qmenta-sdk-lib 2.0.1.dev3469__tar.gz → 2.0.1.dev3470__tar.gz

{qmenta_sdk_lib-2.0.1.dev3469 → qmenta_sdk_lib-2.0.1.dev3470}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta_sdk_lib
-Version: 2.0.1.dev3469
+Version: 2.0.1.dev3470
 Summary: QMENTA SDK for tool development.
 Author: QMENTA
 Maintainer: Marc Ramos

{qmenta_sdk_lib-2.0.1.dev3469 → qmenta_sdk_lib-2.0.1.dev3470}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "qmenta_sdk_lib"
-version = "2.0.1.dev3469"
+version = "2.0.1.dev3470"
 description = "QMENTA SDK for tool development."
 authors = ["QMENTA"]
 packages = [

{qmenta_sdk_lib-2.0.1.dev3469 → qmenta_sdk_lib-2.0.1.dev3470}/python/qmenta/sdk/context.py

@@ -51,8 +51,7 @@ class AnalysisContext:
 
     def __init__(self, analysis_id, comm):
         """
-        Context object that interfaces with the QMENTA platform. Should not be
-        created directly.
+        Context object that interfaces with the QMENTA platform. Should not be created directly.
         """
         self.analysis_id = analysis_id
         self.__comm = comm
@@ -74,19 +73,15 @@ class AnalysisContext:
         Returns
         -------
         dict
-            Dictionary that contains important information about the
-            current analysis, such as:
+            Dictionary that contains important information about the current analysis, such as:
                 * state (str) : State of the analysis
                 * name (str) : Name of the analysis
                 * script_name (str) : Name of the script
-                * analysis_id (str) : A unique identifier for the
-                current analysis
-                * user_id (str) : Username of the user that started
-                the analysis
+                * analysis_id (str) : A unique identifier for the current analysis
+                * user_id (str) : Username of the user that started the analysis
                 * patient_secret_name (str) : Name of the subject
                 * ssid (str) : Timepoint identifier
-                * settings (dict) : Settings dictionary. See documentation in
-                method `get_settings`
+                * settings (dict) : Settings dictionary. See documentation in method `get_settings`
                 * tags (list) : List of tags
                 * version (str) : Tool version
         """
@@ -110,17 +105,14 @@ class AnalysisContext:
         Returns
         -------
         dict
-            Dictionary that contains important information about the current
-            analysis, such as:
+            Dictionary that contains important information about the current analysis, such as:
                 * state (str) : State of the analysis
                 * name (str) : Name of the analysis
                 * script_name (str) : Name of the script
-                * user_id (str) : Username of the user that started the
-                analysis
+                * user_id (str) : Username of the user that started the analysis
                 * patient_secret_name (str) : Name of the subject
                 * ssid (str) : Timepoint identifier
-                * settings (dict) : Settings dictionary. See documentation in
-                method `get_settings`
+                * settings (dict) : Settings dictionary. See documentation in method `get_settings`
                 * tags (list) : List of tags
                 * version (str) : Tool version
         """
@@ -162,8 +154,7 @@ class AnalysisContext:
 
     def get_communication_object(self):
         """
-        Return the communication object used for communication
-        with the platform
+        Return the communication object used for communication with the platform
 
