galaxy-commits January 2015

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248 discussions

commit/galaxy-central: dan: merge
by commits-noreply＠bitbucket.org 09 Jan '15

09 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5c3327071012/ Changeset: 5c3327071012 User: dan Date: 2015-01-09 19:58:19+00:00 Summary: merge Affected #: 2 files 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: dan: Add gemini.sqlite datatype.
by commits-noreply＠bitbucket.org 09 Jan '15

09 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7fe5cbb6b66e/ Changeset: 7fe5cbb6b66e Branch: next-stable User: dan Date: 2015-01-09 19:48:56+00:00 Summary: Add gemini.sqlite datatype. Affected #: 3 files diff -r 13f767186d5e281a9d647f8e497d6aca48d03417 -r 7fe5cbb6b66e0debec7775a88a8c553384784a00 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -180,7 +180,8 @@ <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="True" /><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> @@ -270,6 +271,7 @@ --><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/><sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/> diff -r 13f767186d5e281a9d647f8e497d6aca48d03417 -r 7fe5cbb6b66e0debec7775a88a8c553384784a00 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -20,7 +20,7 @@ from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE from galaxy.util import sqlite -from galaxy.datatypes.metadata import MetadataElement,ListParameter,DictParameter +from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListParameter, DictParameter from galaxy.datatypes import metadata import dataproviders @@ -630,8 +630,66 @@ return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) +#Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) + + +class GeminiSQLite( SQlite ): + """Class describing a Gemini Sqlite database """ + MetadataElement( name="gemini_version", default='0.10.0' , param=MetadataParameter, desc="Gemini Version", + readonly=True, visible=True, no_value='0.10.0' ) + file_ext = "gemini.sqlite" + + def set_meta( self, dataset, overwrite = True, **kwd ): + super( GeminiSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd ) + try: + conn = sqlite.connect( dataset.file_name ) + c = conn.cursor() + tables_query = "SELECT version FROM version" + result = c.execute( tables_query ).fetchall() + for version, in result: + dataset.metadata.gemini_version = version + # TODO: Can/should we detect even more attributes, such as use of PED file, what was input annotation type, etc. + except Exception, e: + log.warn( '%s, set_meta Exception: %s', self, e ) + + def sniff( self, filename ): + if super( GeminiSQLite, self ).sniff( filename ): + gemini_table_names = [ "gene_detailed", "gene_summary", "resources", "sample_genotype_counts", "sample_genotypes", "samples", + "variant_impacts", "variants", "version" ] + try: + conn = sqlite.connect( filename ) + c = conn.cursor() + tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name" + result = c.execute( tables_query ).fetchall() + result = map( lambda x: x[0], result ) + for table_name in gemini_table_names: + if table_name not in result: + return False + return True + except Exception, e: + log.warn( '%s, sniff Exception: %s', self, e ) + return False + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' ) + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' ) + +Binary.register_sniffable_binary_format( "gemini.sqlite", "gemini.sqlite", GeminiSQLite ) +# FIXME: We need to register gemini.sqlite before sqlite, since register_sniffable_binary_format and is_sniffable_binary called in upload.py +# ignores sniff order declared in datatypes_conf.xml Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) + class Xlsx(Binary): """Class for Excel 2007 (xlsx) files""" file_ext="xlsx" diff -r 13f767186d5e281a9d647f8e497d6aca48d03417 -r 7fe5cbb6b66e0debec7775a88a8c553384784a00 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -113,6 +113,8 @@ ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) # Is dataset content supported sniffable binary? else: + # FIXME: This ignores the declared sniff order in datatype_conf.xml + # resulting in improper behavior type_info = Binary.is_sniffable_binary( dataset.path ) if type_info: data_type = type_info[0] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add gemini.sqlite datatype.
by commits-noreply＠bitbucket.org 09 Jan '15

09 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55553f94d810/ Changeset: 55553f94d810 User: dan Date: 2015-01-09 19:48:56+00:00 Summary: Add gemini.sqlite datatype. Affected #: 3 files diff -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f -r 55553f94d810f4ce3ff44a46b439690003d848cb config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -181,7 +181,8 @@ <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="True" /><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> @@ -271,6 +272,7 @@ --><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/><sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/> diff -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f -r 55553f94d810f4ce3ff44a46b439690003d848cb lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -20,7 +20,7 @@ from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE from galaxy.util import sqlite -from galaxy.datatypes.metadata import MetadataElement,ListParameter,DictParameter +from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListParameter, DictParameter from galaxy.datatypes import metadata import dataproviders @@ -640,8 +640,66 @@ return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) +#Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) + + +class GeminiSQLite( SQlite ): + """Class describing a Gemini Sqlite database """ + MetadataElement( name="gemini_version", default='0.10.0' , param=MetadataParameter, desc="Gemini Version", + readonly=True, visible=True, no_value='0.10.0' ) + file_ext = "gemini.sqlite" + + def set_meta( self, dataset, overwrite = True, **kwd ): + super( GeminiSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd ) + try: + conn = sqlite.connect( dataset.file_name ) + c = conn.cursor() + tables_query = "SELECT version FROM version" + result = c.execute( tables_query ).fetchall() + for version, in result: + dataset.metadata.gemini_version = version + # TODO: Can/should we detect even more attributes, such as use of PED file, what was input annotation type, etc. + except Exception, e: + log.warn( '%s, set_meta Exception: %s', self, e ) + + def sniff( self, filename ): + if super( GeminiSQLite, self ).sniff( filename ): + gemini_table_names = [ "gene_detailed", "gene_summary", "resources", "sample_genotype_counts", "sample_genotypes", "samples", + "variant_impacts", "variants", "version" ] + try: + conn = sqlite.connect( filename ) + c = conn.cursor() + tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name" + result = c.execute( tables_query ).fetchall() + result = map( lambda x: x[0], result ) + for table_name in gemini_table_names: + if table_name not in result: + return False + return True + except Exception, e: + log.warn( '%s, sniff Exception: %s', self, e ) + return False + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' ) + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' ) + +Binary.register_sniffable_binary_format( "gemini.sqlite", "gemini.sqlite", GeminiSQLite ) +# FIXME: We need to register gemini.sqlite before sqlite, since register_sniffable_binary_format and is_sniffable_binary called in upload.py +# ignores sniff order declared in datatypes_conf.xml Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) + class Xlsx(Binary): """Class for Excel 2007 (xlsx) files""" file_ext="xlsx" diff -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f -r 55553f94d810f4ce3ff44a46b439690003d848cb tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -113,6 +113,8 @@ ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) # Is dataset content supported sniffable binary? else: + # FIXME: This ignores the declared sniff order in datatype_conf.xml + # resulting in improper behavior type_info = Binary.is_sniffable_binary( dataset.path ) if type_info: data_type = type_info[0] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] 2f879e: Increase memory for join1.
by GitHub 08 Jan '15

08 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f879e75e7258805ee919c0d043611e57cfd40a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/2f879e75e7258805… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-08 (Thu, 08 Jan 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase memory for join1.

