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https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
Allow the Apply Rules tool to attach tags to output datasets.
This commit is contained in:
John Chilton
@@ -788,7 +788,7 @@ const MAPPING_TARGETS = {
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help: _l(
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"Add a general purpose tag based on the specified column value, use : to separate key-value pairs if desired. These tags are not propagated to derived datasets the way name and group tags are."
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),
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modes: ["raw", "ftp", "datasets", "library_datasets"],
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modes: ["raw", "ftp", "datasets", "library_datasets", "collection_contents"],
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},
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group_tags: {
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multiple: true,
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@@ -796,7 +796,7 @@ const MAPPING_TARGETS = {
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help: _l(
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"Add a group tag based on the specified column value, use : to separate key-value pairs. These tags are propagated to derived datasets and may be useful for factorial experiments."
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),
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modes: ["raw", "ftp", "datasets", "library_datasets"],
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modes: ["raw", "ftp", "datasets", "library_datasets", "collection_contents"],
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},
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name: {
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label: _l("Name"),
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@@ -499,6 +499,7 @@ class DatasetCollectionManager:
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def _build_elements_from_rule_data(self, collection_type_description, rule_set, data, sources, handle_dataset):
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identifier_columns = rule_set.identifier_columns
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mapping_as_dict = rule_set.mapping_as_dict
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elements = OrderedDict()
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for data_index, row_data in enumerate(data):
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# For each row, find place in depth for this element.
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@@ -518,7 +519,22 @@ class DatasetCollectionManager:
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else:
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raise Exception("Unknown indicator of paired status encountered - only values of F, R, 1, 2, R1, R2, forward, or reverse are allowed.")
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elements_at_depth[identifier] = handle_dataset(sources[data_index]["dataset"])
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tags = []
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if "group_tags" in mapping_as_dict:
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columns = mapping_as_dict["group_tags"]["columns"]
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for tag_column in columns:
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tag = row_data[tag_column]
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tags.append("group:%s" % tag)
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if "tags" in mapping_as_dict:
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columns = mapping_as_dict["tags"]["columns"]
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for tag_column in columns:
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tag = row_data[tag_column]
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tags.append(tag)
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effective_dataset = handle_dataset(sources[data_index]["dataset"], tags)
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elements_at_depth[identifier] = effective_dataset
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# log.info("Handling dataset [%s] with sources [%s], need to add tags [%s]" % (effective_dataset, sources, tags))
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else:
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collection_type_at_depth = collection_type_at_depth.child_collection_type_description()
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found = False
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@@ -3158,9 +3158,11 @@ class ApplyRulesTool(DatabaseOperationTool):
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rule_set = RuleSet(incoming["rules"])
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copied_datasets = []
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def copy_dataset(dataset):
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def copy_dataset(dataset, tags):
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copied_dataset = dataset.copy(flush=False)
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copied_datasets.append(copied_dataset)
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if tags is not None:
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self.app.tag_handler.set_tags_from_list(trans.get_user(), copied_dataset, tags)
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return copied_dataset
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new_elements = self.app.dataset_collections_service.apply_rules(
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@@ -1,6 +1,6 @@
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<tool id="__APPLY_RULES__"
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name="Apply Rule to Collection"
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version="1.0.0"
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version="1.1.0"
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tool_type="apply_rules_to_collection">
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<type class="ApplyRulesTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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@@ -553,6 +553,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
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def test_apply_rules_4(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_4)
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def test_apply_rules_5(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_5)
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def test_apply_rules_6(self):
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self._apply_rules_and_check(rules_test_data.EXAMPLE_6)
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@skip_without_tool("multi_select")
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def test_multi_select_as_list(self):
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with self.dataset_populator.test_history() as history_id:
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@@ -37,6 +37,39 @@ def check_example_4(hdca, dataset_populator):
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assert "object" in i1_element, hdca
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assert "element_identifier" in i1_element
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assert i1_element["element_identifier"] == "i1", hdca
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assert len(i1_element["object"]["tags"]) == 0
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def check_example_5(hdca, dataset_populator):
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assert hdca["collection_type"] == "list:list"
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assert hdca["element_count"] == 2
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first_collection_level = hdca["elements"][0]
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assert first_collection_level["element_identifier"] == "single", hdca
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assert first_collection_level["element_type"] == "dataset_collection"
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second_collection_level = first_collection_level["object"]
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assert "elements" in second_collection_level, hdca
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assert len(second_collection_level["elements"]) == 1, hdca
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i1_element = second_collection_level["elements"][0]
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assert "object" in i1_element, hdca
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assert "element_identifier" in i1_element
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assert i1_element["element_identifier"] == "i1", hdca
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tags = i1_element["object"]["tags"]
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assert len(tags) > 0
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assert "group:single" in tags, tags
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assert "i1" in tags, tags
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def check_example_6(hdca, dataset_populator):
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assert hdca["collection_type"] == "list"
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assert hdca["element_count"] == 3
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i1_element = hdca["elements"][0]
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assert "object" in i1_element, hdca
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assert "element_identifier" in i1_element
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assert i1_element["element_identifier"] == "i1", hdca
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tags = i1_element["object"]["tags"]
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assert len(tags) == 2
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assert "random" in tags
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assert "group:type:single" in tags
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EXAMPLE_1 = {
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@@ -208,3 +241,110 @@ EXAMPLE_4 = {
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"check": check_example_4,
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"output_hid": 8,
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}
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EXAMPLE_5 = {
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"rules": {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_column_group_tag_value",
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"value": "type",
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"default_value": "unused"
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}
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [1, 0],
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},
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{
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"type": "group_tags",
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"columns": [1],
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},
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{
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"type": "tags",
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"columns": [0],
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},
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],
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},
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"test_data": {
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"type": "list",
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"elements": [
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{
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"identifier": "i1",
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"contents": "0",
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"class": "File",
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"tags": ["random", "group:type:single"]
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},
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{
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"identifier": "i2",
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"contents": "1",
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"class": "File",
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"tags": ["random", "group:type:paired"]
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},
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{
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"identifier": "i3",
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"contents": "2",
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"class": "File",
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"tags": ["random", "group:type:paired"]
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},
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]
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},
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"check": check_example_5,
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"output_hid": 8,
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}
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EXAMPLE_6 = {
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"rules": {
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"rules": [
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{
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"type": "add_column_metadata",
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"value": "identifier0",
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},
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{
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"type": "add_column_metadata",
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"value": "tags",
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}
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],
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"mapping": [
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{
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"type": "list_identifiers",
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"columns": [0],
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},
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{
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"type": "tags",
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"columns": [1],
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},
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],
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},
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"test_data": {
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"type": "list",
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"elements": [
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{
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"identifier": "i1",
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"contents": "0",
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"class": "File",
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"tags": ["random", "group:type:single"]
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},
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{
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"identifier": "i2",
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"contents": "1",
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"class": "File",
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"tags": ["random", "group:type:paired"]
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},
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{
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"identifier": "i3",
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"contents": "2",
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"class": "File",
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"tags": ["random", "group:type:paired"]
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},
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]
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},
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"check": check_example_6,
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"output_hid": 8,
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}
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