         Returns
         -------
@@ -187,13 +178,11 @@ class AnalysisContext:
         status : QCStatus
             QCStatus.PASS or QCStatus.FAIL
         comments : str, optional
-            Additional comments explaining why the QC status has been
-            set to pass or fail.
+            Additional comments explaining why the QC status has been set to pass or fail.
         entity : QCEntity, optional
             QCEntity.ANALYSIS or QCEntity.SESSION
         input_id : str, optional
-            The id of the session in the settings definition when
-            entity is QCEntity.SESSION
+            The id of the session in the settings definition when entity is QCEntity.SESSION
         """
         if entity == self.QCEntity.ANALYSIS:
             item_id = self.analysis_id
@@ -243,8 +232,7 @@ class AnalysisContext:
                 "patient_manager/get_patient_list",
                 req_headers={"X-Range": "items=0-9999"},
                 req_data={
-                    "pars_patient_secret_name": "string;"
-                    f"{self.analysis_data['patient_secret_name']}"
+                    "pars_patient_secret_name": f"string;{self.analysis_data['patient_secret_name']}"
                 },
             )
             self.logger.info(data_sessions[0])
@@ -361,8 +349,7 @@ class AnalysisContext:
         Parameters
         ----------
         value : int, optional
-            Number between 0 and 100 indicating the current status of the
-            execution
+            Number between 0 and 100 indicating the current status of the execution
         message : str, optional
             Progress message.
         """
@@ -379,14 +366,12 @@ class AnalysisContext:
             value = int(value)  # Cast to int to avoid float/string problems
             if value > 100:
                 self.logger.warning(
-                    "The progress value should be between 0 and 100 "
-                    "(using 100 instead)"
+                    "The progress value should be between 0 and 100 (using 100 instead)"
                 )
                 value = 100
             elif value < 0:
                 self.logger.warning(
-                    "The progress value should be between 0 and 100 "
-                    "(using 0 instead)"
+                    "The progress value should be between 0 and 100 (using 0 instead)"
                 )
                 value = 0
             data_to_send["value"] = value
@@ -406,10 +391,8 @@ class AnalysisContext:
         Returns
         -------
         dict
-            Settings for the current analysis. This includes all the
-            parameters defined in the tool specification
-            (checkboxes, input fields, etc.) and can be accessed using their
-            identifier.
+            Settings for the current analysis. This includes all the parameters defined in the tool specification
+            (checkboxes, input fields, etc.) and can be accessed using their identifier.
         """
         return self.analysis_data["settings"]
 
@@ -421,13 +404,10 @@ class AnalysisContext:
         reg_expression=None,
         file_filter_condition_name=None,
         subject_container_id=None,
-        unpack=True,
     ):
         """
-        Returns the files in the input container specified by
-        `input_id` that match the modality, tags
-        and regular expression, if any. (X)OR that are selected by
-        the file filter condition
+        Returns the files in the input container specified by `input_id` that match the modality, tags
+        and regular expression, if any. (X)OR that are selected by the file filter condition
         defined in the tool settings.
 
         Parameters
@@ -438,47 +418,38 @@ class AnalysisContext:
             Optional modality, will allow any modalities if None given.
             Default is None.
         tags : set, optional
-            Optional set of tags, will allow any tags if None given,
-            and will match any set of tags (including
+            Optional set of tags, will allow any tags if None given, and will match any set of tags (including
             the empty set) otherwise.
             Default is None.
         reg_expression : str, optional
-            Regular expression to match with the file names in the specified
-            container, will allow any file names
+            Regular expression to match with the file names in the specified container, will allow any file names
             if None given.
             Default is None.
         file_filter_condition_name : str, optional
             File filter specified in the settings of the tool.
             Default is None.
         subject_container_id : str, optional
-        unpack: bool, optional
 
         Examples
         --------
 
-        Get all files that passed c_TEST (including any selection
-        the user may have done using the GUI)
+        Get all files that passed c_TEST (including any selection the user may have done using the GUI)
 
         >>> context.get_files('input', file_filter_condition_name='c_TEST')
 
         Get all files that passed c_TEST and have no tags
 
-        >>> context.get_files('input', file_fitler_condition_name='c_TEST',
-        tags=set()
+        >>> context.get_files('input', file_fitler_condition_name='c_TEST', tags=set()
 
-        Get all files that passed c_TEST and have the DTI tag in their
-        list of tags
+        Get all files that passed c_TEST and have the DTI tag in their list of tags
 
-        >>> context.get_files('input', file_fitler_condition_name='c_TEST',
-        tags={'DTI'})
+        >>> context.get_files('input', file_fitler_condition_name='c_TEST', tags={'DTI'})
 