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[galaxyproject/usegalaxy-playbook] 1eff0f: Set the bigwig implicit converter to use more memo...
by GitHub 08 Jan '15

08 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1eff0fac7c5826823f89852268218e3429658e1a https://github.com/galaxyproject/usegalaxy-playbook/commit/1eff0fac7c582682… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-08 (Thu, 08 Jan 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Set the bigwig implicit converter to use more memory.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 07 Jan '15

07 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65cd7c0eee89/ Changeset: 65cd7c0eee89 User: jmchilton Date: 2015-01-07 21:33:11+00:00 Summary: Update to brew_exts to latest platform-brew. Affected #: 1 file diff -r 8c57fc528cb7255ab11d20b03b5dd8509e3ea5a0 -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 lib/galaxy/tools/deps/brew_exts.py --- a/lib/galaxy/tools/deps/brew_exts.py +++ b/lib/galaxy/tools/deps/brew_exts.py @@ -28,6 +28,7 @@ import os import re import sys +import string import subprocess WHITESPACE_PATTERN = re.compile("[\s]+") @@ -43,6 +44,7 @@ CANNOT_DETERMINE_TAP_ERROR_MESSAGE = "Cannot determine tap of specified recipe - please use fully qualified recipe (e.g. homebrew/science/samtools)." VERBOSE = False RELAXED = False +BREW_ARGS = [] class BrewContext(object): @@ -104,6 +106,7 @@ def main(): global VERBOSE global RELAXED + global BREW_ARGS parser = argparse.ArgumentParser(description=DESCRIPTION) parser.add_argument("--brew", help="Path to linuxbrew 'brew' executable to target") actions = ["vinstall", "vuninstall", "vdeps", "vinfo", "env"] @@ -114,11 +117,13 @@ parser.add_argument('version', metavar='version', help="Version for action (e.g. 0.1.19).") parser.add_argument('--relaxed', action='store_true', help="Relaxed processing - for instance allow use of env on non-vinstall-ed recipes.") parser.add_argument('--verbose', action='store_true', help="Verbose output") + parser.add_argument('restargs', nargs=argparse.REMAINDER) args = parser.parse_args() if args.verbose: VERBOSE = True if args.relaxed: RELAXED = True + BREW_ARGS = args.restargs if not action: action = args.action brew_context = BrewContext(args) @@ -159,7 +164,7 @@ return self.message -def versioned_install(recipe_context, package=None, version=None): +def versioned_install(recipe_context, package=None, version=None, installed_deps=[]): if package is None: package = recipe_context.recipe version = recipe_context.version @@ -176,10 +181,15 @@ versioned = version_info[2] if versioned: dep_to_version[dep] = dep_version + if dep in installed_deps: + continue versioned_install(recipe_context, dep, dep_version) + installed_deps.append(dep) else: # Install latest. dep_to_version[dep] = None + if dep in installed_deps: + continue unversioned_install(dep) try: for dep in deps: @@ -198,7 +208,16 @@ } deps_metadata.append(dep_metadata) - brew_execute(["install", package]) + cellar_root = recipe_context.brew_context.homebrew_cellar + cellar_path = recipe_context.cellar_path + env_actions = build_env_actions(deps_metadata, cellar_root, cellar_path, custom_only=True) + env = EnvAction.build_env(env_actions) + args = ["install"] + if VERBOSE: + args.append("--verbose") + args.extend(BREW_ARGS) + args.append(package) + brew_execute(args, env=env) deps = brew_execute(["deps", package]) deps = [d.strip() for d in deps.split("\n") if d] metadata = { @@ -278,10 +297,10 @@ pass -def brew_execute(args): +def brew_execute(args, env=None): os.environ["HOMEBREW_NO_EMOJI"] = "1" # simplify brew parsing. cmds = ["brew"] + args - return execute(cmds) + return execute(cmds, env=env) def build_env_statements_from_recipe_context(recipe_context, **kwds): @@ -290,11 +309,20 @@ return env_statements -def build_env_statements(cellar_root, cellar_path, relaxed=None): +def build_env_statements(cellar_root, cellar_path, relaxed=None, custom_only=False): deps = load_versioned_deps(cellar_path, relaxed=relaxed) + actions = build_env_actions(deps, cellar_root, cellar_path, relaxed, custom_only) + env_statements = [] + for action in actions: + env_statements.extend(action.to_statements()) + return "\n".join(env_statements) + + +def build_env_actions(deps, cellar_root, cellar_path, relaxed=None, custom_only=False): path_appends = [] ld_path_appends = [] + actions = [] def handle_keg(cellar_path): bin_path = os.path.join(cellar_path, "bin") @@ -303,6 +331,14 @@ lib_path = os.path.join(cellar_path, "lib") if os.path.isdir(lib_path): ld_path_appends.append(lib_path) + env_path = os.path.join(cellar_path, "platform_environment.json") + if os.path.exists(env_path): + with open(env_path, "r") as f: + env_metadata = json.load(f) + if "actions" in env_metadata: + def to_action(desc): + return EnvAction(cellar_path, desc) + actions.extend(map(to_action, env_metadata["actions"])) for dep in deps: package = dep['name'] @@ -311,14 +347,54 @@ handle_keg( dep_cellar_path ) handle_keg( cellar_path ) - env_statements = [] - if path_appends: - env_statements.append("PATH=" + ":".join(path_appends) + ":$PATH") - env_statements.append("export PATH") - if ld_path_appends: - env_statements.append("LD_LIBRARY_PATH=" + ":".join(ld_path_appends) + ":$LD_LIBRARY_PATH") - env_statements.append("export LD_LIBRARY_PATH") - return "\n".join(env_statements) + if not custom_only: + if path_appends: + actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "PATH", "value": ":".join(path_appends)})) + if ld_path_appends: + actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "LD_LIBRARY_PATH", "value": ":".join(path_appends)})) + return actions + + +class EnvAction(object): + + def __init__(self, keg_root, action_description): + self.variable = action_description["variable"] + self.action = action_description["action"] + self.value = string.Template(action_description["value"]).safe_substitute({ + 'KEG_ROOT': keg_root, + }) + + @staticmethod + def build_env(env_actions): + new_env = os.environ.copy() + map(lambda env_action: env_action.modify_environ(new_env), env_actions) + return new_env + + def modify_environ(self, environ): + if self.action == "set" or not environ.get(self.variable, ""): + environ[self.variable] = self.__eval("${value}") + elif self.action == "prepend": + environ[self.variable] = self.__eval("${value}:%s" % environ[self.variable]) + else: + environ[self.variable] = self.__eval("%s:${value}" % environ[self.variable]) + + def __eval(self, template): + return string.Template(template).safe_substitute( + variable=self.variable, + value=self.value, + ) + + def to_statements(self): + if self.action == "set": + template = '''${variable}="${value}"''' + elif self.action == "prepend": + template = '''${variable}="${value}:$$${variable}"''' + else: + template = '''${variable}="$$${variable}:${value}"''' + return [ + self.__eval(template), + "export %s" % self.variable + ] @contextlib.contextmanager @@ -350,8 +426,15 @@ return execute(cmds) -def execute(cmds): - p = subprocess.Popen(cmds, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) +def execute(cmds, env=None): + subprocess_kwds = dict( + shell=False, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + if env: + subprocess_kwds["env"] = env + p = subprocess.Popen(cmds, **subprocess_kwds) #log = p.stdout.read() global VERBOSE stdout, stderr = p.communicate() @@ -363,7 +446,10 @@ def brew_deps(package): - stdout = brew_execute(["deps", package]) + args = ["deps"] + args.extend(BREW_ARGS) + args.append(package) + stdout = brew_execute(args) return [p.strip() for p in stdout.split("\n") if p] https://bitbucket.org/galaxy/galaxy-central/commits/63d901ca0e6e/ Changeset: 63d901ca0e6e User: jmchilton Date: 2015-01-07 21:33:11+00:00 Summary: Implement dependency resolver for Homebrew "tapped" tool shed packages (highly beta). Homebrew/Linuxbrew can be configured the same way the more vanilla Homebrew resolver works (added in 6b7782f). When this resolver is active, if the tool has been installed via the Tool Shed and the dependencies also installed it will use the database information to determine the dependent packages - otherwise it will just try to find the tool_dependencies.xml file on disk and recover the dependencies from that. This is for dependencies installed via Platform Brew (https://github.com/jmchilton/platform-brew) and converted from Tool Shed repositories usiing the shed2tap WIP code (e.g. https://github.com/jmchilton/homebrew-toolshed). Affected #: 7 files diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1843,7 +1843,8 @@ """Return a list of commands to be run to populate the current environment to include this tools requirements.""" return