Commit d8e94e71 authored by mvdbeek's avatar mvdbeek
Browse files

Fix running metadata tool on LDDAs 

The library tests were producing datasets with failed_metadata states,
but we never asserted the state, so we never noticed this.
parent e2ac10eb

lib/galaxy/tools/parameters/basic.py

+7 −8
Original line number Diff line number Diff line
@@ -1894,13 +1894,12 @@ class DataToolParameter(BaseDataToolParameter): 
                        rval.append(trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(decoded_id))

                    else:

                        raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])

                elif isinstance(single_value, trans.app.model.HistoryDatasetCollectionAssociation):

                    rval.append(single_value)

                elif isinstance(single_value, trans.app.model.DatasetCollectionElement):

                    rval.append(single_value)

                elif isinstance(single_value, trans.app.model.HistoryDatasetAssociation):

                    rval.append(single_value)

                elif isinstance(single_value, trans.app.model.LibraryDatasetDatasetAssociation):

                elif isinstance(single_value, (

                        trans.app.model.HistoryDatasetCollectionAssociation,

                        trans.app.model.DatasetCollectionElement,

                        trans.app.model.HistoryDatasetAssociation,

                        trans.app.model.LibraryDatasetDatasetAssociation

                )):

                    rval.append(single_value)

                else:

                    if len(str(single_value)) == 16:
@@ -1913,7 +1912,7 @@ class DataToolParameter(BaseDataToolParameter): 
                for val in rval:

                    if not isinstance(val, trans.app.model.HistoryDatasetCollectionAssociation):

                        raise ParameterValueError("if collections are supplied to multiple data input parameter, only collections may be used", self.name)

        elif isinstance(value, trans.app.model.HistoryDatasetAssociation):

        elif isinstance(value, (trans.app.model.HistoryDatasetAssociation, trans.app.model.LibraryDatasetDatasetAssociation)):

            rval = value

        elif isinstance(value, dict) and 'src' in value and 'id' in value:

            if value['src'] == 'hda':

lib/galaxy_test/api/test_libraries.py

+26 −28
Original line number Diff line number Diff line 
import json

import time

import unittest



from galaxy_test.base.populators import (
@@ -284,44 +283,43 @@ class LibrariesApiTestCase(ApiTestCase, TestsDatasets): 
        container_update_time = container_fetch_response.json()['folder_contents'][0]['update_time']

        assert dataset_update_time == container_update_time, container_fetch_response



    def test_update_dataset_in_folder(self):

        ld = self._create_dataset_in_folder_in_library("ForUpdateDataset")

        data = {'name': 'updated_name', 'file_ext': 'fastq', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'}

        create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data)

    def _patch_library_dataset(self, library_dataset_id, data):

        create_response = self._patch("libraries/datasets/{}".format(library_dataset_id), data=data)

        self._assert_status_code_is(create_response, 200)

        self._assert_has_keys(create_response.json(), "name", "file_ext", "misc_info", "genome_build")

        ld = create_response.json()

        library_id = ld['parent_library_id']

        return self.library_populator.wait_on_library_dataset(library={'id': library_id}, dataset=ld)



    def test_update_dataset_in_folder(self):

        ld = self._create_dataset_in_folder_in_library("ForUpdateDataset", content=">seq\nATGC", wait=True).json()

        data = {'name': 'updated_name', 'file_ext': 'fasta', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'}

        ld_updated = self._patch_library_dataset(ld['id'], data)

        self._assert_has_keys(ld_updated, "name", "file_ext", "misc_info", "genome_build")



    def test_update_dataset_tags(self):

        ld = self._create_dataset_in_folder_in_library("ForTagtestDataset")

        ld = self._create_dataset_in_folder_in_library("ForTagtestDataset", wait=True).json()

        data = {"tags": ["#Lancelot", "name:Holy Grail", "blue"]}

        create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data)

        self._assert_status_code_is(create_response, 200)

        self._assert_has_keys(create_response.json(), "tags")

        assert create_response.json()["tags"] == "name:Lancelot, name:HolyGrail, blue"

        ld_updated = self._patch_library_dataset(ld['id'], data)

        self._assert_has_keys(ld_updated, "tags")

        assert ld_updated["tags"] == "name:Lancelot, name:HolyGrail, blue"



    def test_invalid_update_dataset_in_folder(self):

        ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset")

        ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset", wait=True).json()

        data = {'file_ext': 'nonexisting_type'}

        create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data)

        create_response = self._patch("libraries/datasets/{}".format(ld["id"]), data=data)

        self._assert_status_code_is(create_response, 400)

        assert 'This Galaxy does not recognize the datatype of:' in create_response.json()['err_msg']



    def test_detect_datatype_of_dataset_in_folder(self):

        ld = self._create_dataset_in_folder_in_library("ForDetectDataset")

        # Wait for metadata job to finish.

        time.sleep(2)

        ld = self._create_dataset_in_folder_in_library("ForDetectDataset", wait=True).json()

        data = {'file_ext': 'data'}

        create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data)

        self._assert_status_code_is(create_response, 200)

        self._assert_has_keys(create_response.json(), "file_ext")

        assert create_response.json()["file_ext"] == "data"

        # Wait for metadata job to finish.

        time.sleep(2)

        ld_updated = self._patch_library_dataset(ld['id'], data)

        self._assert_has_keys(ld_updated, "file_ext")

        assert ld_updated["file_ext"] == "data"

        data = {'file_ext': 'auto'}

        create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data)

        self._assert_status_code_is(create_response, 200)

        self._assert_has_keys(create_response.json(), "file_ext")

        assert create_response.json()["file_ext"] == "txt"

        ld_updated = self._patch_library_dataset(ld['id'], data)

        self._assert_has_keys(ld_updated, "file_ext")

        assert ld_updated["file_ext"] == "txt"



    def test_ldda_collection_import_to_history(self):

        self._import_to_history(visible=True)
@@ -426,13 +424,13 @@ class LibrariesApiTestCase(ApiTestCase, TestsDatasets): 
        )

        return self._post("folders/%s" % containing_folder_id, data=create_data)



    def _create_dataset_in_folder_in_library(self, library_name):

    def _create_dataset_in_folder_in_library(self, library_name, content="1 2 3", wait=False):

        library = self.library_populator.new_private_library(library_name)

        folder_response = self._create_folder(library)

        self._assert_status_code_is(folder_response, 200)

        folder_id = folder_response.json()[0]['id']

        history_id = self.dataset_populator.new_history()

        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id']

        hda_id = self.dataset_populator.new_dataset(history_id, content=content, wait=wait)['id']

        payload = {'from_hda_id': hda_id, 'create_type': 'file', 'folder_id': folder_id}

        ld = self._post("libraries/%s/contents" % folder_id, payload)

        return ld

lib/galaxy_test/base/populators.py

+1 −1
Original line number Diff line number Diff line
@@ -1570,7 +1570,7 @@ def wait_on_state(state_func, desc="state", skip_states=None, ok_states=None, as 
            return state



    if skip_states is None:

        skip_states = ["running", "queued", "new", "ready", "stop", "stopped"]

        skip_states = ["running", "queued", "new", "ready", "stop", "stopped", "setting_metadata"]

    if ok_states is None:

        ok_states = ["ok", "scheduled"]

    try: