Merge pull request #13 from kikkomep/feature/dataset-type-support

Feature/dataset type support
phnmnl · Feb 27, 2017 · 40b8dcc · 40b8dcc
2 parents 1410964 + dc70afd
commit 40b8dcc
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Showing 2 changed files with 19 additions and 5 deletions.
diff --git a/docs/config-file.rst b/docs/config-file.rst
@@ -115,6 +115,16 @@ should be used for that input.
 
 The relative path is interpreted relative to the `Base path`_.
 
+By default Galaxy automatically detects the type of the input dataset by its file extension.
+If you need to specify the type of the input dataset you can use the following extended syntax:
+
+.. code-block:: YAML
+
+      inputs:
+        DataMatrix:
+            file: "sacurine/input/dataMatrix.tsv"
+            type: "tsv"
+
 
 Specifying workflow outputs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/wft4galaxy/core.py b/wft4galaxy/core.py
@@ -283,9 +283,9 @@ def set_inputs(self, inputs):
         :return: a dictionary of mappings (see :class:`WorkflowTestConfiguration`)
         """
         for name, config in inputs.items():
-            self.add_input(name, config["file"])
+            self.add_input(name, config["file"], config["type"] if "type" in config else None)
 
-    def add_input(self, name, file):
+    def add_input(self, name, file, type=None):
         """
         Add a new input mapping.
 
@@ -297,7 +297,7 @@ def add_input(self, name, file):
         """
         if not name:
             raise ValueError("Input name not defined")
-        self._inputs[name] = {"name": name, "file": file if isinstance(file, list) else [file]}
+        self._inputs[name] = {"name": name, "file": file if isinstance(file, list) else [file], "type": type}
 
     def remove_input(self, name):
         """
@@ -1151,8 +1151,12 @@ def run_test(self, base_path=None, inputs=None, params=None, expected_outputs=No
                 for label, config in inputs.items():
                     datamap[label] = []
                     for filename in config["file"]:
-                        datamap[label].append(history.upload_dataset(filename if _os.path.isabs(filename)
-                                                                     else _os.path.join(base_path, filename)))
+                        dataset_filename = filename if _os.path.isabs(filename) else _os.path.join(base_path, filename)
+                        if config["type"]:
+                            datamap[label].append(
+                                history.upload_dataset(dataset_filename, file_type=config["type"]))
+                        else:
+                            datamap[label].append(history.upload_dataset(dataset_filename))
 
                 # run the workflow
                 _logger.info("Workflow '%s' (id: %s) running ...", workflow.name, workflow.id)