self.app.toolbox.dependency_manager.dependency_shell_commands( self.requirements, - installed_tool_dependencies=self.installed_tool_dependencies + installed_tool_dependencies=self.installed_tool_dependencies, + tool_dir=self.tool_dir, ) @property diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py --- /dev/null +++ b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py @@ -0,0 +1,150 @@ +""" +This dependency resolver resolves tool shed dependencies (those defined +tool_dependencies.xml) installed using Platform Homebrew and converted +via shed2tap (e.g. https://github.com/jmchilton/homebrew-toolshed). +""" +import logging +import os +from xml.etree import ElementTree as ET + +from .resolver_mixins import ( + UsesHomebrewMixin, + UsesToolDependencyDirMixin, + UsesInstalledRepositoriesMixin, +) +from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY + +log = logging.getLogger(__name__) + + +class HomebrewToolShedDependencyResolver( + DependencyResolver, + UsesHomebrewMixin, + UsesToolDependencyDirMixin, + UsesInstalledRepositoriesMixin, +): + resolver_type = "tool_shed_tap" + + def __init__(self, dependency_manager, **kwds): + self._init_homebrew(**kwds) + self._init_base_path(dependency_manager, **kwds) + + def resolve(self, name, version, type, **kwds): + if type != "package": + return INDETERMINATE_DEPENDENCY + + if version is None: + return INDETERMINATE_DEPENDENCY + + return self._find_tool_dependencies(name, version, type, **kwds) + + def _find_tool_dependencies(self, name, version, type, **kwds): + installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds) + if installed_tool_dependency: + return self._resolve_from_installed_tool_dependency(name, version, installed_tool_dependency) + + if "tool_dir" in kwds: + tool_directory = os.path.abspath(kwds["tool_dir"]) + tool_depenedencies_path = os.path.join(tool_directory, "tool_dependencies.xml") + if os.path.exists(tool_depenedencies_path): + return self._resolve_from_tool_dependencies_path(name, version, tool_depenedencies_path) + + return INDETERMINATE_DEPENDENCY + + def _resolve_from_installed_tool_dependency(self, name, version, installed_tool_dependency): + tool_shed_repository = installed_tool_dependency.tool_shed_repository + recipe_name = build_recipe_name( + package_name=name, + package_version=version, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + ) + return self._find_dep_default(recipe_name, None) + + def _resolve_from_tool_dependencies_path(self, name, version, tool_dependencies_path): + try: + raw_dependencies = RawDependencies(tool_dependencies_path) + except Exception: + log.debug("Failed to parse dependencies in file %s" % tool_dependencies_path) + return INDETERMINATE_DEPENDENCY + + raw_dependency = raw_dependencies.find(name, version) + if not raw_dependency: + return INDETERMINATE_DEPENDENCY + + recipe_name = build_recipe_name( + package_name=name, + package_version=version, + repository_owner=raw_dependency.repository_owner, + repository_name=raw_dependency.repository_name + ) + dep = self._find_dep_default(recipe_name, None) + return dep + + +class RawDependencies(object): + + def __init__(self, dependencies_file): + self.root = ET.parse(dependencies_file).getroot() + dependencies = [] + package_els = self.root.findall("package") or [] + for package_el in package_els: + repository_el = package_el.find("repository") + if repository_el is None: + continue + dependency = RawDependency(self, package_el, repository_el) + dependencies.append(dependency) + self.dependencies = dependencies + + def find(self, package_name, package_version): + target_dependency = None + + for dependency in self.dependencies: + if dependency.package_name == package_name and dependency.package_version == package_version: + target_dependency = dependency + break + return target_dependency + + +class RawDependency(object): + + def __init__(self, dependencies, package_el, repository_el): + self.dependencies = dependencies + self.package_el = package_el + self.repository_el = repository_el + + def __repr__(self): + temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]" + return temp % ( + self.package_el.attrib["name"], + self.package_el.attrib["version"], + self.repository_el.attrib["name"] + ) + + @property + def repository_owner(self): + return self.repository_el.attrib["owner"] + + @property + def repository_name(self): + return self.repository_el.attrib["name"] + + @property + def package_name(self): + return self.package_el.attrib["name"] + + @property + def package_version(self): + return self.package_el.attrib["version"] + + +def build_recipe_name(package_name, package_version, repository_owner, repository_name): + # TODO: Consider baking package_name and package_version into name? (would be more "correct") + owner = repository_owner.replace("-", "") + name = repository_name + name = name.replace("_", "").replace("-", "") + base = "%s_%s" % (owner, name) + return base + + +__all__ = [HomebrewToolShedDependencyResolver] diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/deps/resolvers/galaxy_packages.py --- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py +++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py @@ -1,12 +1,13 @@ -from os.path import join, islink, realpath, basename, exists, abspath +from os.path import join, islink, realpath, basename, exists from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY, Dependency +from .resolver_mixins import UsesToolDependencyDirMixin import logging log = logging.getLogger( __name__ ) -class GalaxyPackageDependencyResolver(DependencyResolver): +class GalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependencyDirMixin): resolver_type = "galaxy_packages" def __init__(self, dependency_manager, **kwds): @@ -16,7 +17,7 @@ ## resolver that will just grab 'default' version of exact version ## unavailable. self.versionless = str(kwds.get('versionless', "false")).lower() == "true" - self.base_path = abspath( kwds.get('base_path', dependency_manager.default_base_path) ) + self._init_base_path( dependency_manager, **kwds ) def resolve( self, name, version, type, **kwds ): """ diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/deps/resolvers/homebrew.py --- a/lib/galaxy/tools/deps/resolvers/homebrew.py +++ b/lib/galaxy/tools/deps/resolvers/homebrew.py @@ -12,20 +12,19 @@ incompatible changes coming. """ -import os -from ..brew_exts import DEFAULT_HOMEBREW_ROOT, recipe_cellar_path, build_env_statements -from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY, Dependency +from .resolver_mixins import UsesHomebrewMixin +from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY # TODO: Implement prefer version linked... PREFER_VERSION_LINKED = 'linked' PREFER_VERSION_LATEST = 'latest' -UNKNOWN_PREFER_VERSION_MESSAGE_TEMPLATE = "HomebrewDependencyResolver prefer_version must be latest %s" +UNKNOWN_PREFER_VERSION_MESSAGE_TEMPLATE = "HomebrewDependencyResolver prefer_version must be %s" UNKNOWN_PREFER_VERSION_MESSAGE = UNKNOWN_PREFER_VERSION_MESSAGE_TEMPLATE % (PREFER_VERSION_LATEST) DEFAULT_PREFER_VERSION = PREFER_VERSION_LATEST -class HomebrewDependencyResolver(DependencyResolver): +class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin): resolver_type = "homebrew" def __init__(self, dependency_manager, **kwds): @@ -38,11 +37,7 @@ if self.versionless and self.prefer_version not in [PREFER_VERSION_LATEST]: raise Exception(UNKNOWN_PREFER_VERSION_MESSAGE) - cellar_root = kwds.get('cellar', None) - if cellar_root is None: - cellar_root = os.path.join(DEFAULT_HOMEBREW_ROOT, "Cellar") - - self.cellar_root = cellar_root + self._init_homebrew(**kwds) def resolve(self, name, version, type, **kwds): if type != "package": @@ -53,41 +48,6 @@ else: return self._find_dep_versioned(name, version) - def _find_dep_versioned(self, name, version): - recipe_path = recipe_cellar_path(self.cellar_root, name, version) - if not os.path.exists(recipe_path) or not os.path.isdir(recipe_path): - return INDETERMINATE_DEPENDENCY - - commands = build_env_statements(self.cellar_root, recipe_path, relaxed=True) - return HomebrewDependency(commands) - - def _find_dep_default(self, name, version): - installed_versions = self._installed_versions(name) - if not installed_versions: - return INDETERMINATE_DEPENDENCY - - # Just grab newest installed version - may make sense some day to find - # the linked version instead. - default_version = sorted(installed_versions, reverse=True)[0] - return self._find_dep_versioned(name, default_version) - - def _installed_versions(self, recipe): - recipe_base_path = os.path.join(self.cellar_root, recipe) - if not os.path.exists(recipe_base_path): - return [] - - names = os.listdir(recipe_base_path) - return filter(lambda n: os.path.isdir(os.path.join(recipe_base_path, n)), names) - - -class