         Get all files that passed c_TEST whose name match the given regexp
 
-        >>> context.get_files('input', file_filter_condition_name='c_TEST',
-        reg_expression='^some_expression[0-9]')
+        >>> context.get_files('input', file_filter_condition_name='c_TEST', reg_expression='^some_expression[0-9]')
 
-        Alternatively, you can use no file_filter_condition_name to browse
-        through the whole input container
+        Alternatively, you can use no file_filter_condition_name to browse through the whole input container
 
         >>> context.get_files('input')
 
@@ -504,10 +475,7 @@ class AnalysisContext:
         )
 
         if is_subject_setting and subject_container_id is None:
-            msg = (
-                "must define subject_container_id for subjects with"
-                " multiple sessions"
-            )
+            msg = "must define subject_container_id for subjects with multiple sessions"
             self.logger.error(msg)
             raise Exception(msg)
 
@@ -557,8 +525,7 @@ class AnalysisContext:
             ]
 
         if file_filter_condition_name:
-            # Get the files that passed the file_filter and take those that
-            #  have the required conditions
+            # Get the files that passed the file_filter and take those that have the required conditions
 
             selected_files = []
 
@@ -568,8 +535,9 @@ class AnalysisContext:
                         file_filter_condition_name
                     ]
                 except KeyError:
-                    msg = f"File filter condition {file_filter_condition_name}"
-                    f"not specified in the container {input_id} settings !"
+                    msg = "File filter condition {} not specified in the container {} settings !".format(
+                        file_filter_condition_name, input_id
+                    )
                     self.logger.error(msg)
                     raise Exception(msg)
 
@@ -607,8 +575,7 @@ class AnalysisContext:
 
             return selected_files
         else:
-            # in case the file filter condition name is not specified then we
-            # need to take the other
+            # in case the file filter condition name is not specified then we need to take the other
             # concrete search conditions i.e. modality, tags, reg_expression
 
             # filter the files according to the filter defined
@@ -640,8 +607,7 @@ class AnalysisContext:
         selected_files = []
         for file_data in container_data["meta"]:
 
-            # TODO: Here we are assuming that file metadata has a name and a
-            # metadata attribute. Need of jsonschema
+            # TODO: Here we are assuming that file metadata has a name and a metadata attribute. Need of jsonschema
 
             fname, fmetadata, ftags = (
                 file_data["name"],
@@ -685,15 +651,13 @@ class AnalysisContext:
         patient_metadata_id=None,
     ):
         """
-        Add a new scan session. Only functional for analysis tools of type
-        `data`.
+        Add a new scan session. Only functional for analysis tools of type `data`.
 
         Parameters
         ----------
         ssid : int, optional
         date_at_scan : str, optional
-            Possible formats: '%d.%m.%Y' / '%Y-%m-%d'.
-            Examples: '01.01.2000' / '2000-01-01'
+            Possible formats: '%d.%m.%Y' / '%Y-%m-%d'. Examples: '01.01.2000' / '2000-01-01'
         age_at_scan : int, optional
         backup_age : int, optional
         patient_metadata_id : int, optional
@@ -707,15 +671,13 @@ class AnalysisContext:
             patient_secret_name = self.analysis_data["patient_secret_name"]
         except KeyError:
             raise RuntimeError(
-                "Patient secret name not available in analysis information. "
-                "Check platform failures."
+                "Patient secret name not available in analysis information. Check platform failures."
             )
         try:
             md5_original_file = self.get_settings()["md5_original_file"]
         except KeyError:
             raise RuntimeError(
-                "MD5 hash not available via analysis settings. "
-                "Check platform failures."
+                "MD5 hash not available via analysis settings. Check platform failures."
             )
 
