Unverified Commit dbc264c3 authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_24.2' into dev

parents 8f9dfaab 1d31d5b3

client/src/components/Panels/Common/ToolSearch.vue

+3 −1
Original line number Diff line number Diff line
@@ -80,7 +80,9 @@ const localFilterText = computed({ 
        return props.query !== null ? props.query : "";

    },

    set: (newVal: any) => {

        if (newVal.trim() || props.query.trim()) {

            checkQuery(newVal);

        }

    },

});

client/src/viz/trackster.js

+17 −10
Original line number Diff line number Diff line
@@ -74,23 +74,30 @@ export class TracksterUI extends Backbone.Model { 
            },

            bookmarks: bookmarks,

        };



        // Make call to save visualization.

        return $.ajax({

            url: `${getAppRoot()}visualization/save`,

            type: "POST",

        const request = {

            dataType: "json",

            data: {

            contentType: "application/json; charset=utf-8",

            data: JSON.stringify({

                id: this.view.vis_id,

                title: this.view.config.get_value("name"),

                dbkey: this.view.dbkey,

                type: "trackster",

                vis_json: JSON.stringify(viz_config),

            },

        })

                config: viz_config,

            }),

        };

        if (!this.view.vis_id) {

            request.url = `${getAppRoot()}api/visualizations`;

            request.type = "POST";

        } else {

            request.url = `${getAppRoot()}api/visualizations/${this.view.vis_id}`;

            request.type = "PUT";

        }



        // Make call to save visualization.

        return $.ajax(request)

            .success((vis_info) => {

                Galaxy.modal.hide();

                this.view.vis_id = vis_info.vis_id;

                this.view.vis_id = vis_info.id;

                this.view.has_changes = false;



                // Needed to set URL when first saving a visualization.

lib/galaxy/managers/jobs.py

+7 −2
Original line number Diff line number Diff line
@@ -345,7 +345,7 @@ class JobManager: 


    def stop(self, job, message=None):

        if not job.finished:

            job.mark_deleted(self.app.config.track_jobs_in_database)

            job.mark_deleted(self.app.config.track_jobs_in_database, message)

            session = self.app.model.session

            session.commit()

            self.app.job_manager.stop(job, message=message)
@@ -391,7 +391,12 @@ class JobSearch: 
                current_case = param_dump

                for p in path:

                    current_case = current_case[p]

                src = current_case["src"]

                src = current_case.get("src")

                if src is None:

                    # just a parameter named id.

                    # TODO: dispatch on tool parameter type instead of values,

                    # maybe with tool state variant

                    return key, value

                current_case = param

                for i, p in enumerate(path):

                    if p == "values" and i == len(path) - 2:

lib/galaxy/model/__init__.py

+28 −17
Original line number Diff line number Diff line
@@ -1893,7 +1893,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
        else:

            self.state = Job.states.STOPPED



    def mark_deleted(self, track_jobs_in_database=False):

    def mark_deleted(self, track_jobs_in_database=False, message=None):

        """

        Mark this job as deleted, and mark any output datasets as discarded.

        """
@@ -1904,7 +1904,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
            self.state = Job.states.DELETING

        else:

            self.state = Job.states.DELETED

        self.info = "Job output deleted by user before job completed."

        info = message or "Job output deleted by user before job completed."

        self.info = info

        for jtoda in self.output_datasets:

            output_hda = jtoda.dataset

            output_hda.deleted = True
@@ -1914,7 +1915,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable): 
                shared_hda.deleted = True

                shared_hda.blurb = "deleted"

                shared_hda.peek = "Job deleted"

                shared_hda.info = "Job output deleted by user before job completed"

                shared_hda.info = info



    def mark_failed(self, info="Job execution failed", blurb=None, peek=None):

        """
@@ -3686,6 +3687,10 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable 
        """Return all active contents ordered by hid."""

        return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)



    @property

    def visible_contents(self):

        return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)



    def contents_iter(self, **kwds):

        """

        Fetch filtered list of contents of history.
@@ -4979,11 +4984,16 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
    def display_info(self):

        return self.datatype.display_info(self)



    def get_converted_files_by_type(self, file_type):

    def get_converted_files_by_type(self, file_type, include_errored=False):

        for assoc in self.implicitly_converted_datasets:

            if not assoc.deleted and assoc.type == file_type:

                item = assoc.dataset or assoc.dataset_ldda

                if not item.deleted and item.state in Dataset.valid_input_states:

                valid_states = (

                    (Dataset.states.ERROR, *Dataset.valid_input_states)

                    if include_errored

                    else Dataset.valid_input_states

                )

                if not item.deleted and item.state in valid_states:

                    return item

        return None
@@ -4998,7 +5008,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
            depends_list = []

        return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}



    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):

    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):

        """

        Return converted dataset(s) if they exist, along with a dict of dependencies.

        If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -5010,7 +5020,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 
        converted_dataset = self.get_metadata_dataset(target_ext)

        if converted_dataset:

            return converted_dataset

        converted_dataset = self.get_converted_files_by_type(target_ext)

        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)

        if converted_dataset:

            return converted_dataset

        deps = {}
@@ -5232,7 +5242,8 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): 


        # Get converted dataset; this will start the conversion if necessary.

        try:

            converted_dataset = self.get_converted_dataset(trans, target_type)

            # Include errored datasets here, we let user chose to retry or view error

            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)

        except NoConverterException:

            return self.conversion_messages.NO_CONVERTER

        except ConverterDependencyException as dep_error:
@@ -7871,7 +7882,7 @@ class Workflow(Base, Dictifiable, RepresentById): 
    source_metadata: Mapped[Optional[Dict[str, str]]] = mapped_column(JSONType)

    uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)



    steps = relationship(

    steps: Mapped[List["WorkflowStep"]] = relationship(

        "WorkflowStep",

        back_populates="workflow",

        primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
@@ -7921,7 +7932,7 @@ class Workflow(Base, Dictifiable, RepresentById): 
        return rval



    @property

    def steps_by_id(self):

    def steps_by_id(self) -> Dict[int, "WorkflowStep"]:

        steps = {}

        for step in self.steps:

            step_id = step.id
@@ -8096,7 +8107,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime): 
        back_populates="workflow_step",

    )

    post_job_actions = relationship("PostJobAction", back_populates="workflow_step")

    inputs = relationship("WorkflowStepInput", back_populates="workflow_step")

    inputs: Mapped[List["WorkflowStepInput"]] = relationship("WorkflowStepInput", back_populates="workflow_step")

    workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship(back_populates="workflow_step")

    output_connections: Mapped[List["WorkflowStepConnection"]] = relationship(

        primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
@@ -8436,16 +8447,16 @@ class WorkflowStepConnection(Base, RepresentById): 
    output_name: Mapped[Optional[str]] = mapped_column(TEXT)

    input_subworkflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)



    input_step_input = relationship(

    input_step_input: Mapped["WorkflowStepInput"] = relationship(

        "WorkflowStepInput",

        back_populates="connections",

        cascade="all",

        primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),

    )

    input_subworkflow_step = relationship(

    input_subworkflow_step: Mapped[Optional["WorkflowStep"]] = relationship(

        "WorkflowStep", primaryjoin=(lambda: WorkflowStepConnection.input_subworkflow_step_id == WorkflowStep.id)

    )

    output_step = relationship(

    output_step: Mapped["WorkflowStep"] = relationship(

        "WorkflowStep",

        back_populates="output_connections",

        cascade="all",
@@ -8469,7 +8480,7 @@ class WorkflowStepConnection(Base, RepresentById): 


    @property

    def input_step(self) -> Optional[WorkflowStep]:

        return self.input_step_input and self.input_step_input.workflow_step

        return self.input_step_input.workflow_step



    @property

    def input_step_id(self):
@@ -8678,7 +8689,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl 
        back_populates="workflow_invocation",

        order_by=lambda: WorkflowInvocationStep.order_index,

    )

    workflow = relationship("Workflow")

    workflow: Mapped[Workflow] = relationship("Workflow")

    output_dataset_collections = relationship(

        "WorkflowInvocationOutputDatasetCollectionAssociation",

        back_populates="workflow_invocation",
@@ -9594,7 +9605,7 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable): 
        ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True

    )

    workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"))

    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)

    value: Mapped[Optional[Dict[str, Any]]] = mapped_column(MutableJSONType)

    workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()

    workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="step_states")

lib/galaxy/tool_util/toolbox/__init__.py

+2 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
from .base import (

    AbstractToolBox,

    AbstractToolTagManager,

    ToolLoadConfigurationConflict,

    ToolLoadError,

)

from .panel import (
@@ -15,6 +16,7 @@ __all__ = ( 
    "AbstractToolBox",

    "AbstractToolTagManager",

    "panel_item_types",

    "ToolLoadConfigurationConflict",

    "ToolLoadError",

    "ToolSection",

    "ToolSectionLabel",