HomebrewDependency(Dependency): - - def __init__(self, commands): - self.commands = commands - - def shell_commands(self, requirement): - return self.commands.replace("\n", ";") + "\n" - def _string_as_bool( value ): return str( value ).lower() == "true" diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/deps/resolvers/resolver_mixins.py --- /dev/null +++ b/lib/galaxy/tools/deps/resolvers/resolver_mixins.py @@ -0,0 +1,73 @@ +import os +from ..brew_exts import DEFAULT_HOMEBREW_ROOT, recipe_cellar_path, build_env_statements +from ..resolvers import INDETERMINATE_DEPENDENCY, Dependency + + +class UsesHomebrewMixin: + + def _init_homebrew(self, **kwds): + cellar_root = kwds.get('cellar', None) + if cellar_root is None: + cellar_root = os.path.join(DEFAULT_HOMEBREW_ROOT, "Cellar") + + self.cellar_root = cellar_root + + def _find_dep_versioned(self, name, version): + recipe_path = recipe_cellar_path(self.cellar_root, name, version) + if not os.path.exists(recipe_path) or not os.path.isdir(recipe_path): + return INDETERMINATE_DEPENDENCY + + commands = build_env_statements(self.cellar_root, recipe_path, relaxed=True) + return HomebrewDependency(commands) + + def _find_dep_default(self, name, version): + installed_versions = self._installed_versions(name) + if not installed_versions: + return INDETERMINATE_DEPENDENCY + + # Just grab newest installed version - may make sense some day to find + # the linked version instead. + default_version = sorted(installed_versions, reverse=True)[0] + return self._find_dep_versioned(name, default_version) + + def _installed_versions(self, recipe): + recipe_base_path = os.path.join(self.cellar_root, recipe) + if not os.path.exists(recipe_base_path): + return [] + + names = os.listdir(recipe_base_path) + return filter(lambda n: os.path.isdir(os.path.join(recipe_base_path, n)), names) + + +class UsesToolDependencyDirMixin: + + def _init_base_path(self, dependency_manager, **kwds): + self.base_path = os.path.abspath( kwds.get('base_path', dependency_manager.default_base_path) ) + + +class UsesInstalledRepositoriesMixin: + + def _get_installed_dependency( self, name, type, version=None, **kwds ): + installed_tool_dependencies = kwds.get("installed_tool_dependencies", []) + for installed_tool_dependency in (installed_tool_dependencies or []): + name_and_type_equal = installed_tool_dependency.name == name and installed_tool_dependency.type == type + if version: + if name_and_type_equal and installed_tool_dependency.version == version: + return installed_tool_dependency + else: + if name_and_type_equal: + return installed_tool_dependency + return None + + +class HomebrewDependency(Dependency): + + def __init__(self, commands): + self.commands = commands + + def shell_commands(self, requirement): + raw_commands = self.commands.replace("\n", ";") + return raw_commands + + def __repr__(self): + return "PlatformBrewDependency[commands=%s]" % self.commands diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/tools/deps/resolvers/tool_shed_packages.py --- a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py @@ -1,10 +1,11 @@ from os.path import abspath, join, exists +from .resolver_mixins import UsesInstalledRepositoriesMixin from .galaxy_packages import GalaxyPackageDependencyResolver, GalaxyPackageDependency from ..resolvers import INDETERMINATE_DEPENDENCY -class ToolShedPackageDependencyResolver(GalaxyPackageDependencyResolver): +class ToolShedPackageDependencyResolver(GalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin): resolver_type = "tool_shed_packages" def __init__(self, dependency_manager, **kwds): @@ -12,9 +13,8 @@ def _find_dep_versioned( self, name, version, type='package', **kwds ): installed_tool_dependency = self._get_installed_dependency( name, type, version=version, **kwds ) - base_path = self.base_path if installed_tool_dependency: - path = self._get_package_installed_dependency_path( installed_tool_dependency, base_path, name, version ) + path = self._get_package_installed_dependency_path( installed_tool_dependency, name, version ) return self._galaxy_package_dep(path, version) else: return INDETERMINATE_DEPENDENCY @@ -29,26 +29,17 @@ return GalaxyPackageDependency(dependency.script, dependency.path, None) return INDETERMINATE_DEPENDENCY - def _get_installed_dependency( self, name, type, version=None, **kwds ): - installed_tool_dependencies = kwds.get("installed_tool_dependencies", []) - for installed_tool_dependency in (installed_tool_dependencies or []): - name_and_type_equal = installed_tool_dependency.name == name and installed_tool_dependency.type == type - if version: - if name_and_type_equal and installed_tool_dependency.version == version: - return installed_tool_dependency - else: - if name_and_type_equal: - return installed_tool_dependency - return None - - def _get_package_installed_dependency_path( self, installed_tool_dependency, base_path, name, version ): + def _get_package_installed_dependency_path( self, installed_tool_dependency, name, version ): tool_shed_repository = installed_tool_dependency.tool_shed_repository - return join( base_path, - name, - version, - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) + base_path = self.base_path + return join( + base_path, + name, + version, + tool_shed_repository.owner, + tool_shed_repository.name, + tool_shed_repository.installed_changeset_revision + ) def _get_set_environment_installed_dependency_script_path( self, installed_tool_dependency, name ): tool_shed_repository = installed_tool_dependency.tool_shed_repository @@ -64,4 +55,5 @@ return GalaxyPackageDependency(script, path, None) return INDETERMINATE_DEPENDENCY + __all__ = [ToolShedPackageDependencyResolver] diff -r 65cd7c0eee89e2d32a3369b1eb88742f23034560 -r 63d901ca0e6e9cfa405bae41f7088e3fa6bf243f lib/galaxy/util/plugin_config.py --- a/lib/galaxy/util/plugin_config.py +++ b/lib/galaxy/util/plugin_config.py @@ -24,7 +24,7 @@ for plugin_module in submodules( module ): # FIXME: this is not how one is suppose to use __all__ why did you do # this past John? - for clazz in plugin_module.__all__: + for clazz in getattr( plugin_module, "__all__", [] ): plugin_type = getattr( clazz, plugin_type_identifier, None ) if plugin_type: plugin_dict[ plugin_type ] = clazz 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: Clarify source of errors reported by anonymous users who don't provide a contact email address.
by commits-noreply＠bitbucket.org 07 Jan '15

07 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c57fc528cb7/ Changeset: 8c57fc528cb7 User: dannon Date: 2015-01-07 19:10:42+00:00 Summary: Clarify source of errors reported by anonymous users who don't provide a contact email address. Affected #: 1 file diff -r 81e27001166b0e01b89eabc79d32b0adf72d5ef5 -r 8c57fc528cb7255ab11d20b03b5dd8509e3ea5a0 lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -86,7 +86,7 @@ if user and user.email != email: email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email) else: - email_str = "'%s'" % email + email_str = "'%s'" % (email or 'anonymously') self.report = string.Template( error_report_template ) \ .safe_substitute( host=host, dataset_id=hda.dataset_id, 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: Use set_tags_from_list for PJA instead of apply_item_tags.
by commits-noreply＠bitbucket.org 07 Jan '15

07 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81e27001166b/ Changeset: 81e27001166b User: dannon Date: 2015-01-07 18:45:12+00:00 Summary: Use set_tags_from_list for PJA instead of apply_item_tags. Affected #: 2 files diff -r 53e839193da1f58b15834b07a61a3c131267795f -r 81e27001166b0e01b89eabc79d32b0adf72d5ef5 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -428,12 +428,11 @@ @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): if action.action_arguments: - tags = ','.join([t.strip() for t in action.action_arguments.get('tags', '').split(',')]) + tags = [t.strip() for t in action.action_arguments.get('tags', '').split(',')] if tags: for dataset_assoc in job.output_datasets: if action.output_name == '' or dataset_assoc.name == action.output_name: - app.tag_handler.apply_item_tags( job.user, dataset_assoc.dataset, - unicode(tags.encode('utf-8'), 'utf-8')) + app.tag_handler.set_tags_from_list( job.user, dataset_assoc.dataset, tags) sa_session.flush() @classmethod diff -r 53e839193da1f58b15834b07a61a3c131267795f -r 81e27001166b0e01b89eabc79d32b0adf72d5ef5 lib/galaxy/managers/tags.py --- a/lib/galaxy/managers/tags.py +++ b/lib/galaxy/managers/tags.py @@ -1,5 +1,5 @@ +import logging import re -import logging from sqlalchemy.sql import select from sqlalchemy.sql.expression import func 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: Tag manager PEP8.