         data = {
@@ -770,8 +732,9 @@ class AnalysisContext:
                     return True
                 else:
                     raise RuntimeError(
-                        "Intermediate chunk upload "
-                        f"failed: {response.text} != {expected_response}"
+                        "Intermediate chunk upload failed: {!r} != {!r}".format(
+                            response.text, expected_response
+                        )
                     )
         except Exception as e:
             logger.error(
@@ -850,8 +813,7 @@ class AnalysisContext:
         file_info : dict, optional
             File information metadata.
         file_format : str, optional
-            Use "dicom" when .zip file with .dcm slices (uploading a "nifti"
-            file is automatically recognized as such).
+            Use "dicom" when .zip file with .dcm slices (uploading a "nifti" file is automatically recognized as such).
         protocol : str, optional
         container_id : str, optional
         replace : str, optional
@@ -900,7 +862,7 @@ class AnalysisContext:
                 ) and chunk_retry_count <= self.__max_chunk_retries:
                     start_position = chunk_num * self.__comm.chunk_size
                     self.logger.debug(
-                        "Chunk size " f"is {self.__comm.chunk_size}"
+                        "Chunk size is {}".format(self.__comm.chunk_size)
                     )
                     end_position = start_position + self.__comm.chunk_size - 1
                     bytes_to_send = self.__comm.chunk_size
@@ -921,8 +883,9 @@ class AnalysisContext:
                         "Content-Range": bytes_range,
                         "Session-ID": str(session_id),
                         "Content-Length": str(bytes_to_send),
-                        "Content-Disposition": "attachment; "
-                        f"filename={file_name}",
+                        "Content-Disposition": "attachment; filename={}".format(
+                            file_name
+                        ),
                     }
 
                     # If it is the last chunk, define more header fields
@@ -930,30 +893,35 @@ class AnalysisContext:
                         chunk_num * self.__comm.chunk_size + bytes_to_send
                     )
                     if accumulated_bytes == total_bytes:
-                        last_data = {
-                            "X-Mint-Analysis-Output": str(self.analysis_id),
-                            "X-Mint-File-Destination-Path": destination_path,
-                            "X-Mint-File-Tags": ",".join(tags),
-                        }
                         self.logger.debug("Sending last data chunk")
-                        req_headers.update(last_data)
+                        req_headers.update(
+                            {
+                                "X-Mint-Analysis-Output": str(
+                                    self.analysis_id
+                                ),
+                                "X-Mint-File-Destination-Path": destination_path,
+                                "X-Mint-File-Tags": ",".join(tags),
+                            }
+                        )
 
                         # Conditional headers
-                        for key, value, attr in [
-                            ("X-Mint-File-Info", file_info, None),
-                            ("X-Mint-File-Format", file_format, str),
-                            ("X-Mint-Protocol", protocol, str),
-                            ("X-Mint-Container", container_id, str),
-                            (
-                                "X-Mint-Replace-Flag",
-                                replace,
-                                lambda x: x.value,
-                            ),
-                        ]:
-                            if value:
-                                req_headers[key] = (
-                                    str(value) if attr is None else attr(value)
-                                )
+                        if file_info:
+                            req_headers["X-Mint-File-Info"] = json.dumps(
+                                file_info
+                            )
+                        if file_format:
+                            req_headers["X-Mint-File-Format"] = str(
+                                file_format
+                            )
+                        if protocol:
+                            req_headers["X-Mint-Protocol"] = str(protocol)
+                        if container_id:
+                            req_headers["X-Mint-Container"] = str(container_id)
+                        if replace:
+                            assert isinstance(
+                                replace, AnalysisContext.ReplaceFlag
+                            )
+                            req_headers["X-Mint-Replace-Flag"] = replace.value
                         req_headers["X-Requested-With"] = "XMLHttpRequest"
 
                     # Send data chunk
@@ -975,8 +943,9 @@ class AnalysisContext:
                         wait_time = 2 * wait_time
                         time.sleep(wait_time)
 
