Merge branch 'release_20.05' into dev

galaxyproject · Jun 1, 2020 · 3aebb5f · 3aebb5f
2 parents 98b5480 + 49c6f1d
commit 3aebb5f
Show file tree

Hide file tree

Showing 8 changed files with 184 additions and 15 deletions.
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
@@ -236,7 +236,11 @@ def __resolvers_dict(self):
 
     def find_best_container_description(self, enabled_container_types, tool_info, **kwds):
         """Yield best container description of supplied types matching tool info."""
-        resolved_container_description = self.resolve(enabled_container_types, tool_info, **kwds)
+        try:
+            resolved_container_description = self.resolve(enabled_container_types, tool_info, **kwds)
+        except Exception:
+            log.exception("Could not get container description for tool '%s'", tool_info.tool_id)
+            return None
         return None if resolved_container_description is None else resolved_container_description.container_description
 
     def resolve(self, enabled_container_types, tool_info, index=None, resolver_type=None, install=True, resolution_cache=None):

diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
@@ -18,6 +18,7 @@
 QUAY_REPOSITORY_API_ENDPOINT = 'https://quay.io/api/v1/repository'
 BUILD_NUMBER_REGEX = re.compile(r'\d+$')
 PARSED_TAG = collections.namedtuple('ParsedTag', 'tag version build_string build_number')
+QUAY_IO_TIMEOUT = 10
 
 
 def create_repository(namespace, repo_name, oauth_token):
@@ -29,7 +30,7 @@ def create_repository(namespace, repo_name, oauth_token):
         "description": "",
         "visibility": "public",
     }
-    requests.post("https://quay.io/api/v1/repository", json=data, headers=headers)
+    requests.post("https://quay.io/api/v1/repository", json=data, headers=headers, timeout=QUAY_IO_TIMEOUT)
 
 
 def quay_versions(namespace, pkg_name):
@@ -49,7 +50,7 @@ def quay_repository(namespace, pkg_name):
     assert namespace is not None
     assert pkg_name is not None
     url = 'https://quay.io/api/v1/repository/%s/%s' % (namespace, pkg_name)
-    response = requests.get(url, timeout=None)
+    response = requests.get(url, timeout=QUAY_IO_TIMEOUT)
     data = response.json()
     return data
 
@@ -65,7 +66,7 @@ def _namespace_has_repo_name(namespace, repo_name, resolution_cache):
         repos_parameters = {'public': 'true', 'namespace': namespace}
         repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'}
         repos_response = requests.get(
-            QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=None)
+            QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=QUAY_IO_TIMEOUT)
 
         repos = repos_response.json()['repositories']
         repo_names = [r["name"] for r in repos]

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -4865,6 +4865,8 @@ A contrived example of a tool that uses this is the test tool
 
 By default this file will not contain paths for data or collection inputs. To include simple
 paths for data parameters set the ``data_style`` attribute to ``paths`` (see [inputs_as_json_with_paths.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/inputs_as_json_with_paths.xml) for an example).
+
+For tools with profile >= 20.05 a select with ``multiple="true"`` is rendered as an array which is empty if nothing is selected. For older profile versions select lists are rendered as comma separated strings or a literal ``null`` in case nothing is selected.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:simpleContent>

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -2413,7 +2413,7 @@ def exec_before_job(self, app, inp_data, out_data, param_dict=None):
             raise Exception("Internal error - param_dict is empty.")
 
         job = {}
-        json_wrap(self.inputs, param_dict, job, handle_files='OBJECT')
+        json_wrap(self.inputs, param_dict, self.profile, job, handle_files='OBJECT')
         expression_inputs = {
             'job': job,
             'script': self._expression,

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
@@ -607,7 +607,10 @@ def __build_config_file_text(self, content):
             message = template % content_format
             raise Exception(message)
 
-        return json.dumps(wrapped_json.json_wrap(self.tool.inputs, self.param_dict, handle_files=handle_files)), False
+        return json.dumps(wrapped_json.json_wrap(self.tool.inputs,
+                                                 self.param_dict,
+                                                 self.tool.profile,
+                                                 handle_files=handle_files)), False
 
     def __write_workdir_file(self, config_filename, content, context, is_template=True, strip=False):
         parent_dir = os.path.dirname(config_filename)

diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py
@@ -1,25 +1,28 @@
 import logging
 
+import packaging.version
+
 log = logging.getLogger(__name__)
 