by commits-noreply＠bitbucket.org 07 Jan '15

07 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53e839193da1/ Changeset: 53e839193da1 User: dannon Date: 2015-01-07 18:26:22+00:00 Summary: Tag manager PEP8. Affected #: 1 file diff -r 504fd0cce279c54003fb9c38ad9107ae9fea6ce6 -r 53e839193da1f58b15834b07a61a3c131267795f lib/galaxy/managers/tags.py --- a/lib/galaxy/managers/tags.py +++ b/lib/galaxy/managers/tags.py @@ -7,7 +7,7 @@ log = logging.getLogger( __name__ ) -#Item-specific information needed to perform tagging. +# Item-specific information needed to perform tagging. class ItemTagAssocInfo( object ): def __init__( self, item_class, tag_assoc_class, item_id_col ): self.item_class = item_class @@ -36,8 +36,8 @@ self.item_tag_assoc_info = {} def set_tags_from_list( self, user, item, new_tags_list ): - #precondition: item is already security checked against user - #precondition: incoming tags is a list of sanitized/formatted strings + # precondition: item is already security checked against user + # precondition: incoming tags is a list of sanitized/formatted strings self.delete_item_tags( user, item ) new_tags_str = ','.join( new_tags_list ) @@ -83,7 +83,7 @@ def get_tool_tags( self ): result_set = self.app.model.context.execute( select( columns=[ self.app.model.ToolTagAssociation.table.c.tag_id ], - from_obj=self.app.model.ToolTagAssociation.table ).distinct() ) + from_obj=self.app.model.ToolTagAssociation.table ).distinct() ) tags = [] for row in result_set: @@ -289,6 +289,7 @@ name_value_pair.append( None ) return name_value_pair + class GalaxyTagManager( TagManager ): def __init__( self, app ): from galaxy import model @@ -313,5 +314,4 @@ class CommunityTagManager( TagManager): def __init__( self, app ): - from galaxy.webapps.tool_shed import model # ?huh? TagManager.__init__( self, app ) 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: 4 new changesets
by commits-noreply＠bitbucket.org 07 Jan '15

07 Jan '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dcc40b6cdb65/ Changeset: dcc40b6cdb65 User: dannon Date: 2015-01-06 21:09:47+00:00 Summary: Initial commit of TagManager refactor. Affected #: 5 files diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dcc40b6cdb65043fa0800c2852b60059b81bab91 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -7,7 +7,7 @@ import galaxy.security from galaxy.managers.collections import DatasetCollectionManager import galaxy.quota -from galaxy.tags.tag_handler import GalaxyTagHandler +from galaxy.managers.tags import GalaxyTagManager from galaxy.visualization.genomes import Genomes from galaxy.visualization.data_providers.registry import DataProviderRegistry from galaxy.visualization.registry import VisualizationsRegistry @@ -58,7 +58,7 @@ # Security helper self._configure_security() # Tag handler - self.tag_handler = GalaxyTagHandler() + self.tag_handler = GalaxyTagManager( self ) # Dataset Collection Plugins self.dataset_collections_service = DatasetCollectionManager(self) diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dcc40b6cdb65043fa0800c2852b60059b81bab91 lib/galaxy/managers/collections.py --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -36,7 +36,7 @@ self.security = app.security self.hda_manager = hdas.HDAManager() self.history_manager = histories.HistoryManager() - self.tag_manager = tags.TagsManager( app ) + self.tag_manager = tags.TagManager( app ) self.ldda_manager = lddas.LDDAManager( ) def create( @@ -163,7 +163,7 @@ dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] ) changed[ 'annotation' ] = new_data[ 'annotation' ] if 'tags' in new_data.keys() and trans.get_user(): - self.tag_manager.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) + self.tag_manager.set_tags_from_list( trans.get_user(), dataset_collection_instance, new_data[ 'tags' ] ) if changed.keys(): trans.sa_session.flush() diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dcc40b6cdb65043fa0800c2852b60059b81bab91 lib/galaxy/managers/tags.py --- a/lib/galaxy/managers/tags.py +++ b/lib/galaxy/managers/tags.py @@ -1,20 +1,317 @@ +import re +import logging +from sqlalchemy.sql import select +from sqlalchemy.sql.expression import func -class TagsManager( object ): - """ Manages CRUD operations related to tagging objects. +log = logging.getLogger( __name__ ) + + +#Item-specific information needed to perform tagging. +class ItemTagAssocInfo( object ): + def __init__( self, item_class, tag_assoc_class, item_id_col ): + self.item_class = item_class + self.tag_assoc_class = tag_assoc_class + self.item_id_col = item_id_col + + +class TagManager( object ): + """ + Manages CRUD operations related to tagging objects. """ def __init__( self, app ): self.app = app - self.tag_handler = app.tag_handler + # Minimum tag length. + self.min_tag_len = 2 + # Maximum tag length. + self.max_tag_len = 255 + # Tag separator. + self.tag_separators = ',;' + # Hierarchy separator. + self.hierarchy_separator = '.' + # Key-value separator. + self.key_value_separators = "=:" + # Initialize with known classes - add to this in subclasses. + self.item_tag_assoc_info = {} - def set_tags_from_list( self, trans, item, new_tags_list, user=None ): + def set_tags_from_list( self, user, item, new_tags_list ): #precondition: item is already security checked against user #precondition: incoming tags is a list of sanitized/formatted strings - user = user or trans.user - self.tag_handler.delete_item_tags( trans, user, item ) + self.delete_item_tags( user, item ) new_tags_str = ','.join( new_tags_list ) - self.tag_handler.apply_item_tags( trans, user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) ) - trans.sa_session.flush() + self.apply_item_tags( user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) ) + self.app.model.context.flush() return item.tags + + def get_tag_assoc_class( self, item_class ): + """Returns tag association class for item class.""" + return self.item_tag_assoc_info[item_class.__name__].tag_assoc_class + + def get_id_col_in_item_tag_assoc_table( self, item_class ): + """Returns item id column in class' item-tag association table.""" + return self.item_tag_assoc_info[item_class.__name__].item_id_col + + def get_community_tags( self, item=None, limit=None ): + """Returns community tags for an item.""" + # Get item-tag association class. + item_class = item.__class__ + item_tag_assoc_class = self.get_tag_assoc_class( item_class ) + if not item_tag_assoc_class: + return [] + # Build select statement. + cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count( '*' ) ] + from_obj = item_tag_assoc_class.table.join( item_class.table ).join( self.app.model.Tag.table ) + where_clause = ( self.get_id_col_in_item_tag_assoc_table( item_class ) == item.id ) + order_by = [ func.count( "*" ).desc() ] + group_by = item_tag_assoc_class.table.c.tag_id + # Do query and get result set. + query = select( columns=cols_to_select, + from_obj=from_obj, + whereclause=where_clause, + group_by=group_by, + order_by=order_by, + limit=limit ) + result_set = self.app.model.context.execute( query ) + # Return community tags. + community_tags = [] + for row in result_set: + tag_id = row[0] + community_tags.append( self.get_tag_by_id( tag_id ) ) + return community_tags + + def get_tool_tags( self ): + result_set = self.app.model.context.execute( select( columns=[ self.app.model.ToolTagAssociation.table.c.tag_id ], + from_obj=self.app.model.ToolTagAssociation.table ).distinct() ) + + tags = [] + for row in result_set: + tag_id = row[0] + tags.append( self.get_tag_by_id( tag_id ) ) + return tags + + def remove_item_tag( self, user, item, tag_name ): + """Remove a tag from an item.""" + # Get item tag association. + item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) + # Remove association. + if item_tag_assoc: + # Delete association. + self.app.model.context.delete( item_tag_assoc ) + item.tags.remove( item_tag_assoc ) + return True + return False + + def delete_item_tags( self, user, item ): + """Delete tags from an item.""" + # Delete item-tag associations. + for tag in item.tags: + self.app.model.context.delete( tag ) + # Delete tags from item. + del item.tags[:] + + def item_has_tag( self, user, item, tag ): + """Returns true if item is has a given tag.""" + # Get tag name. + if isinstance( tag, basestring ): + tag_name = tag + elif isinstance( tag, self.app.model.Tag ): + tag_name = tag.name + # Check for an item-tag association to see if item has a given tag. + item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) + if item_tag_assoc: + return True + return False + + def apply_item_tag( self, user, item, name, value=None ): + # Use lowercase name for searching/creating tag. + lc_name = name.lower() + # Get or create item-tag association. + item_tag_assoc = self._get_item_tag_assoc( user, item, lc_name ) + if not item_tag_assoc: + # Create item-tag association. + # Create tag; if None, skip the tag (and log error). + tag = self._get_or_create_tag( lc_name ) + if not tag: + log.warn( "Failed to create tag with name %s" % lc_name ) + return + # Create tag association based on item class. + item_tag_assoc_class = self.get_tag_assoc_class( item.__class__ ) + item_tag_assoc = item_tag_assoc_class() + # Add tag to association. + item.tags.append( item_tag_assoc ) + item_tag_assoc.tag = tag + item_tag_assoc.user = user + # Apply attributes to item-tag association. Strip whitespace from user name and tag. + lc_value = None + if value: + lc_value = value.lower() + item_tag_assoc.user_tname = name + item_tag_assoc.user_value = value + item_tag_assoc.value = lc_value + return item_tag_assoc + + def apply_item_tags( self, user, item, tags_str ): + """Apply tags to an item.""" + # Parse tags. + parsed_tags = self.parse_tags( tags_str ) + # Apply each tag. + for name, value in parsed_tags.items(): + self.apply_item_tag( user, item, name, value ) + + def get_tags_str( self, tags ): + """Build a string from an item's tags.""" + # Return empty string if there are no tags. + if not tags: + return "" + # Create string of tags. + tags_str_list = list() + for tag in tags: + tag_str = tag.user_tname + if tag.value is not None: + tag_str += ":" + tag.user_value + tags_str_list.append( tag_str ) + return ", ".join( tags_str_list ) + + def get_tag_by_id( self, tag_id ): + """Get a Tag object from a tag id.""" + return self.app.model.context.query( self.app.model.Tag ).filter_by( id=tag_id ).first() + + def get_tag_by_name( self, tag_name ): + """Get a Tag object from a tag name (string).""" + if tag_name: + return self.app.model.context.query( self.app.model.Tag ).filter_by( name=tag_name.lower() ).first() + return None + + def _create_tag( self, tag_str ): + """Create a Tag object from a tag string.""" + tag_hierarchy = tag_str.split( self.hierarchy_separator ) + tag_prefix = "" + parent_tag = None + for sub_tag in tag_hierarchy: + # Get or create subtag. + tag_name = tag_prefix + self._scrub_tag_name( sub_tag ) + tag = self.app.model.context.query( self.app.model.Tag ).filter_by( name=tag_name).first() + if not tag: + tag = self.app.model.Tag( type=0, name=tag_name ) + # Set tag parent. + tag.parent = parent_tag + # Update parent and tag prefix. + parent_tag = tag + tag_prefix = tag.name + self.hierarchy_separator + return tag + + def _get_or_create_tag( self, tag_str ): + """Get or create a Tag object from a tag string.""" + # Scrub tag; if tag is None after being scrubbed, return None. + scrubbed_tag_str = self._scrub_tag_name( tag_str ) + if not scrubbed_tag_str: + return None + # Get item tag. + tag = self.get_tag_by_name( scrubbed_tag_str ) + # Create tag if necessary. + if tag is None: + tag = self._create_tag( scrubbed_tag_str ) + return tag + + def _get_item_tag_assoc( self, user, item, tag_name ): + """ + Return ItemTagAssociation object for a user, item, and tag string; returns None if there is + no such association. + """ + scrubbed_tag_name = self._scrub_tag_name( tag_name ) + for item_tag_assoc in item.tags: + if ( item_tag_assoc.user == user ) and ( item_tag_assoc.user_tname == scrubbed_tag_name ): + return item_tag_assoc + return None + + def parse_tags( self, tag_str ): + """ + Returns a list of raw (tag-name, value) pairs derived from a string; method scrubs tag names and values as well. + Return value is a dictionary where tag-names are keys. + """ + # Gracefully handle None. + if not tag_str: + return dict() + # Split tags based on separators. + reg_exp = re.compile( '[' + self.tag_separators + ']' ) + raw_tags = reg_exp.split( tag_str ) + # Extract name-value pairs. + name_value_pairs = dict() + for raw_tag in raw_tags: + nv_pair = self._get_name_value_pair( raw_tag ) + scrubbed_name = self._scrub_tag_name( nv_pair[0] ) + scrubbed_value = self._scrub_tag_value( nv_pair[1] ) + name_value_pairs[scrubbed_name] = scrubbed_value + return name_value_pairs + + def _scrub_tag_value( self, value ): + """Scrub a tag value.""" + # Gracefully handle None: + if not value: + return None + # Remove whitespace from value. + reg_exp = re.compile( '\s' ) + scrubbed_value = re.sub( reg_exp, "", value ) + return scrubbed_value + + def _scrub_tag_name( self, name ): + """Scrub a tag name.""" + # Gracefully handle None: + if not name: + return None + # Remove whitespace from name. + reg_exp = re.compile( '\s' ) + scrubbed_name = re.sub( reg_exp, "", name ) + # Ignore starting ':' char. + if scrubbed_name.startswith( self.hierarchy_separator ): + scrubbed_name = scrubbed_name[1:] + # If name is too short or too long, return None. + if len( scrubbed_name ) < self.min_tag_len or len( scrubbed_name ) > self.max_tag_len: + return None + return scrubbed_name + + def _scrub_tag_name_list( self, tag_name_list ): + """Scrub a tag name list.""" + scrubbed_tag_list = list() + for tag in tag_name_list: + scrubbed_tag_list.append( self._scrub_tag_name( tag ) ) + return scrubbed_tag_list + + def _get_name_value_pair( self, tag_str ): + """Get name, value pair from a tag string.""" + # Use regular expression to parse name, value. + reg_exp = re.compile( "[" + self.key_value_separators + "]" ) + name_value_pair = reg_exp.split( tag_str ) + # Add empty slot if tag does not have value. + if len( name_value_pair ) < 2: + name_value_pair.append( None ) + return name_value_pair + +class GalaxyTagManager( TagManager ): + def __init__( self, app ): + from galaxy import model + TagManager.__init__( self, app ) + self.item_tag_assoc_info["History"] = ItemTagAssocInfo( model.History, + model.HistoryTagAssociation, + model.HistoryTagAssociation.table.c.history_id ) + self.item_tag_assoc_info["HistoryDatasetAssociation"] = \ + ItemTagAssocInfo( model.HistoryDatasetAssociation, + model.HistoryDatasetAssociationTagAssociation, + model.HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id ) + self.item_tag_assoc_info["Page"] = ItemTagAssocInfo( model.Page, + model.PageTagAssociation, + model.PageTagAssociation.table.c.page_id ) + self.item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo( model.StoredWorkflow, + model.StoredWorkflowTagAssociation, + model.StoredWorkflowTagAssociation.table.c.stored_workflow_id ) + self.item_tag_assoc_info["Visualization"] = ItemTagAssocInfo( model.Visualization, + model.VisualizationTagAssociation, + model.VisualizationTagAssociation.table.c.visualization_id ) + + +class CommunityTagManager( TagManager): + def __init__( self ): + from galaxy.webapps.tool_shed import model # ?huh? + TagManager.