict( **kwd ) + env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) + return_code = self.file_append( env_entry, env_file, make_executable=make_executable ) + self.return_code = self.return_code or return_code + return self.return_code + + @staticmethod + def create_or_update_env_shell_file( install_dir, env_var_dict ): + env_var_action = env_var_dict[ 'action' ] + env_var_value = env_var_dict[ 'value' ] + if env_var_action in [ 'prepend_to', 'set_to', 'append_to' ]: + env_var_name = env_var_dict[ 'name' ] + if env_var_action == 'prepend_to': + changed_value = '%s:$%s' % ( env_var_value, env_var_name ) + elif env_var_action == 'set_to': + changed_value = '%s' % env_var_value + elif env_var_action == 'append_to': + changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) + elif env_var_action == "source": + line = "if [ -f %s ] ; then . %s ; fi" % ( env_var_value, env_var_value ) + else: + raise Exception( "Unknown shell file action %s" % env_var_action ) + env_shell_file_path = os.path.join( install_dir, 'env.sh' ) + return line, env_shell_file_path + + def file_append( self, text, file_path, make_executable=True ): + """ + Append a line to a file unless the line already exists in the file. This method creates the file if + it doesn't exist. If make_executable is True, the permissions on the file are set to executable by + the owner. + """ + file_dir = os.path.dirname( file_path ) + if not os.path.exists( file_dir ): + try: + os.makedirs( file_dir ) + except Exception, e: + log.exception( str( e ) ) + return 1 + if os.path.exists( file_path ): + try: + new_env_file_contents = [] + env_file_contents = file( file_path, 'r' ).readlines() + # Clean out blank lines from the env.sh file. + for line in env_file_contents: + line = line.rstrip() + if line: + new_env_file_contents.append( line ) + env_file_contents = new_env_file_contents + except Exception, e: + log.exception( str( e ) ) + return 1 + else: + env_file_handle = open( file_path, 'w' ) + env_file_handle.close() + env_file_contents = [] + if make_executable: + # Explicitly set the file's executable bits. + try: + os.chmod( file_path, int( '111', base=8 ) | os.stat( file_path )[ stat.ST_MODE ] ) + except Exception, e: + log.exception( str( e ) ) + return 1 + # Convert the received text to a list, in order to support adding one or more lines to the file. + if isinstance( text, basestring ): + text = [ text ] + for line in text: + line = line.rstrip() + if line and line not in env_file_contents: + env_file_contents.append( line ) + try: + file( file_path, 'w' ).write( '\n'.join( env_file_contents ) ) + except Exception, e: + log.exception( str( e ) ) + return 1 + return 0 + + def handle_action_shell_file_paths( self, action_dict ): + shell_file_paths = action_dict.get( 'action_shell_file_paths', [] ) + for shell_file_path in shell_file_paths: + self.append_line( action="source", value=shell_file_path ) + + +class InstallEnvironment( object ): + """Object describing the environment built up as part of the process of building and installing a package.""" + + + def __init__( self ): + self.env_shell_file_paths = [] + + def __call__( self, install_dir ): + with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ): + with prefix( self.__setup_environment() ): + yield + + def add_env_shell_file_paths( self, paths ): + for path in paths: + self.env_shell_file_paths.append( str( path ) ) + + def build_command( self, command, action_type='shell_command' ): + """ + Build command line for execution from simple command, but + configuring environment described by this object. + """ + env_cmds = self.environment_commands( action_type ) + return '\n'.join( env_cmds + [ command ] ) + + def close_file_descriptor( self, fd ): + """Attempt to close a file descriptor.""" + start_timer = time.time() + error = '' + while True: + try: + fd.close() + break + except IOError, e: + # Undoubtedly close() was called during a concurrent operation on the same file object. + log.debug( 'Error closing file descriptor: %s' % str( e ) ) + time.sleep( .5 ) + current_wait_time = time.time() - start_timer + if current_wait_time >= 600: + error = 'Error closing file descriptor: %s' % str( e ) + break + return error + + def enqueue_output( self, stdout, stdout_queue, stderr, stderr_queue ): + """ + This method places streamed stdout and stderr into a threaded IPC queue target. Received data + is printed and saved to that thread's queue. The calling thread can then retrieve the data using + thread.stdout and thread.stderr. + """ + stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) + stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) + for line in iter( stdout.readline, '' ): + output = line.rstrip() + stdout_logger.debug( output ) + stdout_queue.put( output ) + stdout_queue.put( None ) + for line in iter( stderr.readline, '' ): + output = line.rstrip() + stderr_logger.debug( output ) + stderr_queue.put( output ) + stderr_queue.put( None ) + + def environment_commands( self, action_type ): + """Build a list of commands used to construct the environment described by this object.""" + cmds = [] + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmds.append( env_setting.strip( '\n' ) ) + else: + log.debug( 'Invalid file %s specified, ignoring %s action.' % ( str( env_shell_file_path ), str( action_type ) ) ) + return cmds + + def environment_dict( self, action_type='template_command' ): + env_vars = dict() + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + else: + log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) ) + return env_vars + + def handle_command( self, app, tool_dependency, install_dir, cmd, return_output=False ): + """Handle a command and log the results.""" + context = app.install_model.context + command = str( cmd ) + output = self.handle_complex_command( command ) + self.log_results( cmd, output, os.path.join( install_dir, td_common_util.INSTALLATION_LOG ) ) + stdout = output.stdout + stderr = output.stderr + if len( stdout ) > DATABASE_MAX_STRING_SIZE: + print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) + stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if len( stderr ) > DATABASE_MAX_STRING_SIZE: + print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) + stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if output.return_code not in [ 0 ]: + tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR + if stderr: + tool_dependency.error_message = unicodify( stderr ) + elif stdout: + tool_dependency.error_message = unicodify( stdout ) + else: + # We have a problem if there was no stdout and no stderr. + tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ + ( str( cmd ), str( output.return_code ) ) + context.add( tool_dependency ) + context.flush() + if return_output: + return output + return output.return_code + + def handle_complex_command( self, command ): + """ + Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will + be captured and logged in nearly real time. This is similar to fabric.local, but allows us to + retain control over the process. This method is named "complex" because it uses queues and + threads to execute a command while capturing and displaying the output. + """ + # Launch the command as subprocess. A bufsize of 1 means line buffered. + process_handle = subprocess.Popen( str( command ), + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + bufsize=1, + close_fds=False, + shell=True, + cwd=state.env[ 'lcwd' ] ) + pid = process_handle.pid + # Launch the asynchronous readers of the process' stdout and stderr. + stdout_queue = Queue.Queue() + stdout_reader = AsynchronousReader( process_handle.stdout, stdout_queue ) + stdout_reader.start() + stderr_queue = Queue.Queue() + stderr_reader = AsynchronousReader( process_handle.stderr, stderr_queue ) + stderr_reader.start() + # Place streamed stdout and stderr into a threaded IPC queue target so it can + # be printed and stored for later retrieval when generating the INSTALLATION.log. + stdio_thread = threading.Thread( target=self.enqueue_output, + args=( process_handle.stdout, + stdout_queue, + process_handle.stderr, + stderr_queue ) ) + thread_lock = threading.Lock() + thread_lock.acquire() + stdio_thread.start() + # Check the queues for output until there is nothing more to get. + start_timer = time.time() + while not stdout_reader.installation_complete() or not stderr_reader.installation_complete(): + # Show what we received from standard output. + while not stdout_queue.empty(): + try: + line = stdout_queue.get() + except Queue.Empty: + line = None + break + if line: + print line + start_timer = time.time() + else: + break + # Show what we received from standard error. + while not stderr_queue.empty(): + try: + line = stderr_queue.get() + except Queue.Empty: + line = None + break + if line: + print line + start_timer = time.time() + else: + stderr_queue.task_done() + break + # Sleep a bit before asking the readers again. + time.sleep( .1 ) + current_wait_time = time.time() - start_timer + if stdout_queue.empty() and stderr_queue.empty() and current_wait_time > td_common_util.NO_OUTPUT_TIMEOUT: + err_msg = "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n" % \ + ( pid, td_common_util.NO_OUTPUT_TIMEOUT ) + stderr_reader.lines.append( err_msg ) + process_handle.kill() + break + thread_lock.release() + # Wait until each of the threads we've started terminate. The following calls will block each thread + # until it terminates