Merge pull request #843 from jmchilton/collection_inputs

Tests for collection inputs to workflows.

Author: jmchilton

requirements.txt

@@ -13,6 +13,6 @@ virtualenv
 lxml
 gxformat2>=0.2.0
 ephemeris>=0.8
-galaxy-lib>=18.5.12
+galaxy-lib>=18.5.13
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09
 cwltool==1.0.20180508202931

tests/data/cat_list.xml

@@ -0,0 +1,16 @@
+<tool id="cat_list" name="Concatenate multiple datasets (for test workflows)">
+    <description>tail-to-head</description>
+    <command>
+        cat #for $q in $input1# $q #end for# > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset" multiple="true" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>

tests/data/wf5-collection-input.gxwf-test.yml

@@ -0,0 +1,20 @@
+- doc: Test Explicit Collection Creation.
+  job:
+    input1:
+      class: Collection
+      collection_type: list
+      elements:
+        - identifier: el1
+          class: File
+          path: hello.txt
+  outputs:
+    wf_output_1:
+      checksum: "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b"
+- doc: Test CWL-style list inputs.
+  job:
+    input1:
+      - class: File
+        path: hello.txt
+  outputs:
+    wf_output_1:
+      checksum: "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b"

tests/data/wf5-collection-input.gxwf.yml

@@ -0,0 +1,18 @@
+class: GalaxyWorkflow
+name: "Test Workflow - Collection Inputs"
+
+inputs:
+  - id: input1
+    type: collection
+    collection_type: list
+
+outputs:
+  - id: wf_output_1
+    source: first_cat#out_file1
+
+steps:
+  - tool_id: cat_list
+    label: first_cat
+    state:
+      input1:
+        $link: input1

tests/test_cmd_test.py

@@ -62,7 +62,7 @@ def test_workflow_test_simple_ga(self):
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_workflow_test_distro_tool(self):
-        """Test testing a simple GA workflow with Galaxy."""
+        """Test testing a workflow that uses distro tools."""
         with self._isolate():
             test_artifact = os.path.join(TEST_DATA_DIR, "wf4-distro-tools.gxwf.yml")
             test_command = [
@@ -82,6 +82,30 @@ def test_workflow_test_distro_tool(self):
             #        print(o.read())
             #    raise
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_workflow_test_collection_inputs(self):
+        """Test testing a workflow with collection inputs Galaxy."""
+        with self._isolate():
+            test_artifact = os.path.join(TEST_DATA_DIR, "wf5-collection-input.gxwf.yml")
+            cat_list = os.path.join(TEST_DATA_DIR, "cat_list.xml")
+            test_command = [
+                "--verbose",
+                "test"
+            ]
+            test_command = self.append_profile_argument_if_needed(test_command)
+            test_command += [
+                "--no_dependency_resolution",
+                "--galaxy_branch", "release_18.01",  # Much better workflow output detection than master for now (pre-release of 18.01)
+                "--extra_tools", cat_list,
+                test_artifact,
+            ]
+            # try:
+            self._check_exit_code(test_command, exit_code=0)
+            # except Exception:
+            #    with open(os.path.join(f, "tool_test_output.json"), "r") as o:
+            #        print(o.read())
+            #    raise
+
     @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
     def test_cwltool_tool_test(self):
         """Test testing a CWL tool with cwltool."""