__init__( self ) diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dcc40b6cdb65043fa0800c2852b60059b81bab91 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py +++ b/lib/galaxy/tags/tag_handler.py @@ -1,301 +0,0 @@ -import re -import logging -from sqlalchemy.sql.expression import func -from sqlalchemy.sql.expression import and_ -from sqlalchemy.sql import select - -log = logging.getLogger( __name__ ) - -# Item-specific information needed to perform tagging. -class ItemTagAssocInfo( object ): - def __init__( self, item_class, tag_assoc_class, item_id_col ): - self.item_class = item_class - self.tag_assoc_class = tag_assoc_class - self.item_id_col = item_id_col - -class TagHandler( object ): - def __init__( self ): - # Minimum tag length. - self.min_tag_len = 2 - # Maximum tag length. - self.max_tag_len = 255 - # Tag separator. - self.tag_separators = ',;' - # Hierarchy separator. - self.hierarchy_separator = '.' - # Key-value separator. - self.key_value_separators = "=:" - # Initialize with known classes - add to this in subclasses. - self.item_tag_assoc_info = {} - - def get_tag_assoc_class( self, item_class ): - """Returns tag association class for item class.""" - return self.item_tag_assoc_info[item_class.__name__].tag_assoc_class - - def get_id_col_in_item_tag_assoc_table( self, item_class ): - """Returns item id column in class' item-tag association table.""" - return self.item_tag_assoc_info[item_class.__name__].item_id_col - - def get_community_tags( self, trans, item=None, limit=None ): - """Returns community tags for an item.""" - # Get item-tag association class. - item_class = item.__class__ - item_tag_assoc_class = self.get_tag_assoc_class( item_class ) - if not item_tag_assoc_class: - return [] - # Build select statement. - cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count( '*' ) ] - from_obj = item_tag_assoc_class.table.join( item_class.table ).join( trans.app.model.Tag.table ) - where_clause = ( self.get_id_col_in_item_tag_assoc_table( item_class ) == item.id ) - order_by = [ func.count( "*" ).desc() ] - group_by = item_tag_assoc_class.table.c.tag_id - # Do query and get result set. - query = select( columns=cols_to_select, - from_obj=from_obj, - whereclause=where_clause, - group_by=group_by, - order_by=order_by, - limit=limit ) - result_set = trans.sa_session.execute( query ) - # Return community tags. - community_tags = [] - for row in result_set: - tag_id = row[0] - community_tags.append( self.get_tag_by_id( trans, tag_id ) ) - return community_tags - - def get_tool_tags( self, trans ): - result_set = trans.sa_session.execute( select( columns=[ trans.app.model.ToolTagAssociation.table.c.tag_id ], - from_obj=trans.app.model.ToolTagAssociation.table ).distinct() ) - - tags = [] - for row in result_set: - tag_id = row[0] - tags.append( self.get_tag_by_id( trans, tag_id ) ) - return tags - - def remove_item_tag( self, trans, user, item, tag_name ): - """Remove a tag from an item.""" - # Get item tag association. - item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) - # Remove association. - if item_tag_assoc: - # Delete association. - trans.sa_session.delete( item_tag_assoc ) - item.tags.remove( item_tag_assoc ) - return True - return False - - def delete_item_tags( self, trans, user, item ): - """Delete tags from an item.""" - # Delete item-tag associations. - for tag in item.tags: - trans.sa_session.delete( tag ) - # Delete tags from item. - del item.tags[:] - - def item_has_tag( self, trans, user, item, tag ): - """Returns true if item is has a given tag.""" - # Get tag name. - if isinstance( tag, basestring ): - tag_name = tag - elif isinstance( tag, trans.app.model.Tag ): - tag_name = tag.name - # Check for an item-tag association to see if item has a given tag. - item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) - if item_tag_assoc: - return True - return False - - def apply_item_tag( self, trans, user, item, name, value=None ): - # Use lowercase name for searching/creating tag. - lc_name = name.lower() - # Get or create item-tag association. - item_tag_assoc = self._get_item_tag_assoc( user, item, lc_name ) - if not item_tag_assoc: - # Create item-tag association. - # Create tag; if None, skip the tag (and log error). - tag = self._get_or_create_tag( trans, lc_name ) - if not tag: - log.warn( "Failed to create tag with name %s" % lc_name ) - return - # Create tag association based on item class. - item_tag_assoc_class = self.get_tag_assoc_class( item.__class__ ) - item_tag_assoc = item_tag_assoc_class() - # Add tag to association. - item.tags.append( item_tag_assoc ) - item_tag_assoc.tag = tag - item_tag_assoc.user = user - # Apply attributes to item-tag association. Strip whitespace from user name and tag. - lc_value = None - if value: - lc_value = value.lower() - item_tag_assoc.user_tname = name - item_tag_assoc.user_value = value - item_tag_assoc.value = lc_value - return item_tag_assoc - - def apply_item_tags( self, trans, user, item, tags_str ): - """Apply tags to an item.""" - # Parse tags. - parsed_tags = self.parse_tags( tags_str ) - # Apply each tag. - for name, value in parsed_tags.items(): - self.apply_item_tag( trans, user, item, name, value ) - - def get_tags_str( self, tags ): - """Build a string from an item's tags.""" - # Return empty string if there are no tags. - if not tags: - return "" - # Create string of tags. - tags_str_list = list() - for tag in tags: - tag_str = tag.user_tname - if tag.value is not None: - tag_str += ":" + tag.user_value - tags_str_list.append( tag_str ) - return ", ".join( tags_str_list ) - - def get_tag_by_id( self, trans, tag_id ): - """Get a Tag object from a tag id.""" - return trans.sa_session.query( trans.app.model.Tag ).filter_by( id=tag_id ).first() - - def get_tag_by_name( self, trans, tag_name ): - """Get a Tag object from a tag name (string).""" - if tag_name: - return trans.sa_session.query( trans.app.model.Tag ).filter_by( name=tag_name.lower() ).first() - return None - - def _create_tag( self, trans, tag_str ): - """Create a Tag object from a tag string.""" - tag_hierarchy = tag_str.split( self.hierarchy_separator ) - tag_prefix = "" - parent_tag = None - for sub_tag in tag_hierarchy: - # Get or create subtag. - tag_name = tag_prefix + self._scrub_tag_name( sub_tag ) - tag = trans.sa_session.query( trans.app.model.Tag ).filter_by( name=tag_name).first() - if not tag: - tag = trans.app.model.Tag( type=0, name=tag_name ) - # Set tag parent. - tag.parent = parent_tag - # Update parent and tag prefix. - parent_tag = tag - tag_prefix = tag.name + self.hierarchy_separator - return tag - - def _get_or_create_tag( self, trans, tag_str ): - """Get or create a Tag object from a tag string.""" - # Scrub tag; if tag is None after being scrubbed, return None. - scrubbed_tag_str = self._scrub_tag_name( tag_str ) - if not scrubbed_tag_str: - return None - # Get item tag. - tag = self.get_tag_by_name( trans, scrubbed_tag_str ) - # Create tag if necessary. - if tag is None: - tag = self._create_tag( trans, scrubbed_tag_str ) - return tag - - def _get_item_tag_assoc( self, user, item, tag_name ): - """ - Return ItemTagAssociation object for a user, item, and tag string; returns None if there is - no such association. - """ - scrubbed_tag_name = self._scrub_tag_name( tag_name ) - for item_tag_assoc in item.tags: - if ( item_tag_assoc.user == user ) and ( item_tag_assoc.user_tname == scrubbed_tag_name ): - return item_tag_assoc - return None - - def parse_tags( self, tag_str ): - """ - Returns a list of raw (tag-name, value) pairs derived from a string; method scrubs tag names and values as well. - Return value is a dictionary where tag-names are keys. - """ - # Gracefully handle None. - if not tag_str: - return dict() - # Split tags based on separators. - reg_exp = re.compile( '[' + self.tag_separators + ']' ) - raw_tags = reg_exp.split( tag_str ) - # Extract name-value pairs. - name_value_pairs = dict() - for raw_tag in raw_tags: - nv_pair = self._get_name_value_pair( raw_tag ) - scrubbed_name = self._scrub_tag_name( nv_pair[0] ) - scrubbed_value = self._scrub_tag_value( nv_pair[1] ) - name_value_pairs[scrubbed_name] = scrubbed_value - return name_value_pairs - - def _scrub_tag_value( self, value ): - """Scrub a tag value.""" - # Gracefully handle None: - if not value: - return None - # Remove whitespace from value. - reg_exp = re.compile( '\s' ) - scrubbed_value = re.sub( reg_exp, "", value ) - return scrubbed_value - - def _scrub_tag_name( self, name ): - """Scrub a tag name.""" - # Gracefully handle None: - if not name: - return None - # Remove whitespace from name. - reg_exp = re.compile( '\s' ) - scrubbed_name = re.sub( reg_exp, "", name ) - # Ignore starting ':' char. - if scrubbed_name.startswith( self.hierarchy_separator ): - scrubbed_name = scrubbed_name[1:] - # If name is too short or too long, return None. - if len( scrubbed_name ) < self.min_tag_len or len( scrubbed_name ) > self.max_tag_len: - return None - return scrubbed_name - - def _scrub_tag_name_list( self, tag_name_list ): - """Scrub a tag name list.""" - scrubbed_tag_list = list() - for tag in tag_name_list: - scrubbed_tag_list.append( self._scrub_tag_name( tag ) ) - return scrubbed_tag_list - - def _get_name_value_pair( self, tag_str ): - """Get name, value pair from a tag string.""" - # Use regular expression to parse name, value. - reg_exp = re.compile( "[" + self.key_value_separators + "]" ) - name_value_pair = reg_exp.split( tag_str ) - # Add empty slot if tag does not have value. - if len( name_value_pair ) < 2: - name_value_pair.append( None ) - return name_value_pair - - -class GalaxyTagHandler( TagHandler ): - def __init__( self ): - from galaxy import model - TagHandler.