either normally, through an unhandled exception, or until the timeout occurs. + stdio_thread.join( td_common_util.NO_OUTPUT_TIMEOUT ) + stdout_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) + stderr_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) + # Close subprocess' file descriptors. + error = self.close_file_descriptor( process_handle.stdout ) + error = self.close_file_descriptor( process_handle.stderr ) + stdout = '\n'.join( stdout_reader.lines ) + stderr = '\n'.join( stderr_reader.lines ) + # Handle error condition (deal with stdout being None, too) + output = _AttributeString( stdout.strip() if stdout else "" ) + errors = _AttributeString( stderr.strip() if stderr else "" ) + # Make sure the process has finished. + process_handle.poll() + output.return_code = process_handle.returncode + output.stderr = errors + return output + + def log_results( self, command, fabric_AttributeString, file_path ): + """Write attributes of fabric.operations._AttributeString to a specified log file.""" + if os.path.exists( file_path ): + logfile = open( file_path, 'ab' ) + else: + logfile = open( file_path, 'wb' ) + logfile.write( "\n#############################################\n" ) + logfile.write( '%s\nSTDOUT\n' % command ) + logfile.write( str( fabric_AttributeString.stdout ) ) + logfile.write( "\n#############################################\n" ) + logfile.write( "\n#############################################\n" ) + logfile.write( '%s\nSTDERR\n' % command ) + logfile.write( str( fabric_AttributeString.stderr ) ) + logfile.write( "\n#############################################\n" ) + logfile.close() + + @contextmanager + def make_tmp_dir( self ): + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-mtd" ) + yield work_dir + if os.path.exists( work_dir ): + try: + shutil.rmtree( work_dir ) + except Exception, e: + log.exception( str( e ) ) + + def __setup_environment( self ): + return "&&".join( [ ". %s" % file for file in self.__valid_env_shell_file_paths() ] ) + + def __valid_env_shell_file_paths( self ): + return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ] + + +class RecipeManager( object ): + + def __init__( self ): + self.step_handlers_by_type = self.load_step_handlers() + + def get_step_handler_by_type( self, type ): + return self.step_handlers_by_type.get( type, None ) + + def execute_step( self, app, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions, + env_file_builder, install_environment, work_dir, install_dir, current_dir=None, initial_download=False ): + if actions: + step_handler = self.get_step_handler_by_type( action_type ) + tool_dependency, filtered_actions, dir = step_handler.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=current_dir, + initial_download=initial_download ) + else: + dir = None + return tool_dependency, filtered_actions, dir + + def load_step_handlers( self ): + step_handlers_by_type = dict( autoconf=step_handler.Autoconf(), + change_directory=step_handler.ChangeDirectory(), + chmod=step_handler.Chmod(), + download_binary=step_handler.DownloadBinary(), + download_by_url=step_handler.DownloadByUrl(), + download_file=step_handler.DownloadFile(), + make_directory=step_handler.MakeDirectory(), + make_install=step_handler.MakeInstall(), + move_directory_files=step_handler.MoveDirectoryFiles(), + move_file=step_handler.MoveFile(), + set_environment=step_handler.SetEnvironment(), + set_environment_for_install=step_handler.SetEnvironmentForInstall(), + setup_perl_environment=step_handler.SetupPerlEnvironment(), + setup_r_environment=step_handler.SetupREnvironment(), + setup_ruby_environment=step_handler.SetupRubyEnvironment(), + setup_virtual_env=step_handler.SetupVirtualEnv(), + shell_command=step_handler.ShellCommand(), + template_command=step_handler.TemplateCommand() ) + return step_handlers_by_type + + def prepare_step( self, app, tool_dependency, action_type, action_elem, action_dict, install_dir, is_binary_download ): + """ + Prepare the recipe step for later execution. This generally alters the received action_dict + with new information needed during this step's execution. + """ + if action_elem is not None: + step_handler = self.get_step_handler_by_type( action_type ) + action_dict = step_handler.prepare_step( app=app, + tool_dependency=tool_dependency, + action_elem=action_elem, + action_dict=action_dict, + install_dir=install_dir, + is_binary_download=is_binary_download ) + return action_dict + \ No newline at end of file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Client app: extract method on client app init to javascript_app so it isn't called twice when using parent.javascripts()
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/369bb0f7ebef/ Changeset: 369bb0f7ebef User: carlfeberhard Date: 2014-04-24 16:34:24 Summary: Client app: extract method on client app init to javascript_app so it isn't called twice when using parent.javascripts() Affected #: 5 files diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -12,6 +12,7 @@ ${self.metas()} ${self.stylesheets()} ${self.javascripts()} + ${self.javascript_app()} </head><body class="inbound"> ${next.body()} @@ -83,8 +84,6 @@ }); </script> - ${ galaxy_client.load( app=self.js_app ) } - %if not form_input_auto_focus is UNDEFINED and form_input_auto_focus: <script type="text/javascript"> $(document).ready( function() { @@ -98,5 +97,9 @@ </%def> +<%def name="javascript_app()"> + ${ galaxy_client.load( app=self.js_app ) } +</%def> + ## Additional metas can be defined by templates inheriting from this one. <%def name="metas()"></%def> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -1,6 +1,6 @@ <!DOCTYPE HTML> +<%namespace name="galaxy_client" file="/galaxy_client_app.mako" /> -<%namespace name="galaxy_client" file="/galaxy_client_app.mako" /><% self.has_left_panel = hasattr( self, 'left_panel' ) self.has_right_panel = hasattr( self, 'right_panel' ) @@ -20,7 +20,10 @@ ## Default stylesheets <%def name="stylesheets()"> - ${h.css('base','jquery.rating')} + ${h.css( + 'base', + 'jquery.rating' + )} <style type="text/css"> #center { %if not self.has_left_panel: @@ -67,9 +70,9 @@ root: '${h.url_for( "/" )}' }; - ## load additional style sheet - if (window != window.top) - $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); + //## load additional style sheet + //if (window != window.top) + // $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); // console protection window.console = window.console || { @@ -91,16 +94,24 @@ }); </script> +</%def> + +<%def name="javascript_app()"> ## load the Galaxy global js var ${ galaxy_client.load() } - </%def> ## Default late-load javascripts <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - ${h.js( 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.form', 'libs/jquery/jquery.rating', 'galaxy.panels' )} + ${h.js( + 'libs/jquery/jquery.event.drag', + 'libs/jquery/jquery.event.hover', + 'libs/jquery/jquery.form', + 'libs/jquery/jquery.rating', + 'galaxy.panels' + )} <script type="text/javascript"> ensure_dd_helper(); @@ -295,6 +306,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> ${self.stylesheets()} ${self.javascripts()} + ${self.javascript_app()} </head><% diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -1,4 +1,5 @@ <%inherit file="/base/base_panels.mako"/> +<%namespace name="mod_masthead" file="/webapps/galaxy/galaxy.masthead.mako"/> ## Default title @@ -17,4 +18,4 @@ <% mod_masthead.load(self.active_view); %> -</%def> \ No newline at end of file +</%def> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -101,6 +101,11 @@ }); var galaxy_config = ${ h.to_json_string( self.galaxy_config ) }; + </script> +</%def> + +<%def name="javascript_app()"> + <script type="text/javascript"> // load any app configured define( 'app', function(){ var jscript = galaxy_config.app.jscript; @@ -116,6 +121,7 @@ } }); </script> + ## load the Galaxy global js var and run 'app' from above ${ galaxy_client.load( app='app' ) } @@ -125,7 +131,6 @@ ##${ galaxy_client.load( app=( app_config[ 'jscript' ] if 'jscript' in app_config else None )) } ##TODO: at that point, we can think about optimizing the various apps - </%def> ## default late-load javascripts @@ -165,6 +170,7 @@ ## load scripts ${self.javascripts()} + ${self.javascript_app()} </head><body scroll="no" class="full-content"> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -8,13 +8,16 @@ ## ----------------------------------------------------------------------------- <%def name="javascripts()"> ${ parent.javascripts() } - <script type="text/javascript"> $(function(){ $( 'body' ).addClass( 'historyPage' ).addClass( 'history-panel' ) .css({ margin: '0px', padding: '0px' }); }); +</script> +</%def> +<%def name="javascript_app()"> +<script type="text/javascript"> define( 'app', function(){ require([ 'mvc/history/current-history-panel' @@ -34,8 +37,7 @@ }); }); }); -}) +}); </script> ${ galaxy_client.load( app='app', history=history, hdas=hdas, show_deleted=show_deleted, show_hidden=show_hidden ) } - </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Update LWR client through LWR changeset bd8d1cc.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/641f7063ce3c/ Changeset: 641f7063ce3c User: jmchilton Date: 2014-04-24 07:31:57 Summary: Update LWR client through LWR changeset bd8d1cc. Needed for LWR runner to be able to use env tags from job conf file. Affected #: 4 files diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c 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 @@ -39,6 +39,7 @@ ) else: job_directory = None + self.env = destination_params.get( "env", [] ) self.files_endpoint = destination_params.get("files_endpoint", None) self.job_directory = job_directory @@ -81,7 +82,7 @@ super(JobClient, self).