Allow multiple simultaneous uploads via single POST.

lib/galaxy/tools/parameters/__init__.py

@@ -298,11 +298,10 @@ def populate_state(request_context, inputs, incoming, state, errors={}, prefix='
         elif input.type == 'section':
             populate_state(request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context, check=check)
         elif input.type == 'upload_dataset':
-            d_type = input.get_datatype(request_context, context=context)
-            writable_files = d_type.writable_files
-            while len(group_state) > len(writable_files):
+            file_count = input.get_file_count(request_context, context)
+            while len(group_state) > file_count:
                 del group_state[-1]
-            while len(writable_files) > len(group_state):
+            while file_count > len(group_state):
                 new_state = {'__index__' : len(group_state)}
                 for upload_item in input.inputs.values():
                     new_state[upload_item.name] = upload_item.get_initial_value(request_context, context)

lib/galaxy/tools/parameters/grouping.py

@@ -219,17 +219,30 @@ def get_file_base_name(self, context):
         fd = context.get('files_metadata|base_name', 'Galaxy_Composite_file')
         return fd
 
-    def get_file_type(self, context):
-        return context.get(self.file_type_name, self.default_file_type)
-
-    def get_datatype_ext(self, trans, context):
-        ext = self.get_file_type(context)
+    def get_file_type(self, context, parent_context=None):
+        file_type = context.get(self.file_type_name, None)
+        if file_type == "":
+            if parent_context:
+                file_type = parent_context.get(self.file_type_name, self.default_file_type)
+            else:
+                file_type = self.default_file_type
+        return file_type
+
+    def get_dbkey(self, context, parent_context=None):
+        dbkey = context.get("dbkey", None)
+        if dbkey == "":
+            if parent_context:
+                dbkey = parent_context.get("dbkey", dbkey)
+        return dbkey
+
+    def get_datatype_ext(self, trans, context, parent_context=None):
+        ext = self.get_file_type(context, parent_context=parent_context)
         if ext in self.file_type_to_ext:
             ext = self.file_type_to_ext[ext]  # when using autodetect, we will use composite info from 'text', i.e. only the main file
         return ext
 
-    def get_datatype(self, trans, context):
-        ext = self.get_datatype_ext(trans, context)
+    def get_datatype(self, trans, context, parent_context=None):
+        ext = self.get_datatype_ext(trans, context, parent_context=parent_context)
         return trans.app.datatypes_registry.get_datatype_by_extension(ext)
 
     @property
@@ -249,6 +262,8 @@ def title_by_index(self, trans, index, context):
                 if composite_file.optional:
                     rval = "%s [optional]" % rval
                 return rval
+        if index < self.get_file_count(trans, context):
+            return "Extra primary file"
         return None
 
     def value_to_basic(self, value, app):
@@ -279,10 +294,14 @@ def value_from_basic(self, value, app, ignore_errors=False):
             rval.append(rval_dict)
         return rval
 
+    def get_file_count(self, trans, context):
+        file_count = context.get("file_count", "auto")
+        return len(self.get_datatype(trans, context).writable_files) if file_count == "auto" else int(file_count)
+
     def get_initial_value(self, trans, context):
-        d_type = self.get_datatype(trans, context)
+        file_count = self.get_file_count(trans, context)
         rval = []
-        for i, (composite_name, composite_file) in enumerate(d_type.writable_files.items()):
+        for i in range(file_count):
             rval_dict = {}
             rval_dict['__index__'] = i  # create __index__
             for input in self.inputs.values():
@@ -356,6 +375,8 @@ def get_one_filename(context):
             name = context.get('NAME', None)
             info = context.get('INFO', None)
             uuid = context.get('uuid', None) or None  # Turn '' to None
+            file_type = context.get('file_type', None)
+            dbkey = self.get_dbkey(context)
             warnings = []
             to_posix_lines = False
             if context.get('to_posix_lines', None) not in ["None", None, False]:
@@ -405,6 +426,10 @@ def get_one_filename(context):
             file_bunch.auto_decompress = auto_decompress
             file_bunch.space_to_tab = space_to_tab
             file_bunch.uuid = uuid
+            if file_type is not None:
+                file_bunch.file_type = file_type
+            if dbkey is not None:
+                file_bunch.dbkey = dbkey
             return file_bunch, warnings
 