__init__( self ) - self.item_tag_assoc_info["History"] = ItemTagAssocInfo( model.History, - model.HistoryTagAssociation, - model.HistoryTagAssociation.table.c.history_id ) - self.item_tag_assoc_info["HistoryDatasetAssociation"] = \ - ItemTagAssocInfo( model.HistoryDatasetAssociation, - model.HistoryDatasetAssociationTagAssociation, - model.HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id ) - self.item_tag_assoc_info["Page"] = ItemTagAssocInfo( model.Page, - model.PageTagAssociation, - model.PageTagAssociation.table.c.page_id ) - self.item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo( model.StoredWorkflow, - model.StoredWorkflowTagAssociation, - model.StoredWorkflowTagAssociation.table.c.stored_workflow_id ) - self.item_tag_assoc_info["Visualization"] = ItemTagAssocInfo( model.Visualization, - model.VisualizationTagAssociation, - model.VisualizationTagAssociation.table.c.visualization_id ) - - -class CommunityTagHandler( TagHandler ): - def __init__( self ): - from galaxy.webapps.tool_shed import model - TagHandler.__init__( self ) diff -r d50ee9520583c225e48c577ab977f18fd6cb7d6a -r dcc40b6cdb65043fa0800c2852b60059b81bab91 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2523,8 +2523,8 @@ def set_tags_from_list( self, trans, item, new_tags_list, user=None ): # Method deprecated - try to use TagsHandler instead. - tags_manager = tags.TagsManager( trans.app ) - return tags_manager.set_tags_from_list( trans, item, new_tags_list, user=user ) + tags_manager = tags.GalaxyTagManager( trans.app ) + return tags_manager.set_tags_from_list( user, item, new_tags_list ) def get_user_tags_used( self, trans, user=None ): """ https://bitbucket.org/galaxy/galaxy-central/commits/6bb0ddd5a4cc/ Changeset: 6bb0ddd5a4cc User: dannon Date: 2015-01-06 21:14:30+00:00 Summary: Update toolshed tag handler, but I don't think it's ever used. Affected #: 2 files diff -r dcc40b6cdb65043fa0800c2852b60059b81bab91 -r 6bb0ddd5a4cc1cba6e42fb838fabcfe818fc8ddb lib/galaxy/managers/tags.py --- a/lib/galaxy/managers/tags.py +++ b/lib/galaxy/managers/tags.py @@ -312,6 +312,6 @@ class CommunityTagManager( TagManager): - def __init__( self ): + def __init__( self, app ): from galaxy.webapps.tool_shed import model # ?huh? - TagManager.__init__( self ) + TagManager.__init__( self, app ) diff -r dcc40b6cdb65043fa0800c2852b60059b81bab91 -r 6bb0ddd5a4cc1cba6e42fb838fabcfe818fc8ddb lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -8,7 +8,7 @@ from galaxy.openid.providers import OpenIDProviders from galaxy.util.dbkeys import GenomeBuilds from galaxy.web import security -from galaxy.tags.tag_handler import CommunityTagHandler +from galaxy.managers.tags import CommunityTagManager from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager import tool_shed.repository_registry import tool_shed.repository_types.registry @@ -47,7 +47,7 @@ # Initialize the Tool SHed security helper. self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # initialize the Tool Shed tag handler. - self.tag_handler = CommunityTagHandler() + self.tag_handler = CommunityTagManager( self ) # Initialize the Tool Shed tool data tables. Never pass a configuration file here # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) https://bitbucket.org/galaxy/galaxy-central/commits/cb061e5ef947/ Changeset: cb061e5ef947 User: dannon Date: 2015-01-06 23:27:54+00:00 Summary: Minor typo in comment. Affected #: 1 file diff -r 6bb0ddd5a4cc1cba6e42fb838fabcfe818fc8ddb -r cb061e5ef9475f61c30c90a0e9e3c9ad614cc728 lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -44,7 +44,7 @@ self.model = mapping.init( self.config.file_path, db_url, self.config.database_engine_options ) - # Initialize the Tool SHed security helper. + # Initialize the Tool Shed security helper. self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # initialize the Tool Shed tag handler. self.tag_handler = CommunityTagManager( self ) https://bitbucket.org/galaxy/galaxy-central/commits/504fd0cce279/ Changeset: 504fd0cce279 User: dannon Date: 2015-01-07 18:08:14+00:00 Summary: Add Tagging PJA. Affected #: 1 file diff -r cb061e5ef9475f61c30c90a0e9e3c9ad614cc728 -r 504fd0cce279c54003fb9c38ad9107ae9fea6ce6 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -1,5 +1,6 @@ """ -Actions to be run at job completion. Currently only used in workflows. +Actions to be run at job completion (or output hda creation, as in the case of +immediate_actions listed below. Currently only used in workflows. """ import datetime @@ -420,6 +421,43 @@ return "Delete parent datasets of this step created in this workflow that aren't flagged as outputs." +class TagDatasetAction(DefaultJobAction): + name = "TagDatasetAction" + verbose_name = "Add tag to dataset" + + @classmethod + def execute(cls, app, sa_session, action, job, replacement_dict): + if action.action_arguments: + tags = ','.join([t.strip() for t in action.action_arguments.get('tags', '').split(',')]) + if tags: + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + app.tag_handler.apply_item_tags( job.user, dataset_assoc.dataset, + unicode(tags.encode('utf-8'), 'utf-8')) + sa_session.flush() + + @classmethod + def get_config_form(cls, trans): + form = """ + if (pja.action_arguments && pja.action_arguments.tags){ + p_str += "<label for='pja__"+pja.output_name+"__TagDatasetAction__tags'>Tags:</label>\ + <input type='text' name='pja__"+pja.output_name+"__TagDatasetAction__tags' value=\\"" + pja.action_arguments.tags.replace(/"/g, """) + "\\"/>"; + } + else{ + p_str += "<label for='pja__"+pja.output_name+"__TagDatasetAction__tags'>Tags:</label>\ + <input type='text' name='pja__"+pja.output_name+"__TagDatasetAction__tags' value=''/>"; + } + """ + return get_form_template(cls.name, cls.verbose_name, form, "This action will set tags for the dataset.") + + @classmethod + def get_short_str(cls, pja): + if pja.action_arguments and pja.action_arguments.get('tags', ''): + return "Add tag(s) '%s' to '%s'." % (pja.action_arguments['tags'], pja.output_name) + else: + return "Tag addition action used without a tag specified. No tag will be added." + + class ActionBox(object): actions = { "RenameDatasetAction": RenameDatasetAction, @@ -428,11 +466,13 @@ "ColumnSetAction": ColumnSetAction, "EmailAction": EmailAction, "DeleteIntermediatesAction": DeleteIntermediatesAction, + "TagDatasetAction": TagDatasetAction, } public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction', - 'DeleteIntermediatesAction'] - immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction'] + 'DeleteIntermediatesAction', 'TagDatasetAction'] + immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction', + 'TagDatasetAction'] @classmethod def get_short_str(cls, action): 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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galaxy-commits January 2015