Source code for galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages

"""
Backup resolvers for when dependencies can not be loaded from the database.
Mainly suited for testing stage.

Ideally all dependencies will be stored in the database
when a tool is added from a Tool Shed.

That should remain the preferred way of locating dependencies.

In cases where that is not possible
for example during testing this resolver can act as a backup.

This resolver looks not just for manually added dependencies
but also ones added from a Tool Shed.

This tool is still under development so the default behaviour could change.
It has been tested when placed in the same directory as galaxy_packages.py

At the time of writing July 3 2015 this resolver has to be plugged in.
See bottom for instructions on how to add this resolver.

"""

import logging
from os import listdir
from os.path import (
    exists,
    getmtime,
    join,
)

from . import (
    Dependency,
    NullDependency,
)
from .galaxy_packages import BaseGalaxyPackageDependencyResolver

log = logging.getLogger(__name__)

MANUAL = "manual"
PREFERRED_OWNERS = f"{MANUAL},iuc,devteam"


[docs]class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver):
    dict_collection_visible_keys = BaseGalaxyPackageDependencyResolver.dict_collection_visible_keys + [
        "preferred_owners",
        "select_by_owner",
    ]
    resolver_type = "unlinked_tool_shed_packages"

[docs]    def __init__(self, dependency_manager, **kwds):
        super().__init__(dependency_manager, **kwds)
        # Provide a list of preferred owners whose dependency to use
        self.preferred_owners = kwds.get("preferred_owners", PREFERRED_OWNERS).split(",")
        # Option to ignore owner and just use last modified time
        self.select_by_owner = str(kwds.get("select_by_owner", "true")).lower() != "false"

    def _find_dep_versioned(self, name, version, type="package", **kwds):
        try:
            possibles = self._find_possible_dependencies(name, version, type)
            if len(possibles) == 0:
                log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type)
                return NullDependency(version=version, name=name)
            elif len(possibles) == 1:
                # Only one candidate found so ignore any preference rules
                return possibles[0].dependency
            else:
                # Pick the preferred one
                return self._select_preferred_dependency(possibles).dependency
        except Exception:
            log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
            return NullDependency(version=version, name=name)

    # Finds all possible dependency to use
    # Should be extended as required
    # Returns CandidateDependency objects with data for preference picking
    def _find_possible_dependencies(self, name, version, type):
        possibles = []
        if exists(self.base_path):
            path = join(self.base_path, name, version)
            if exists(path):
                # First try the way without owner/name/revision
                package = self._galaxy_package_dep(path, version, name, type, True)
                if not isinstance(package, NullDependency):
                    log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, path)
                    possibles.append(CandidateDependency(package, path))
                # now try with an owner/name/revision
                for owner in listdir(path):
                    owner_path = join(path, owner)
                    for package_name in listdir(owner_path):
                        if package_name.lower().startswith(f"package_{name.lower()}"):
                            package_path = join(owner_path, package_name)
                            for revision in listdir(package_path):
                                revision_path = join(package_path, revision)
                                package = self._galaxy_package_dep(revision_path, version, name, type, True)
                                if not isinstance(package, NullDependency):
                                    log.debug(
                                        "Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path
                                    )
                                    possibles.append(CandidateDependency(package, package_path, owner))
        return possibles

    def _select_preferred_dependency(self, possibles, by_owner=None):
        if by_owner is None:
            by_owner = self.select_by_owner
        preferred = []
        if by_owner:
            for owner in self.preferred_owners:
                for candidate in possibles:
                    if candidate.owner == owner:
                        preferred.append(candidate)
                if len(preferred) == 1:
                    log.debug("Picked dependency based on owner '%s'", owner)
                    return preferred[0]
                elif len(preferred) > 1:
                    log.debug("Multiple dependency found with owner '%s'", owner)
                    break
        if len(preferred) == 0:
            preferred = possibles
        latest_modified = 0
        for candidate in preferred:
            modified = getmtime(candidate.path)
            if latest_modified < modified:
                latest_candidate = candidate
                latest_modified = modified
        log.debug("Picking dependency at '%s' as it was the last modified", latest_candidate.path)
        return latest_candidate


class CandidateDependency(Dependency):
    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ["dependency", "path", "owner"]
    dependency_type = "unlinked_tool_shed_package"

    @property
    def exact(self):
        return self.dependency.exact

    def __init__(self, dependency, path, owner=MANUAL):
        self.dependency = dependency
        self.path = path
        self.owner = owner

    def shell_commands(self):
        """
        Return shell commands to enable this dependency.
        """
        return self.dependency.shell_commands()


__all__ = ("UnlinkedToolShedPackageDependencyResolver",)

"""
At the time of writing July 3 2015 this resolver has to be plugged in.

Adding resolver instructions:

1. create a dependency_resolvers_config.xml file
<dependency_resolvers>
  <tool_shed_packages />
  <galaxy_packages />
  <galaxy_packages versionless="true" />
  <unlinked_tool_shed_packages />
</dependency_resolvers>


1a. ALWAYS add <tool_shed_packages /> first!!!!

1b. <galaxy_packages /> is optional as
    this resolver will also find dependency found by that resolver
1bi Current default is to use a dependency to find that way first!
1bii So an alternative version of dependency_resolvers_config.xml
<dependency_resolvers>
  <tool_shed_packages />
  <unlinked_tool_shed_packages />
  <unlinked_tool_shed_packages versionless="true" />
</dependency_resolvers>

1c. See __init__ for optional config values
1ci versionless currently is handled by the super class
    GalaxyPackageDependencyResolver

2. Add a parameter to config.ini
dependency_resolvers_config_file = ./config/dependency_resolvers_config.xml

2a. File name/path can be different
2b. config key must be dependency_resolvers_config_file

3. For planemo it may be required to specify:
--dependency_resolvers_config_file (xml file described in 1 above)
--tool_dependency_dir (root of dependencies typically galaxy/dependency_dir)
See planemo test --help for more information
"""