Unverified Commit e7092b6d authored by Dannon's avatar Dannon Committed by GitHub
Browse files

Merge pull request #15525 from mvdbeek/fix_visible_reverting 

[22.05] Fix visible handling for exisiting datasets on discovery
parents 40b9e8a6 69d2decf

lib/galaxy/model/store/discover.py

+2 −2
Original line number Diff line number Diff line
@@ -100,7 +100,6 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 


        if primary_data is not None:

            primary_data.extension = ext

            primary_data.visible = visible

            primary_data.dbkey = dbkey

        else:

            if not library_folder:
@@ -798,12 +797,13 @@ def persist_hdas(elements, model_persistence_context, final_job_state="ok"): 
                hashes = fields_match.hashes

                created_from_basename = fields_match.created_from_basename

                extra_files = fields_match.extra_files

                visible = fields_match.visible



                info, state = discovered_file.discovered_state(element, final_job_state)

                dataset = model_persistence_context.create_dataset(

                    ext=ext,

                    designation=designation,

                    visible=True,

                    visible=visible,

                    dbkey=dbkey,

                    name=name,

                    filename=discovered_file.path,

lib/galaxy/webapps/galaxy/api/history_contents.py

+2 −2
Original line number Diff line number Diff line
@@ -418,7 +418,7 @@ class FastAPIHistoryContents: 
    @router.get(

        "/api/histories/{history_id}/contents/{id}",

        name="history_content",

        summary="Return detailed information about an HDA within a history.",

        summary="Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.",

        response_model_exclude_unset=True,

        deprecated=True,

    )
@@ -675,7 +675,7 @@ class FastAPIHistoryContents: 
    )

    @router.put(

        "/api/histories/{history_id}/contents/{id}",

        summary="Updates the values for the history content item with the given ``ID``.",

        summary="Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.",

        response_model_exclude_unset=True,

        deprecated=True,

    )

lib/galaxy_test/api/test_tools.py

+17 −0
Original line number Diff line number Diff line
@@ -810,6 +810,23 @@ class ToolsTestCase(ApiTestCase, TestsTools): 
    def test_apply_rules_6(self):

        self._apply_rules_and_check(rules_test_data.EXAMPLE_6)



    @skip_without_tool("galaxy_json_sleep")

    def test_dataset_hidden_after_job_finish(self):

        with self.dataset_populator.test_history() as history_id:

            inputs = {

                "sleep_time": 5,

            }

            response = self._run("galaxy_json_sleep", history_id, inputs, assert_ok=True)

            output = response["outputs"][0]

            response = self._put(

                f"histories/{history_id}/contents/datasets/{output['id']}", data={"visible": False}, json=True

            )

            response.raise_for_status()

            output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output, wait=False)

            assert not output_details["visible"]

            output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output, wait=True)

            assert not output_details["visible"]



    @skip_without_tool("multi_select")

    def test_multi_select_as_list(self):

        with self.dataset_populator.test_history() as history_id:

test/functional/tools/galaxy_json_discover_and_sleep.xml

0 → 100644
+28 −0
Original line number Diff line number Diff line 
<tool id="galaxy_json_sleep" name="galaxy_json_sleep" version="1.0.0" profile="22.05">

    <command><![CDATA[ 

        touch out &&

        sleep $sleep_time &&

        cp '$c1' galaxy.json

    ]]></command>

    <configfiles>

        <configfile name="c1">{"output_tool_supplied_metadata": {

            "name": "my dynamic name",

            "ext": "txt",

            "info": "my dynamic info"

            }}

</configfile>

    </configfiles>

    <inputs>

        <param name="sleep_time" type="integer" value="0" />

    </inputs>

    <outputs>

        <data name="output" format="txt" from_work_dir="out" />

    </outputs>

    <tests>

        <test>

            <param name="input" value="7" />

            <output name="output" md5="d41d8cd98f00b204e9800998ecf8427e">

            </output>

        </test>

    </tests>

</tool>
 
 No newline at end of file

test/functional/tools/samples_tool_conf.xml

+10 −9
Original line number Diff line number Diff line
@@ -30,6 +30,7 @@ 
  <tool file="multi_output_assign_primary_ext_dbkey.xml" />

  <tool file="multi_output_recurse.xml" />

  <tool file="multi_output_recurse_collection.xml" />

  <tool file="galaxy_json_discover_and_sleep.xml" />

  <tool file="tool_provided_metadata_1.xml" />

  <tool file="tool_provided_metadata_2.xml" />

  <tool file="tool_provided_metadata_3.xml" />