qmenta-sdk-lib 2.0.1.dev3463__tar.gz → 2.0.1.dev3465__tar.gz

{qmenta_sdk_lib-2.0.1.dev3463 → qmenta_sdk_lib-2.0.1.dev3465}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta_sdk_lib
-Version: 2.0.1.dev3463
+Version: 2.0.1.dev3465
 Summary: QMENTA SDK for tool development.
 Author: QMENTA
 Maintainer: Marc Ramos

{qmenta_sdk_lib-2.0.1.dev3463 → qmenta_sdk_lib-2.0.1.dev3465}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "qmenta_sdk_lib"
-version = "2.0.1.dev3463"
+version = "2.0.1.dev3465"
 description = "QMENTA SDK for tool development."
 authors = ["QMENTA"]
 packages = [

{qmenta_sdk_lib-2.0.1.dev3463 → qmenta_sdk_lib-2.0.1.dev3465}/python/qmenta/sdk/bids/wrapper.py

@@ -70,7 +70,10 @@ def generate_file_path(original_name, sub_name, modality_name, cat_dir):
 
         # Automatically generate a BIDS compatible name for the file
         extension = "." + ".".join(original_name.split(".")[1:])
-        if extension in [".bval", ".bvec"]:  # In BIDS, bval and bvec use dwi as modality
+        if extension in [
+            ".bval",
+            ".bvec",
+        ]:  # In BIDS, bval and bvec use dwi as modality
             target_name = "{}_dwi{}".format(sub_name, extension)
         else:
             target_name = "{}_{}{}".format(sub_name, modality_name, extension)
@@ -130,22 +133,31 @@ def format_input_data(context, subject, session, path):
     for category in list(bids_ff_names.keys()):
         for modality_name in bids_ff_names[category]:
             try:
-                file_handlers = context.get_files("input", file_filter_condition_name="c_{}".format(modality_name))
+                file_handlers = context.get_files(
+                    "input",
+                    file_filter_condition_name="c_{}".format(modality_name),
+                )
             except:  # noqa: E731,E123,E722
                 continue
 
             for fh in file_handlers:
 
                 # NIFTI IS A MUST FOR BIDS
-                if any([fh.name.endswith(ext) for ext in supported_extensions]):
+                if any(
+                    [fh.name.endswith(ext) for ext in supported_extensions]
+                ):
                     cat_dir = os.path.join(sub_path, category)
                     mkdirs(cat_dir)
 
-                    target_path = generate_file_path(fh.name, subject, modality_name, cat_dir)
+                    target_path = generate_file_path(
+                        fh.name, subject, modality_name, cat_dir
+                    )
 
                     if os.path.isfile(target_path):
                         logger.warning(
-                            "Multiple files with same name ({}). Only the first will be used".format(target_path)
+                            "Multiple files with same name ({}). Only the first will be used".format(
+                                target_path
+                            )
                         )
                         break
 
@@ -156,12 +168,20 @@ def format_input_data(context, subject, session, path):
 
                     metadata = fh.get_file_info()
                     if metadata:
-                        metadata_target_name = "{}_{}{}".format(sub_name, modality_name, ".json")
-                        metadata_target_path = os.path.join(cat_dir, metadata_target_name)
+                        metadata_target_name = "{}_{}{}".format(
+                            sub_name, modality_name, ".json"
+                        )
+                        metadata_target_path = os.path.join(
+                            cat_dir, metadata_target_name
+                        )
                         with open(metadata_target_path, "w") as fp:
                             json.dump(metadata, fp)
                 else:
-                    logger.warning("File {} extension not supported ({})".format(fh.name, supported_extensions))
+                    logger.warning(
+                        "File {} extension not supported ({})".format(
+                            fh.name, supported_extensions
+                        )
+                    )
 
 
 def format_settings(settings):
@@ -193,7 +213,10 @@ def run(context):
 
     # Download data from the platform and store following the BIDS specification
     format_input_data(
-        context, subject=analysis_data["patient_secret_name"], session=analysis_data["ssid"], path=input_path
+        context,
+        subject=analysis_data["patient_secret_name"],
+        session=analysis_data["ssid"],
+        path=input_path,
     )
 
     # Select type of analysis (TODO: add support for group analysis)
@@ -204,14 +227,18 @@ def run(context):
 
     # Run the original BIDS-APP entrypoint
     app_path = os.environ["BIDS_APP_ENTRYPOINT"]
-    context.set_progress(message="Running {}".format(os.path.basename(app_path)))
+    context.set_progress(
+        message="Running {}".format(os.path.basename(app_path))
+    )
     try:
         args = [app_path, input_path, output_path, analysis_type] + options
         logger.info("Calling: {}".format(" ".join(args)))
         ret = check_output(args, stderr=STDOUT)
         logger.info(ret)
     except CalledProcessError as e:
-        raise RuntimeError("Program exited with error: {}\nOutput:\n{}".format(e, e.output))
+        raise RuntimeError(
+            "Program exited with error: {}\nOutput:\n{}".format(e, e.output)
+        )
     except Exception:
         raise
 

