diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py
index 266839a7151..08c6649ec76 100644
--- a/lib/galaxy/tools/parser/xml.py
+++ b/lib/galaxy/tools/parser/xml.py
@@ -127,12 +127,13 @@ class XmlToolSource(ToolSource):
return environment_variables
def parse_interpreter(self):
+ interpreter = None
command_el = self._command_el
- interpreter = (command_el is not None) and command_el.get("interpreter", None)
- if not self.legacy_defaults:
- log.warning("Deprecated interpeter attribute on command element is now ignored.")
+ if command_el is not None:
+ interpreter = command_el.get("interpreter", None)
+ if interpreter and not self.legacy_defaults:
+ log.warning("Deprecated interpreter attribute on command element is now ignored.")
interpreter = None
-
return interpreter
def parse_version_command(self):
diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index f2bda039f76..506f0c0e812 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -471,8 +471,8 @@ This function is called before the tool is executed. If it raises any exceptions
```python
def validate(incoming):
"""Validator for the plotting program"""
-
-
+
+
bins = incoming.get("bins","")
col = incoming.get("col","")
@@ -523,8 +523,8 @@ This code executes after the background process running the tool finishes its ru
from galaxy import datatypes
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
ext = param_dict.get('extension', 'text')
- items = out_data.items()
- for name, data in items:
+ items = out_data.items()
+ for name, data in items:
newdata = datatypes.factory(ext)(id=data.id)
for key, value in data. __dict__.items():
setattr(newdata, key, value)
@@ -2120,7 +2120,7 @@ effectively be a list with one ``None``-like entity in it.
The following idiom can be used to iterate over such a list and build a hypothetical ``-B``
parameter for each file - the ``if`` block is used to handle the case where a ``None``-like
-entity appears in the list because no files were selected:
+entity appears in the list because no files were selected:
```
#for $input in $input1
@@ -2830,7 +2830,7 @@ exclusively use ``filter``s to populate options.
### ``from_data_table``
See Galaxy's
-[data tables documentation](https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables)
+[data tables documentation](https://galaxyproject.org/admin/tools/data-tables)
for information on setting up data tables.
Once a data table has been configured and populated, these can be easily
@@ -3132,7 +3132,7 @@ specified by the ``skip`` attribute.
Tool data table name to check against
if ``type`` is ``dataset_metadata_in_tool_data``. See the documentation for
-[tool data tables](https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables)
+[tool data tables](https://galaxyproject.org/admin/tools/data-tables)
and [data managers](https://galaxyproject.org/admin/tools/data-managers/) for
more information.
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 155bab07e3d..673a217b727 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -307,13 +307,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
# copy from library dataset
hda = None
if source == 'library':
- ld = self.get_library_dataset(trans, content)
- # TODO: why would get_library_dataset NOT return a library dataset?
- if type(ld) is not trans.app.model.LibraryDataset:
- raise exceptions.RequestParameterInvalidException(
- "Library content id ( %s ) is not a dataset" % content)
- # insert into history
- hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
+ hda = self.__create_hda_from_ldda(trans, content, history)
# copy an existing, accessible hda
elif source == 'hda':
@@ -329,6 +323,15 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
return self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
+ def __create_hda_from_ldda(self, trans, content, history):
+ hda = None
+ ld = self.get_library_dataset(trans, content)
+ if type(ld) is not trans.app.model.LibraryDataset:
+ raise exceptions.RequestParameterInvalidException(
+ "Library content id ( %s ) is not a dataset" % content)
+ hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
+ return hda
+
def __create_datasets_from_library_folder(self, trans, history, payload, **kwd):
rval = []
@@ -374,10 +377,54 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
return rval
def __create_dataset_collection(self, trans, history, payload, **kwd):
+ """Create hdca in a history from the list of element identifiers
+
+ :param history: history the new hdca should be added to
+ :type history: History
+ :param source: whether to create a new collection or copy existing one
+ :type source: str
+ :param payload: dictionary structure containing:
+ :param collection_type: type (and depth) of the new collection
+ :type name: str
+ :param element_identifiers: list of elements that should be in the new collection
+ :param element: one member of the collection
+ :param name: name of the element
+ :type name: str
+ :param src: source of the element (hda/ldda)
+ :type src: str
+ :param id: identifier
+ :type id: str
+ :type element: dict
+ :type name: list
+ :param name: name of the collection
+ :type name: str
+ :param hide_source_items: whether to mark the original hdas as hidden
+ :type name: bool
+ :type payload: dict
+
+ .. note:: Elements may be nested depending on the collection_type
+
+ :returns: dataset collection information
+ :rtype: dict
+
+ :raises: RequestParameterInvalidException, RequestParameterMissingException
+ """
source = kwd.get("source", payload.get("source", "new_collection"))
service = trans.app.dataset_collections_service
if source == "new_collection":
create_params = api_payload_to_create_params(payload)
+ converted_identifiers = []
+ changed = False
+ for ei in payload.get('element_identifiers'):
+ # Convert lddas to hdas since there is no direct representation of library items in history.