         def get_filenames(context):
@@ -414,6 +439,8 @@ def get_filenames(context):
             uuid = context.get('uuid', None) or None  # Turn '' to None
             name = context.get('NAME', None)
             info = context.get('INFO', None)
+            file_type = context.get('file_type', None)
+            dbkey = self.get_dbkey(context)
             to_posix_lines = False
             if context.get('to_posix_lines', None) not in ["None", None, False]:
                 to_posix_lines = True
@@ -429,13 +456,23 @@ def get_filenames(context):
                 file_bunch.to_posix_lines = to_posix_lines
                 file_bunch.auto_decompress = auto_decompress
                 file_bunch.space_to_tab = space_to_tab
+                if file_type is not None:
+                    file_bunch.file_type = file_type
+                if dbkey is not None:
+                    file_bunch.dbkey = dbkey
+
                 rval.append(file_bunch)
             for file_bunch in get_url_paste_urls_or_filename(context, override_name=name, override_info=info):
                 if file_bunch.path:
                     file_bunch.uuid = uuid
                     file_bunch.to_posix_lines = to_posix_lines
                     file_bunch.auto_decompress = auto_decompress
                     file_bunch.space_to_tab = space_to_tab
+                    if file_type is not None:
+                        file_bunch.file_type = file_type
+                    if dbkey is not None:
+                        file_bunch.dbkey = dbkey
+
                     rval.append(file_bunch)
             # look for files uploaded via FTP
             valid_files = []
@@ -474,15 +511,20 @@ def get_filenames(context):
                     file_bunch.to_posix_lines = to_posix_lines
                     file_bunch.auto_decompress = auto_decompress
                     file_bunch.space_to_tab = space_to_tab
+                    if file_type is not None:
+                        file_bunch.file_type = file_type
+                    if dbkey is not None:
+                        file_bunch.dbkey = dbkey
                     rval.append(file_bunch)
             return rval
         file_type = self.get_file_type(context)
+        file_count = self.get_file_count(trans, context)
         d_type = self.get_datatype(trans, context)
-        dbkey = context.get('dbkey', None)
+        dbkey = self.get_dbkey(context)
         tag_using_filenames = context.get('tag_using_filenames', False)
         writable_files = d_type.writable_files
         writable_files_offset = 0
-        groups_incoming = [None for _ in writable_files]
+        groups_incoming = [None for _ in range(file_count)]
         for group_incoming in context.get(self.name, []):
             i = int(group_incoming['__index__'])
             groups_incoming[i] = group_incoming
@@ -524,6 +566,10 @@ def get_filenames(context):
                 dataset.to_posix_lines = file_bunch.to_posix_lines
                 dataset.auto_decompress = file_bunch.auto_decompress
                 dataset.space_to_tab = file_bunch.space_to_tab
+                if file_bunch.file_type:
+                    dataset.file_type = file_type
+                if file_bunch.dbkey:
+                    dataset.dbkey = dbkey
                 dataset.warnings.extend(warnings)
             if dataset.primary_file is None:  # remove this before finish, this should create an empty dataset
                 raise Exception('No primary dataset file was available for composite upload')
@@ -544,15 +590,18 @@ def get_filenames(context):
                             dataset.warnings.append("A required composite file (%s) was not specified." % (key))
             return [dataset]
         else:
-            datasets = get_filenames(context[self.name][0])
             rval = []
-            for dataset in datasets:
-                dataset.file_type = file_type
-                dataset.datatype = d_type
-                dataset.ext = self.get_datatype_ext(trans, context)
-                dataset.dbkey = dbkey
-                dataset.tag_using_filenames = tag_using_filenames
-                rval.append(dataset)
+            for i, file_contexts in enumerate(context[self.name]):
+                datasets = get_filenames(file_contexts)
+                for dataset in datasets:
+                    override_file_type = self.get_file_type(context[self.name][i], parent_context=context)
+                    d_type = self.get_datatype(trans, context[self.name][i], parent_context=context)
+                    dataset.file_type = override_file_type
+                    dataset.datatype = d_type
+                    dataset.ext = self.get_datatype_ext(trans, context[self.name][i], parent_context=context)
+                    dataset.dbkey = self.get_dbkey(context[self.name][i], parent_context=context)
+                    dataset.tag_using_filenames = tag_using_filenames
+                    rval.append(dataset)
             return rval
 
 

test/api/test_tools.py

@@ -185,6 +185,99 @@ def _get_roadmaps_content(self, history_id, dataset):
         roadmaps_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=dataset, filename="Roadmaps")
         return roadmaps_content
 
