Unverified Commit a22d7187 authored by mvdbeek's avatar mvdbeek
Browse files

Add `__FETCH_DATA__` support for composite metadata

parent 23a623d9

client/src/api/schema/schema.ts

+2 −0
Original line number Diff line number Diff line
@@ -6749,6 +6749,8 @@ export interface components { 
            hashes?: components["schemas"]["FetchDatasetHash"][] | null;

            /** Info */

            info?: string | null;

            /** Metadata */

            metadata?: Record<string, never> | null;

            /** Name */

            name?: string | number | boolean | null;

            /**

lib/galaxy/model/store/discover.py

+8 −0
Original line number Diff line number Diff line
@@ -80,6 +80,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 
        name,

        filename=None,

        extra_files=None,

        metadata=None,

        metadata_source_name=None,

        info=None,

        library_folder=None,
@@ -152,6 +153,12 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 
        if final_job_state == galaxy.model.Job.states.ERROR and not self.get_implicit_collection_jobs_association_id():

            primary_data.visible = True



        if metadata:

            for key, value in metadata.items():

                metadata_element = primary_data.datatype.metadata_spec.get(key)

                if metadata_element and metadata_element.set_in_upload:

                    setattr(primary_data.metadata, key, value)



        for source_dict in sources:

            source = galaxy.model.DatasetSource()

            source.source_uri = source_dict["source_uri"]
@@ -860,6 +867,7 @@ def persist_hdas(elements, model_persistence_context, final_job_state="ok"): 
                    name=name,

                    filename=discovered_file.path,

                    extra_files=extra_files,

                    metadata=element.get("metadata"),

                    info=info,

                    tag_list=tag_list,

                    link_data=link_data,

lib/galaxy/schema/fetch_data.py

+3 −0
Original line number Diff line number Diff line 
import json

from enum import Enum

from typing import (

    Any,

    Dict,

    List,

    Optional,

    Union,
@@ -181,6 +183,7 @@ class PathDataElement(BaseDataElement): 
class CompositeDataElement(BaseDataElement):

    src: Literal["composite"]

    composite: "CompositeItems"

    metadata: Optional[Dict[str, Any]] = None





class CompositeItems(FetchBaseModel):

lib/galaxy/tool_util/client/staging.py

+2 −0
Original line number Diff line number Diff line
@@ -122,6 +122,8 @@ class StagingInterface(metaclass=abc.ABCMeta): 
                    for i, composite_data in enumerate(upload_target.composite_data):

                        composite_item_src = _attach_file(fetch_payload, composite_data, index=i)

                        composite_items.append(composite_item_src)

                    if "metadata" in upload_target.properties:

                        fetch_payload["targets"][0]["elements"][0]["metadata"] = upload_target.properties["metadata"]

                    fetch_payload["targets"][0]["elements"][0]["src"] = "composite"

                    fetch_payload["targets"][0]["elements"][0]["composite"] = {

                        "items": composite_items,

lib/galaxy/tool_util/cwl/util.py

+2 −0
Original line number Diff line number Diff line
@@ -241,6 +241,8 @@ def galactic_job_json( 
            kwd["decompress"] = value["decompress"]

        if value.get("hashes"):

            kwd["hashes"] = value["hashes"]

        if value.get("metadata"):

            kwd["metadata"] = value["metadata"]

        if composite_data_raw:

            composite_data = []

            for entry in composite_data_raw: