Commit 80518e38 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Add stopped column to job and stopped property to dataset

parent 2a709cb7

lib/galaxy/managers/hdas.py

+1 −0
Original line number Diff line number Diff line
@@ -489,6 +489,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 
                "url",

                "create_time",

                "update_time",

                "stopped"

            ],

        )

        self.add_view(

lib/galaxy/managers/jobs.py

+1 −0
Original line number Diff line number Diff line
@@ -662,6 +662,7 @@ def view_show_job(trans, job, full: bool) -> typing.Dict: 
                job_stderr=job.job_stderr,

                stderr=job.stderr,

                stdout=job.stdout,

                stopped=job.stopped,

                job_messages=job.job_messages,

                dependencies=job.dependencies,

            )

lib/galaxy/model/__init__.py

+12 −0
Original line number Diff line number Diff line
@@ -1353,6 +1353,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
    handler = Column(TrimmedString(255), index=True)

    preferred_object_store_id = Column(String(255), nullable=True)

    object_store_id_overrides = Column(JSONType)

    stopped = Column(Boolean, index=True, default=False)



    user = relationship("User")

    galaxy_session = relationship("GalaxySession")
@@ -1717,6 +1718,10 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
            self.state = Job.states.STOPPING

        else:

            self.state = Job.states.STOPPED

        self.stopped = True

        for jtoda in self.output_datasets:

            output_hda = jtoda.dataset

            output_hda.stopped = True



    def mark_deleted(self, track_jobs_in_database=False):

        """
@@ -5268,6 +5273,13 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot 
                    jobs_to_unpause.update(jtoda.dataset.unpause_dependent_jobs(jobs=jobs_to_unpause))

        return jobs_to_unpause



    @property

    def stopped(self):

        for jtoda in self.creating_job_associations:

            if jtoda.job.stopped:

                return True

        return False



    @property

    def history_content_type(self):

        return "dataset"

lib/galaxy/model/migrations/alembic/versions_gxy/0a5669ff37cc_add_stopped_column_to_job_model.py

0 → 100644
+44 −0
Original line number Diff line number Diff line 
"""add stopped column to job model



Revision ID: 0a5669ff37cc

Revises: e0561d5fc8c7

Create Date: 2023-12-04 15:56:26.362315



"""

from alembic import op

import sqlalchemy as sa



from sqlalchemy import (

    Boolean,

    Column,

)



from galaxy.model.database_object_names import build_index_name

from galaxy.model.migrations.util import (

    add_column,

    drop_column,

    drop_index,

    transaction,

)





# revision identifiers, used by Alembic.

revision = '0a5669ff37cc'

down_revision = 'e0561d5fc8c7'

branch_labels = None

depends_on = None



#database object names used in this revision

table_name = "job"

column_name = "stopped"

index_name = build_index_name(table_name, column_name)





def upgrade():

    add_column(table_name, Column(column_name, Boolean(), default=False, index=True))





def downgrade():

    with transaction():

        drop_index(index_name, table_name)

        drop_column(table_name, column_name)