+    def test_upload_dbkey(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19")
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+            assert datasets[0].get("genome_build") == "hg19", datasets[0]
+
+    def test_upload_multiple_files_1(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+                dbkey="hg19",
+                extra_inputs={
+                    "files_1|url_paste": "SecondOutputContent",
+                    "files_1|NAME": "SecondOutputName",
+                    "files_1|file_type": "tabular",
+                    "files_1|dbkey": "hg18",
+                    "file_count": "2",
+                }
+            )
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+
+            assert len(datasets) == 2, datasets
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
+            assert content.strip() == "Test123"
+            assert datasets[0]["file_ext"] == "txt"
+            assert datasets[0]["genome_build"] == "hg19", datasets
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
+            assert content.strip() == "SecondOutputContent"
+            assert datasets[1]["file_ext"] == "tabular"
+            assert datasets[1]["genome_build"] == "hg18", datasets
+
+    def test_upload_multiple_files_2(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+                file_type="tabular",
+                dbkey="hg19",
+                extra_inputs={
+                    "files_1|url_paste": "SecondOutputContent",
+                    "files_1|NAME": "SecondOutputName",
+                    "files_1|file_type": "txt",
+                    "files_1|dbkey": "hg18",
+                    "file_count": "2",
+                }
+            )
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+
+            assert len(datasets) == 2, datasets
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
+            assert content.strip() == "Test123"
+            assert datasets[0]["file_ext"] == "tabular", datasets
+            assert datasets[0]["genome_build"] == "hg19", datasets
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
+            assert content.strip() == "SecondOutputContent"
+            assert datasets[1]["file_ext"] == "txt"
+            assert datasets[1]["genome_build"] == "hg18", datasets
+
+    def test_upload_multiple_files_3(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+                file_type="tabular",
+                dbkey="hg19",
+                extra_inputs={
+                    "files_0|file_type": "txt",
+                    "files_0|dbkey": "hg18",
+                    "files_1|url_paste": "SecondOutputContent",
+                    "files_1|NAME": "SecondOutputName",
+                    "files_1|file_type": "txt",
+                    "files_1|dbkey": "hg18",
+                    "file_count": "2",
+                }
+            )
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+
+            assert len(datasets) == 2, datasets
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
+            assert content.strip() == "Test123"
+            assert datasets[0]["file_ext"] == "txt", datasets
+            assert datasets[0]["genome_build"] == "hg18", datasets
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
+            assert content.strip() == "SecondOutputContent"
+            assert datasets[1]["file_ext"] == "txt"
+            assert datasets[1]["genome_build"] == "hg18", datasets
+
     def test_unzip_collection(self):
         with self.dataset_populator.test_history() as history_id:
             hdca_id = self.__build_pair(history_id, ["123", "456"])

tools/data_source/upload.py

@@ -408,7 +408,7 @@ def __main__():
         dataset = util.bunch.Bunch(**safe_dict(dataset))
         try:
             output_path = output_paths[int(dataset.dataset_id)][0]
-        except:
+        except Exception:
             print('Output path for dataset %s not found on command line' % dataset.dataset_id, file=sys.stderr)
             sys.exit(1)
         if dataset.type == 'composite':
@@ -422,7 +422,7 @@ def __main__():
     # parent directory is writable by the user.
     try:
         os.remove(sys.argv[3])
-    except:
+    except Exception:
         pass
 
 

tools/data_source/upload.xml

@@ -32,6 +32,7 @@
       </options>
     </param>
     <param name="async_datasets" type="hidden" value="None"/>
+    <param name="file_count" type="hidden" value="auto" />
     <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
         <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail.  To upload large files, use the URL method (below) or FTP (if enabled by the site administrator).">
       </param>
@@ -43,6 +44,10 @@
       <param name="uuid" type="hidden" required="False" />
       <param name="to_posix_lines" type="hidden" value="Yes" />
       <param name="auto_decompress" type="hidden" value="Yes" />
+      <!-- allow per-file override of dbkey -->
+      <param name="file_type" type="hidden" value="" />
+      <param name="dbkey" type="hidden" value="" />
+
       <!--
       <param name="to_posix_lines" type="select" display="checkboxes" multiple="True" label="Convert universal line endings to Posix line endings" help="Turn this option off if you upload a gzip, bz2 or zip archive which contains a binary file." value="Yes"> 
         <option value="Yes" selected="true">Yes</option>