__init__(destination_params, job_id) self.job_manager_interface = job_manager_interface - def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): """ Queue up the execution of the supplied `command_line` on the remote server. Called launch for historical reasons, should be renamed to @@ -98,6 +99,8 @@ launch_params['params'] = dumps(submit_params_dict) if requirements: launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) + if env: + launch_params['env'] = dumps(env) if remote_staging: launch_params['remote_staging'] = dumps(remote_staging) if job_config and self.setup_handler.local: @@ -291,7 +294,7 @@ raise Exception(error_message) self.client_manager = client_manager - def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): """ """ launch_params = dict(command_line=command_line, job_id=self.job_id) @@ -300,6 +303,8 @@ launch_params['params'] = submit_params_dict if requirements: launch_params['requirements'] = [requirement.to_dict() for requirement in requirements] + if env: + launch_params['env'] = env if remote_staging: launch_params['remote_staging'] = remote_staging if job_config and self.setup_handler.local: diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py @@ -32,6 +32,8 @@ Local path created by Galaxy for running this job. requirements : list List of requirements for tool execution. + env: list + List of dict object describing environment variables to populate. version_file : str Path to version file expected on the client server arbitrary_files : dict() @@ -54,6 +56,7 @@ client_outputs, working_directory, requirements, + env=[], arbitrary_files=None, rewrite_paths=True, ): @@ -64,6 +67,7 @@ self.client_outputs = client_outputs self.working_directory = working_directory self.requirements = requirements + self.env = env self.rewrite_paths = rewrite_paths self.arbitrary_files = arbitrary_files or {} @@ -156,5 +160,5 @@ return join(output_directory, self.path_helper.local_name(name)) files_directory = "%s_files%s" % (basename(output_file)[0:-len(".dat")], self.path_helper.separator) - names = filter(lambda o: o.startswith(files_directory), self.output_directory_contents) + names = filter(lambda o: o.startswith(files_directory), self.output_directory_contents) return dict(map(lambda name: (local_path(name), name), names)) diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -80,7 +80,10 @@ if self._attempt_collect_output('output_workdir', path=output_file, name=lwr_name): self.downloaded_working_directory_files.append(lwr_name) # Remove from full output_files list so don't try to download directly. - self.output_files.remove(output_file) + try: + self.output_files.remove(output_file) + except ValueError: + raise Exception("Failed to remove %s from %s" % (output_file, self.output_files)) def __collect_outputs(self): # Legacy LWR not returning list of files, iterate over the list of diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/up.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py @@ -25,6 +25,7 @@ launch_kwds = dict( command_line=rebuilt_command_line, requirements=client_job_description.requirements, + env=client_job_description.env, ) if file_stager.job_config: launch_kwds["job_config"] = file_stager.job_config Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix Python 3 incompat in galaxy.jobs.runners.util.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b172ca94e169/ Changeset: b172ca94e169 User: jmchilton Date: 2014-04-24 03:33:41 Summary: Fix Python 3 incompat in galaxy.jobs.runners.util. Module shared with LWR so hoping for Python 3 compat. Affected #: 2 files diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -3,7 +3,5 @@ processes and interfacing with job managers. This module should contain functionality shared between Galaxy and the LWR. """ -try: - from galaxy.util.bunch import Bunch -except ImportError: - from lwr.util import Bunch + +from galaxy.util.bunch import Bunch diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/condor/__init__.py --- a/lib/galaxy/jobs/runners/util/condor/__init__.py +++ b/lib/galaxy/jobs/runners/util/condor/__init__.py @@ -20,7 +20,8 @@ def submission_params(prefix=SUBMIT_PARAM_PREFIX, **kwds): submission_params = {} - for key, value in kwds.iteritems(): + for key in kwds: + value = kwds[key] key = key.lower() if key.startswith(prefix): condor_key = key[len(prefix):] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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