{qmenta_sdk_lib-2.0.1.dev3463 → qmenta_sdk_lib-2.0.1.dev3465}/python/qmenta/sdk/client.py

@@ -73,11 +73,22 @@ class ExecClient(object):
             One of AnalysisState.RUNNING, AnalysisState.COMPLETED, AnalysisState.EXCEPTION or AnalysisState.NO_FILES
         kwargs : dict
         """
-        assert isinstance(state, AnalysisState), "'state' is {}, not an 'AnalysisState'".format(state)
-        data_to_send = {"analysis_id": self.__analysis_id, "state": state.value}
+        assert isinstance(
+            state, AnalysisState
+        ), "'state' is {}, not an 'AnalysisState'".format(state)
+        data_to_send = {
+            "analysis_id": self.__analysis_id,
+            "state": state.value,
+        }
         data_to_send.update(kwargs)
-        logging.getLogger(__name__).info("State = {state!r} for analysis {analysis_id}".format(**data_to_send))
-        self.__comm.send_request("analysis_manager/set_analysis_state", data_to_send)
+        logging.getLogger(__name__).info(
+            "State = {state!r} for analysis {analysis_id}".format(
+                **data_to_send
+            )
+        )
+        self.__comm.send_request(
+            "analysis_manager/set_analysis_state", data_to_send
+        )
 
     def upload_log(self):
 
@@ -92,7 +103,9 @@ class ExecClient(object):
             # Send file in one single request
             # FIXME Implement chuncked upload
             self.__comm.send_files(
-                "analysis_manager/upload_log", files={"file": ("exec.log", log_contents)}, req_data=data_to_send
+                "analysis_manager/upload_log",
+                files={"file": ("exec.log", log_contents)},
+                req_data=data_to_send,
             )
 
 

{qmenta_sdk_lib-2.0.1.dev3463 → qmenta_sdk_lib-2.0.1.dev3465}/python/qmenta/sdk/communication.py

@@ -11,7 +11,16 @@ except ImportError:
 
 
 class CommunicationObject(object):
-    def __init__(self, url, project_id, token, timeout=900.0, chunk_size=256, verify=True, critical=False):
+    def __init__(
+        self,
+        url,
+        project_id,
+        token,
+        timeout=900.0,
+        chunk_size=256,
+        verify=True,
+        critical=False,
+    ):
         """
         Communications with the platform
 
@@ -112,7 +121,9 @@ class CommunicationObject(object):
 
         if access_point:
             # Add authentication for the platform
-            req_headers["Cookie"] = "AUTH_COOKIE={}; MINT_AP={}".format(self.__token, self.__project_id)
+            req_headers["Cookie"] = "AUTH_COOKIE={}; MINT_AP={}".format(
+                self.__token, self.__project_id
+            )
             req_headers["Mint-Api-Call"] = "1"
             url = urlparse.urljoin(self.__req_url, access_point)
 
@@ -132,10 +143,16 @@ class CommunicationObject(object):
 
                 # log & raise error if we get a HTTP error code
                 if not response.ok:
-                    logger.debug("{!r} HTTP response: {!r}".format(url, response.text))
+                    logger.debug(
+                        "{!r} HTTP response: {!r}".format(url, response.text)
+                    )
                 response.raise_for_status()
 
-            except (requests.HTTPError, requests.Timeout, requests.ConnectionError):
+            except (
+                requests.HTTPError,
+                requests.Timeout,
+                requests.ConnectionError,
+            ):
                 retry_counter += 1
                 if self.__critical or total_retry == retry_counter:
                     raise
@@ -198,7 +215,9 @@ class CommunicationObject(object):
         timeout = timeout or self.timeout
 
         # Add authentication for the platform
-        req_headers["Cookie"] = "AUTH_COOKIE={}; MINT_AP={}".format(self.__token, self.__project_id)
+        req_headers["Cookie"] = "AUTH_COOKIE={}; MINT_AP={}".format(
+            self.__token, self.__project_id
+        )
         req_headers["Mint-Api-Call"] = "1"
 
         retry_counter = 0
@@ -222,7 +241,11 @@ class CommunicationObject(object):
                 logger.info("{!r} HTTP response: {!r}".format(url, result))
                 return result
 
-            except (requests.HTTPError, requests.Timeout, requests.ConnectionError):
+            except (
+                requests.HTTPError,
+                requests.Timeout,
+                requests.ConnectionError,
+            ):
                 retry_counter += 1
                 if self.__critical or total_retry == retry_counter:
                     raise