Commit 7fe3844d authored by Duggan, John's avatar Duggan, John
Browse files

Merge branch 'dev' into 'main' 

Merge 'dev' into 'main'

See merge request !144
parents 3053c327 43999021

.gitlab-ci.yml

+2 −2
Original line number Diff line number Diff line
@@ -9,8 +9,8 @@ variables: 
  CONTAINER_GALAXY_URL: "${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}"

  CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"

  CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"

  GALAXY_VERSION_PYTHON: 25.1.dev3+ornl

  GALAXY_VERSION_DOCKER: 25.1.dev3.ornl

  GALAXY_VERSION_PYTHON: 25.1.dev4+ornl

  GALAXY_VERSION_DOCKER: 25.1.dev4.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/objectstore/rucio.py

+1 −0
Original line number Diff line number Diff line
@@ -165,6 +165,7 @@ class RucioBroker: 
            temp_directory = self.extra_dirs["temp"]

            self.rucio_config_path = os.path.join(temp_directory, "rucio.cfg")

            key_for_pass = "password"

            os.makedirs(temp_directory, exist_ok=True)

            with open(self.rucio_config_path, "w") as f:

                f.write(

                    f"""[client]

lib/galaxy/tools/__init__.py

+8 −0
Original line number Diff line number Diff line
@@ -1472,6 +1472,14 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle): 
        self.resource_requirements = resource_requirements

        self.javascript_requirements = javasscript_requirements

        self.credentials = credentials

        if self.credentials:

            if not self.docker_env_pass_through:

                self.docker_env_pass_through = []

            for credential in self.credentials:

                for secret in credential.secrets:

                    self.docker_env_pass_through.append(secret.inject_as_env)

                for variable in credential.variables:

                    self.docker_env_pass_through.append(variable.inject_as_env)



        required_files = tool_source.parse_required_files()

        if required_files is None:

lib/galaxy/workflow/modules.py

+40 −1
Original line number Diff line number Diff line
@@ -29,6 +29,7 @@ from galaxy.exceptions import ( 
)

from galaxy.job_execution.actions.post import ActionBox

from galaxy.job_execution.compute_environment import ComputeEnvironment

from galaxy.managers.credentials import _build_user_credentials_query

from galaxy.model import (

    Job,

    PostJobAction,
@@ -42,6 +43,11 @@ from galaxy.model.dataset_collections import matching 
from galaxy.model.dataset_collections.query import HistoryQuery

from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY

from galaxy.model.dataset_collections.types.sample_sheet_util import validate_column_definitions

from galaxy.schema.credentials import (

    CredentialsContext,

    SelectedGroup,

    ServiceCredentialsContext,

)

from galaxy.schema.invocation import (

    CancelReason,

    FailureReason,
@@ -2504,7 +2510,7 @@ class ToolModule(WorkflowModule): 
            for pja in step.post_job_actions:

                if pja.action_type == "ValidateOutputsAction":

                    validate_outputs = True



            credentials_context = self._resolve_credentials_context(tool)

            execution_tracker = execute(

                trans=self.trans,

                tool=tool,
@@ -2520,6 +2526,7 @@ class ToolModule(WorkflowModule): 
                ),

                completed_jobs=completed_jobs,

                workflow_resource_parameters=resource_parameters,

                credentials_context=credentials_context,

            )

            complete = True

        except PartialJobExecution as pje:
@@ -2583,6 +2590,38 @@ class ToolModule(WorkflowModule): 
                    self.trans, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict

                )



    def _resolve_credentials_context(self, tool: "Tool") -> Optional[CredentialsContext]:

        """Auto-resolve the user's current credentials for a tool in workflow execution."""

        if not tool.credentials:

            return None

        trans = self.trans

        if not trans.user:

            return None

        stmt = _build_user_credentials_query(

            user_id=trans.user.id,

            source_type="tool",

            source_id=tool.id,

            current_group_only=True,

        )

        results = trans.sa_session.execute(stmt).tuples().all()

        if not results:

            return None

        encode = trans.security.encode_id

        seen = {}

        for user_cred, group, _cred in results:

            key = (user_cred.id, user_cred.name, user_cred.version)

            if key not in seen:

                seen[key] = ServiceCredentialsContext(

                    user_credentials_id=encode(user_cred.id),

                    name=user_cred.name,

                    version=user_cred.version,

                    selected_group=SelectedGroup(

                        id=encode(group.id),

                        name=group.name,

                    ),

                )

        return CredentialsContext(root=list(seen.values()))



    def _handle_post_job_actions(self, step, job, replacement_dict):

        # Create new PJA associations with the created job, to be run on completion.

        # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)

test/unit/tool_shed/test_files/toolshed_community_files.tgz

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