+ if ei['src'] == 'ldda':
+ hda = self.__create_hda_from_ldda(trans, ei['id'], history)
+ converted_identifiers.append({"name": ei["name"], "src": "hda", "id": trans.security.encode_id(hda.id)})
+ changed = True
+ else:
+ converted_identifiers.append(ei)
+ if changed:
+ create_params['element_identifiers'] = converted_identifiers
dataset_collection_instance = service.create(
trans,
parent=history,
diff --git a/templates/user/register.mako b/templates/user/register.mako
index 4bfcf993ab6..659e32a0ebd 100644
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -173,7 +173,7 @@ def inherit(context):
<% subscribe_check_box.checked = True %>
%endif
${subscribe_check_box.get_html()}
- See
+ See
all Galaxy project mailing lists.
%endif
diff --git a/test/api/test_history_contents.py b/test/api/test_history_contents.py
index cb6d31d1a0f..bc2d59824a4 100644
--- a/test/api/test_history_contents.py
+++ b/test/api/test_history_contents.py
@@ -19,6 +19,7 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
super(HistoryContentsApiTestCase, self).setUp()
self.history_id = self._new_history()
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+ self.library_populator = LibraryPopulator(self)
def test_index_hda_summary(self):
hda1 = self._new_dataset(self.history_id)
@@ -57,7 +58,7 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
assert self.__count_contents(second_history_id) == 1
def test_library_copy(self):
- ld = LibraryPopulator(self).new_library_dataset("lda_test_library")
+ ld = self.library_populator.new_library_dataset("lda_test_library")
create_data = dict(
source='library',
content=ld["id"],
@@ -222,6 +223,43 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
self.__check_create_collection_response(create_response)
assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 1
+ def test_hdca_from_library_datasets(self):
+ ld = self.library_populator.new_library_dataset("el1")
+ ldda_id = ld["ldda_id"]
+ element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}]
+ create_data = dict(
+ history_id=self.history_id,
+ type="dataset_collection",
+ name="Test From Library",
+ element_identifiers=json.dumps(element_identifiers),
+ collection_type="list",
+ )
+ create_response = self._post("histories/%s/contents/dataset_collections" % self.history_id, create_data)
+ hdca = self.__check_create_collection_response(create_response)
+ elements = hdca["elements"]
+ assert len(elements) == 1
+ hda = elements[0]["object"]
+ assert hda["hda_ldda"] == "hda"
+ assert hda["history_content_type"] == "dataset"
+ assert hda["copied_from_ldda_id"] == ldda_id
+
+ def test_hdca_from_inaccessible_library_datasets(self):
+ library, library_dataset = self.library_populator.new_library_dataset_in_private_library("HDCACreateInaccesibleLibrary")
+ ldda_id = library_dataset["id"]
+ element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}]
+ create_data = dict(
+ history_id=self.history_id,
+ type="dataset_collection",
+ name="Test From Library",
+ element_identifiers=json.dumps(element_identifiers),
+ collection_type="list",
+ )
+ with self._different_user():
+ second_history_id = self._new_history()
+ create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data)
+ # TODO: This should be 403 and a proper JSON response.
+ self._assert_status_code_is(create_response, 400)
+
def __check_create_collection_response(self, response):
self._assert_status_code_is(response, 200)
dataset_collection = response.json()
diff --git a/test/api/test_libraries.py b/test/api/test_libraries.py
index b89019d106b..8050157e054 100644
--- a/test/api/test_libraries.py
+++ b/test/api/test_libraries.py
@@ -4,7 +4,6 @@ from base.populators import (
DatasetPopulator,
LibraryPopulator,
TestsDatasets,
- wait_on_state
)
@@ -83,20 +82,15 @@ class LibrariesApiTestCase(api.ApiTestCase, TestsDatasets):
create_response = self._post("folders/%s/contents" % folder_id, payload)
self._assert_status_code_is(create_response, 403)
+ def test_show_private_dataset_permissions(self):
+ library, library_dataset = self.library_populator.new_library_dataset_in_private_library("ForCreateDatasets", wait=True)
+ with self._different_user():
+ response = self.library_populator.show_ldda(library["id"], library_dataset["id"])
+ # TODO: this should really be 403 and a proper JSON exception.
+ self._assert_status_code_is(response, 400)
+
def test_create_dataset(self):
- library = self.library_populator.new_private_library("ForCreateDatasets")
- payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test")
- create_response = self._post("libraries/%s/contents" % library["id"], payload, files=files)
- self._assert_status_code_is(create_response, 200)
- library_datasets = create_response.json()
- assert len(library_datasets) == 1
- library_dataset = library_datasets[0]
-
- def show():
- return self._get("libraries/%s/contents/%s" % (library["id"], library_dataset["id"]))
-
- wait_on_state(show, assert_ok=True)
- library_dataset = show().json()
+ library, library_dataset = self.library_populator.new_library_dataset_in_private_library("ForCreateDatasets", wait=True)
self._assert_has_keys(library_dataset, "peek", "data_type")
assert library_dataset["peek"].find("create_test") >= 0
assert library_dataset["file_ext"] == "txt", library_dataset["file_ext"]
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index c0162be0883..4b8c481043e 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1355,6 +1355,29 @@ test_data:
name = content["name"]
assert name == "my new name", name
+ @skip_without_tool("create_2")
+ def test_run_rename_multiple_outputs(self):
+ with self.dataset_populator.test_history() as history_id:
+ self._run_jobs("""
+class: GalaxyWorkflow
+inputs: []
+steps:
+ - tool_id: create_2
+ state:
+ sleep_time: 0
+ outputs:
+ out_file1:
+ rename: "my new name"
+ out_file2:
+ rename: "my other new name"
+test_data: {}
+""", history_id=history_id)
+ details1 = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=True)
+ details2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
+
+ assert details1["name"] == "my new name"
+ assert details2["name"] == "my other new name"
+
@skip_without_tool("cat")
def test_run_rename_based_on_input(self):
history_id = self.dataset_populator.new_history()
diff --git a/test/base/populators.py b/test/base/populators.py
index 0328d416ecd..63b1c407dea 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -471,6 +471,26 @@ class LibraryPopulator(object):
wait_on_state(show, timeout=DEFAULT_TIMEOUT)
return show().json()
+ def show_ldda(self, library_id, library_dataset_id):
+ return self.api_test_case.galaxy_interactor.get("libraries/%s/contents/%s" % (library_id, library_dataset_id))
+
+ def new_library_dataset_in_private_library(self, library_name="private_dataset", wait=True):
+ library = self.new_private_library(library_name)
+ payload, files = self.create_dataset_request(library, file_type="txt", contents="create_test")
+ create_response = self.api_test_case.galaxy_interactor.post("libraries/%s/contents" % library["id"], payload, files=files)
+ api_asserts.assert_status_code_is(create_response, 200)
+ library_datasets = create_response.json()
+ assert len(library_datasets) == 1
+ library_dataset = library_datasets[0]
+ if wait:
+ def show():
+ return self.show_ldda(library["id"], library_dataset["id"])
+
+ wait_on_state(show, assert_ok=True)
+ library_dataset = show().json()
+
+ return library, library_dataset
+
class BaseDatasetCollectionPopulator(object):
diff --git a/test/functional/tools/create_2.xml b/test/functional/tools/create_2.xml
index f9827846f64..f04bab7f4a9 100644
--- a/test/functional/tools/create_2.xml
+++ b/test/functional/tools/create_2.xml
@@ -1,5 +1,5 @@
- '$out_file1';
echo "2" > '$out_file2';
sleep '$sleep_time';
diff --git a/test/integration/test_data_manager_table_reload.py b/test/integration/test_data_manager_table_reload.py
index e2c9cea8fe4..dae7e670ecc 100644
--- a/test/integration/test_data_manager_table_reload.py
+++ b/test/integration/test_data_manager_table_reload.py
@@ -37,8 +37,8 @@ FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {"dbkey_source|dbkey_source_selector": "ne
"dbkey_source|dbkey_name": "NC_001617.1",
"sequence_name": "NC_001617.1",
"sequence_id": "NC_001617.1",
- "reference_source|reference_source_selector": "ncbi",
- "reference_source|requested_identifier": "NC_001617.1",
+ "reference_source|reference_source_selector": "url",
+ "reference_source|user_url": "https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/NC_001617.1.fasta",
"sorting|sort_selector": "as_is"}
SAM_FASTA_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2"
SAM_FASTA_INPUT = {"all_fasta_source": "NC_001617.1", "sequence_name": "", "sequence_id": ""}
diff --git a/tools/data_source/microbial_import.xml b/tools/data_source/microbial_import.xml
index b07f557cb7e..5b817b62c8d 100644
--- a/tools/data_source/microbial_import.xml
+++ b/tools/data_source/microbial_import.xml
@@ -102,13 +102,5 @@ Current datasets available include
-----
Organisms in **bold** are available at the UCSC Browser.
-
------
-
-.. class:: infomark
-
-**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
-
-.. _here: https://wiki.galaxyproject.org/Main/Data%20Libraries/Microbes