 SKIP_INPUT = object()
 
 
-def json_wrap(inputs, input_values, as_dict=None, handle_files="skip"):
+def json_wrap(inputs, input_values, profile, as_dict=None, handle_files="skip"):
     if as_dict is None:
         as_dict = {}
 
     for input in inputs.values():
         input_name = input.name
         value_wrapper = input_values[input_name]
-        json_value = _json_wrap_input(input, value_wrapper, handle_files=handle_files)
+        json_value = _json_wrap_input(input, value_wrapper, profile,
+                                      handle_files=handle_files)
         if json_value is SKIP_INPUT:
             continue
         as_dict[input_name] = json_value
     return as_dict
 
 
-def _json_wrap_input(input, value_wrapper, handle_files="skip"):
+def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
     input_type = input.type
 
     def _data_input_to_path(v):
@@ -32,23 +35,26 @@ def _data_input_to_path(v):
         repeat_job_value = []
         for d in value_wrapper:
             repeat_instance_job_value = {}
-            json_wrap(input.inputs, d, repeat_instance_job_value, handle_files=handle_files)
+            json_wrap(input.inputs, d, profile, repeat_instance_job_value,
+                      handle_files=handle_files)
             repeat_job_value.append(repeat_instance_job_value)
         json_value = repeat_job_value
     elif input_type == "conditional":
         values = value_wrapper
         current = values["__current_case__"]
         conditional_job_value = {}
-        json_wrap(input.cases[current].inputs, values, conditional_job_value, handle_files=handle_files)
+        json_wrap(input.cases[current].inputs, values, profile,
+                  conditional_job_value, handle_files=handle_files)
         test_param = input.test_param
         test_param_name = test_param.name
-        test_value = _json_wrap_input(test_param, values[test_param_name], handle_files=handle_files)
+        test_value = _json_wrap_input(test_param, values[test_param_name],
+                                      profile, handle_files=handle_files)
         conditional_job_value[test_param_name] = test_value
         json_value = conditional_job_value
     elif input_type == "section":
         values = value_wrapper
         section_job_value = {}
-        json_wrap(input.inputs, values, section_job_value, handle_files=handle_files)
+        json_wrap(input.inputs, values, profile, section_job_value, handle_files=handle_files)
         json_value = section_job_value
     elif input_type == "data" and input.multiple:
         if handle_files == "paths":
@@ -88,10 +94,10 @@ def _data_input_to_path(v):
     elif input_type == "boolean":
         json_value = _cast_if_not_none(value_wrapper, bool)
     elif input_type == "select":
-        if input.multiple:
+        if input.multiple and packaging.version.parse(str(profile)) >= packaging.version.parse('20.05'):
             json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]
         else:
-            json_value = _cast_if_not_none(value_wrapper.value, str)
+            json_value = _cast_if_not_none(value_wrapper, str)
     elif input_type == "data_column":
         # value is a SelectToolParameterWrapper()
         if input.multiple:

diff --git a/test/functional/tools/inputs_as_json_profile.xml b/test/functional/tools/inputs_as_json_profile.xml
@@ -0,0 +1,152 @@
+<!-- test if profile version of inputs json generation works, i.e.
+     - multiple selects get comma separated string (lists >= 20.05)
+     - empty optional selects get "None" ([] >= 20.05) -->
+<tool id="inputs_as_json" name="inputs_as_json" profile="20.01" version="1.0.0">
+    <command detect_errors="exit_code"><![CDATA[
+        cat inputs.json &&
+        python $check_inputs inputs.json $test_case
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+        <!-- Can specify with fixed path in working directory instead:
+        <inputs name="inputs" filename="input.json" />
+        -->
+        <configfile name="check_inputs"><![CDATA[
+import json
+import sys
+
+input_json_path = sys.argv[1]
+test_case = sys.argv[2]
+as_dict = json.load(open(input_json_path, "r"))
+
+def assert_equals(x, y):
+    assert x == y, "%s[%s] != %s[%s] " % (x, type(x), y, type(y))
+
+if test_case == "1":
+    assert_equals(as_dict["test_case"], 1)
+    assert_equals(as_dict["text_test"], "foo")
+    assert_equals(as_dict["booltest"], True)
+    assert_equals(as_dict["booltest2"], True)
+    assert_equals(as_dict["inttest"], 12456)
+    assert_equals(as_dict["floattest"], 6.789)
+    assert_equals(as_dict["radio_select"], "a_radio")
+    assert_equals(as_dict["optional_select"], "None")
+    assert_equals(as_dict["optional_multiple_select"], "None")
+    assert_equals(as_dict["repeat"][0]["r"], "000000")
+    assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
+    assert_equals(as_dict["cond"]["more_text"], "fdefault")
+    assert_equals(as_dict["section_example"]["section_text"], "section_default")
+    assert "data_input" not in as_dict
+elif test_case == "2":
+    assert_equals(as_dict["test_case"], 2)
+    assert_equals(as_dict["text_test"], "bar")
+    assert_equals(as_dict["booltest"], False)
+    assert_equals(as_dict["booltest2"], False)
+    assert_equals(as_dict["inttest"], None)
+    assert_equals(as_dict["floattest"], 1.0)
+    assert_equals(as_dict["radio_select"], "a_radio")
+    assert_equals(as_dict["optional_select"], "a")
+    assert_equals(as_dict["optional_multiple_select"], 'a,b')
+    assert_equals(as_dict["repeat"][0]["r"], "000000")
+    assert_equals(as_dict["cond"]["cond_test"], "second")
+    assert_equals(as_dict["cond"]["more_text"], "sdefault")
+    assert_equals(as_dict["section_example"]["section_text"], "section_default")
+    assert "data_input" not in as_dict
+
+with open("output", "w") as f:
+    f.write("okay\n")
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="test_case" type="integer" value="0" />
+        <param name="text_test" type="text" />
+        <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="booltest2" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="inttest" type="integer" optional="true" />
+        <param name="floattest" value="1.0" type="float" />
+        <param name="radio_select" type="select" display="radio">
+            <option value="a_radio" selected="true">A Radio</option>
+            <option value="b_radio">B Radio</option>
+            <option value="c_radio">C Radio</option>
+        </param>
+        <param name="data_input" type="data" optional="true" />
+        <param name="optional_select" type="select" optional="true">
+            <option value="a">A</option>
+            <option value="b">B</option>
+            <option value="c">C</option>
+        </param>
+        <param name="optional_multiple_select" type="select" optional="true" multiple="true">
+            <option value="a">A</option>
+            <option value="b">B</option>
+            <option value="c">C</option>
+        </param>
+        <repeat name="repeat" title="Repeat" min="1">
+            <param name="r" type="color" />
+        </repeat>
+        <conditional name="cond">
+            <param name="cond_test" type="select">
+                <option value="first" selected="true">First</option>
+                <option value="second">Second</option>
+            </param>
+            <when value="first">
+                <param name="more_text" type="text" value="fdefault" />
+            </when>
+            <when value="second">
+                <param name="more_text" type="text" value="sdefault" />
+            </when> 
+        </conditional>
+        <section name="section_example" title="Section Example">
+            <param name="section_text" type="text" value="section_default" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_file1" from_work_dir="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="test_case" value="1" />
+            <param name="text_test" value="foo" />
+            <param name="booltest" value="true" />
+            <param name="booltest2" value="booltrue" />
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <repeat name="repeat">
+                <param name="r" value="000000"/>
+            </repeat>
+            <repeat name="repeat">
+                <param name="r" value="FFFFFF"/>
+            </repeat>
+            <conditional name="cond">
+                <param name="cond_test" value="first" />
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="test_case" value="2" />
+            <param name="text_test" value="bar" />
+            <param name="booltest" value="false" />
+            <param name="booltest2" value="boolfalse" />
+            <param name="data_input" value="simple_line.txt" />
+            <param name="optional_select" value="a"/>
+            <param name="optional_multiple_select" value="a,b"/>
+            <!-- Testing null integers -->
+            <!-- <param name="inttest" value="12456" /> -->
+            <param name="r" value="000000" />
+            <conditional name="cond">
+                <param name="cond_test" value="second" />
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        Test tool demonstrating the special inputs config file.
+    </help>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
@@ -34,6 +34,7 @@
   <tool file="tool_provided_metadata_12.xml" />
   <tool file="empty_datasets.xml" />
   <tool file="inputs_as_json.xml" />
+  <tool file="inputs_as_json_profile.xml" />
   <tool file="inputs_as_json_with_paths.xml" />
   <tool file="filter_static_regexp.xml" />
   <tool file="dbkey_filter_input.xml" />