Commit 844af82c authored by davelopez's avatar davelopez
Browse files

Use correct model_store_format when importing from uri

parent 6a00dc65

lib/galaxy/managers/model_stores.py

+1 −0
Original line number Diff line number Diff line
@@ -168,6 +168,7 @@ class ModelStoreManager: 
            self._app,

            galaxy_user,

            import_options,

            model_store_format=request.model_store_format,

        )

        new_history = history is None and not request.for_library

        if new_history:

lib/galaxy/model/store/__init__.py

+4 −4
Original line number Diff line number Diff line
@@ -2241,7 +2241,7 @@ def source_to_import_store( 
    app: StoreAppProtocol,

    galaxy_user: Optional[model.User],

    import_options: Optional[ImportOptions],

    model_store_format: Optional[str] = None,

    model_store_format: Optional[ModelStoreFormat] = None,

) -> ModelImportStore:

    if isinstance(source, dict):

        if model_store_format is not None:
@@ -2279,8 +2279,8 @@ def source_to_import_store( 
                target_path, import_options=import_options, app=app, user=galaxy_user, tag_handler=tag_handler

            )

        else:

            model_store_format = model_store_format or "tgz"

            if model_store_format in ["tar.gz", "tgz", "tar"]:

            model_store_format = model_store_format or ModelStoreFormat.TGZ

            if ModelStoreFormat.is_compressed(model_store_format):

                try:

                    temp_dir = mkdtemp()

                    target_dir = CompressedFile(target_path).extract(temp_dir)
@@ -2290,7 +2290,7 @@ def source_to_import_store( 
                model_import_store = get_import_model_store_for_directory(

                    target_dir, import_options=import_options, app=app, user=galaxy_user, tag_handler=tag_handler

                )

            elif model_store_format in ["bag.gz", "bag.tar", "bag.zip"]:

            elif ModelStoreFormat.is_bag(model_store_format):

                model_import_store = BagArchiveImportModelStore(

                    target_path, import_options=import_options, app=app, user=galaxy_user

                )

lib/galaxy/schema/schema.py

+8 −0
Original line number Diff line number Diff line
@@ -1291,6 +1291,14 @@ class ModelStoreFormat(str, Enum): 
    BAG_DOT_TAR = "bag.tar"

    BAG_DOT_TGZ = "bag.tgz"



    @classmethod

    def is_compressed(cls, value: "ModelStoreFormat"):

        return value in [cls.TAR_DOT_GZ, cls.TGZ, cls.TAR, cls.ROCRATE_ZIP]



    @classmethod

    def is_bag(cls, value: "ModelStoreFormat"):

        return value in [cls.BAG_DOT_TAR, cls.BAG_DOT_TGZ, cls.BAG_DOT_ZIP]





class StoreContentSource(Model):

    store_content_uri: Optional[str]

lib/galaxy/schema/tasks.py

+2 −0
Original line number Diff line number Diff line
@@ -8,6 +8,7 @@ from pydantic import ( 
from .schema import (

    DatasetSourceType,

    HistoryContentType,

    ModelStoreFormat,

    StoreExportPayload,

    WriteStoreToPayload,

)
@@ -82,6 +83,7 @@ class ImportModelStoreTaskRequest(BaseModel): 
    history_id: Optional[int]

    source_uri: str

    for_library: bool

    model_store_format: Optional[ModelStoreFormat]





class MaterializeDatasetInstanceTaskRequest(BaseModel):

lib/galaxy/webapps/galaxy/services/histories.py

+1 −0
Original line number Diff line number Diff line
@@ -278,6 +278,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores): 
            user=trans.async_request_user,

            source_uri=source_uri,

            for_library=False,

            model_store_format=payload.model_store_format,

        )

        result = import_model_store.delay(request=request)

        return async_task_summary(result)