-                if data or chunk_retry_count != 0:
-                    # Restarted when successful upload
+                if (
+                    data or chunk_retry_count != 0
+                ):  # Restarted when successful upload
                     msg = (
                         "File {} could not be uploaded to the platform.\n"
                         "data - {}\n"
@@ -1008,9 +977,6 @@ class AnalysisContext:
                 ),
                 "container_id": container_id,
             }
-
-            self.logger.info("REQUEST DATA" + str(request_data))
-
             url_request_response = self.__comm.send_request(
                 "file_manager/get_upload_url", req_data=request_data
             )
@@ -1072,16 +1038,13 @@ class AnalysisContext:
                 self.logger.error(msg)
                 raise RuntimeError(msg)
 
-            req_data = {
-                "container_id": container_id,
-                "path": destination_path,
-                "md5": md5_hash,
-            }
-            self.logger.info("VERIFY RESPONSE " + str(req_data))
-
             verification_response = self.__comm.send_request(
                 "file_manager/verify_upload_via_url",
-                req_data=req_data,
+                req_data={
+                    "container_id": container_id,
+                    "path": destination_path,
+                    "md5": md5_hash,
+                },
             )
             if not verification_response.get("success", False):
                 msg = "The upload could not be verified: {}".format(
@@ -1094,8 +1057,7 @@ class AnalysisContext:
 
     def download_resource(self, resource_path, destination_path):
         """
-        Downloads a resource file from the bucket (user/group based resources,
-        or legacy).
+        Downloads a resource file from the bucket (user/group based resources, or legacy).
 
         Parameters
         ----------
@@ -1146,8 +1108,7 @@ class AnalysisContext:
 
     def _get_manual_analysis_data(self):
         """
-        Returns a dictionary with the manual analysis data generated during
-        the manual step (user interaction)
+        Returns a dictionary with the manual analysis data generated during the manual step (user interaction)
 
         Returns
         -------
@@ -1195,13 +1156,11 @@ class AnalysisContext:
         title : str, optional
             How the metadata field should be presented
         readonly : bool, optional
-            Whether the user should be able to edit the value on the platform
-            or not (only by analyses)
+            Whether the user should be able to edit the value on the platform or not (only by analyses)
         patient_secret_name : str, optional
             Manually select the patient_secret_name
         ssid : str, optional
-            Manually select the ssid. This is useful to choose a specific
-            session in a longitudinal analysis.
+            Manually select the ssid. This is useful to choose a specific session in a longitudinal analysis.
         """
 
         if not isinstance(key, str):
@@ -1213,8 +1172,7 @@ class AnalysisContext:
             )
         if not isinstance(value, (int, list, str, float)):
             raise Exception(
-                "Parameter 'value' must be of type 'int', 'list', 'str', "
-                "or 'float'."
+                "Parameter 'value' must be of type 'int', 'list', 'str', or 'float'."
             )
 
         if not self.get_metadata_value(key):
@@ -1283,13 +1241,11 @@ class AnalysisContext:
         Parameters
         ----------
         key : str, optional
-            The ID of the metadata parameter. If not set, it will return all
-            the metadata for the session.
+            The ID of the metadata parameter. If not set, it will return all the metadata for the session.
         patient_secret_name: str, optional
             Manually select the patient_secret_name
         ssid : str, optional
-            Manually select the ssid. This is useful to choose a specific
-            session in a longitudinal analysis.
+            Manually select the ssid. This is useful to choose a specific session in a longitudinal analysis.
 
         Returns
         -------
@@ -1338,8 +1294,7 @@ class AnalysisContext:
         Parameters
         ----------
         params : list
-            The definition of the parameter. It may contain "title", "type",
-            "visible", "readonly" or "order".
+            The definition of the parameter. It may contain "title", "type", "visible", "readonly" or "order".
         """
 
         if not isinstance(params, list):
@@ -1347,10 +1302,7 @@ class AnalysisContext:
 
         for data_to_send in params:
             if not isinstance(data_to_send, dict):
-                msg = (
-                    "Format error. Metadata param configuration should be "
-                    "stored in a dictionary"
-                )
+                msg = "Format error. Metadata param configuration should be stored in a dictionary"
                 self.logger.error(msg)
                 raise TypeError(msg)
 
@@ -1428,8 +1380,9 @@ class AnalysisContext:
         """
         if not isinstance(variables_dict, dict):
             self.logger.error(
-                "The output variables are not of type dictionary ! "
-                "(actual type {})".format(str(type(variables_dict)))
+                "The output variables are not of type dictionary ! (actual type {})".format(
+                    str(type(variables_dict))
+                )
             )
             raise RuntimeError(
                 "The output variables are not of type dictionary !"
@@ -1517,8 +1470,7 @@ class Container:
 class File:
     def __init__(self, container_id, name, metadata, tags, comm):
         """
-        Object that represents a file and all its metadata in the platform.
-        Should not be created directly.
+        Object that represents a file and all its metadata in the platform. Should not be created directly.
         """
         self.__comm = comm
         self.__container_id = container_id
@@ -1552,16 +1504,13 @@ class File:
 
     def get_file_info(self):
         """
-        Get the file information. The type of information depends on the
-        type of file
-        (e.g. nifti files include information such as 'Data strides',
-        'Data type', 'Dimensions' or 'Voxel size').
+        Get the file information. The type of information depends on the type of file
+        (e.g. nifti files include information such as 'Data strides', 'Data type', 'Dimensions' or 'Voxel size').
 
         Returns
         -------
         dict
-            Dictionary of key-value pairs that depend on the format of the
-            file.
+            Dictionary of key-value pairs that depend on the format of the file.
         """
         return self.__metadata.get("info", {})
 
@@ -1591,9 +1540,8 @@ class File:
             If `get_file_path` is called before the file has been downloaded
         """
         if self.__download_path is None:
-            err_msg = (
-                "File {!r} has no path because it has not been"
-                " downloaded".format(self.name)
+            err_msg = "File {!r} has no path because it has not been downloaded".format(
+                self.name
             )
             self.logger.error(err_msg)
             raise RuntimeError(err_msg)
@@ -1651,8 +1599,7 @@ class File:
 
         os.makedirs(os.path.dirname(destination_file_path), exist_ok=True)
         with open(destination_file_path, "wb") as fp:
-            # For Google Cloud Bucket, performance is at its best at 1 MB or
-            # larger chunks.
+            # For Google Cloud Bucket, performance is at its best at 1 MB or larger chunks.
             for chunk in download_response.iter_content(
                 chunk_size=self.__comm.chunk_size
             ):  # Use 10 MB chunk
@@ -1667,16 +1614,14 @@ class File:
 
     def download(self, dest_path, unpack=True):
         """
-        Downloads a file or the contents of a packed file to to the
-        specified `path`.
+        Downloads a file or the contents of a packed file to to the specified `path`.
 
         Parameters
         ----------
         dest_path:
             Path where the file should be downloaded to.
         unpack:
-            Tells the function whether the file should be unpacked to the
-            given folder.
+            Tells the function whether the file should be unpacked to the given folder.
 
         Returns
         -------
@@ -1691,16 +1636,13 @@ class File:
         self.logger.debug("Using path {!r}".format(dest_path))
 
         if source_file.endswith(".zip") and unpack:
-            # Download the zip to a temporary directory and unpack its
-            # contents to the user dir path
+            # Download the zip to a temporary directory and unpack its contents to the user dir path
             with TemporaryDirectory() as temp_dir:
                 temp_path = os.path.join(temp_dir, source_file)
                 self.__download_file(temp_path)
-
                 with zipfile.ZipFile(temp_path, "r") as zip_ref:
                     # file_list = zip_ref.namelist()
-                    # self.logger.info("Decompressing {!r} to
-                    # {!r}".format(file_list, dest_path))
+                    # self.logger.info("Decompressing {!r} to {!r}".format(file_list, dest_path))
                     os.makedirs(dest_path, exist_ok=True)
                     zip_ref.extractall(path=dest_path)
 
@@ -1727,8 +1669,7 @@ def _should_include_file(
     search_tags,
     search_reg_expression,
 ):
-    # Checks if file should be selected or not according to the
-    # specified selectors.
+    # Checks if file should be selected or not according to the specified selectors.
 
     assert fname
 

{qmenta_sdk_lib-2.0.1.dev3469 → qmenta_sdk_lib-2.0.1.dev3470}/python/qmenta/sdk/local/context.py

@@ -1,5 +1,3 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
 import logging
 import os
 import shutil
@@ -12,7 +10,6 @@ from qmenta.sdk.directory_utils import TemporaryDirectory
 
 
 class LocalAnalysisContext:
-
     class QCEntity(Enum):
         """
         Enum with the following options:
@@ -31,16 +28,9 @@ class LocalAnalysisContext:
         PASS = "pass"
         FAIL = "fail"
 
-    def __init__(
-        self,
-        settings,
-        src_folder,
-        out_folder,
-        res_folder,
-    ):
+    def __init__(self, settings, src_folder, out_folder, res_folder):
         """
-        Context object that interfaces with the QMENTA platform. Should not
-        be created directly.
+        Context object that interfaces with the QMENTA platform. Should not be created directly.
         """
 
         self.__settings = settings
@@ -55,21 +45,17 @@ class LocalAnalysisContext:
         Returns
         -------
         dict
-            Dictionary that contains important information about the current
-            analysis, such as:
+            Dictionary that contains important information about the current analysis, such as:
                 * state (str) : State of the analysis
                 * name (str) : Name of the analysis
                 * script_name (str) : Name of the script
-                * user_id (str) : Username of the user that started the
-                analysis
+                * user_id (str) : Username of the user that started the analysis
                 * patient_secret_name (str) : Name of the subject
                 * ssid (str) : Timepoint identifier
-                * settings (dict) : Settings dictionary. See documentation in
-                method `get_settings`
+                * settings (dict) : Settings dictionary. See documentation in method `get_settings`
                 * tags (list) : List of tags
                 * version (str) : Tool version
         """
-
         return {
             "state": "local_running",
             "name": "local",
@@ -97,15 +83,12 @@ class LocalAnalysisContext:
         status : QCStatus
             QCStatus.PASS or QCStatus.FAIL
         comments : str, optional
-            Additional comments explaining why the QC status has been set to
-            pass or fail.
+            Additional comments explaining why the QC status has been set to pass or fail.
         entity : QCEntity, optional
             QCEntity.ANALYSIS or QCEntity.SESSION
         input_id : str, optional
-            The id of the session in the settings definition when entity is
-            QCEntity.SESSION
+            The id of the session in the settings definition when entity is QCEntity.SESSION
         """
-
         logger = logging.getLogger(__name__)
 
         logger.info("Setting QC status to {}: {}".format(status, comments))
@@ -115,7 +98,6 @@ class LocalAnalysisContext:
         Changes the analysis or session QC status.
 
         """
-
         logger = logging.getLogger(__name__)
 
         logger.info("Getting QC status")
@@ -129,17 +111,17 @@ class LocalAnalysisContext:
         path : str
             The location where to store the requirements.r
         """
-
         logger = logging.getLogger(__name__)
 
         if os.path.exists(path):
             raise RuntimeError(
-                "Cannot download session qa because {}"
-                "already exists!".format(path)
+                "Cannot download session qa because {} already exists!".format(
+                    path
+                )
             )
 
         logger.info(
-            "Session QA requirements not supported locally. " "Skipping..."
+            "Session QA requirements not supported locally. Skipping..."
         )
 
     def upload_session_qa_report(self, input_id, path):
@@ -153,10 +135,9 @@ class LocalAnalysisContext:
         path : str
             The json file with the QA status for all files and rules
         """
-
         logger = logging.getLogger(__name__)
         logger.info(
-            "Session QA requirements not supported locally. " "Skipping..."
+            "Session QA requirements not supported locally. Skipping..."
         )
 
     @staticmethod
@@ -167,17 +148,15 @@ class LocalAnalysisContext:
         Parameters
         ----------
         value : int, optional
-            Number between 0 and 100 indicating the current status of
-            the execution
+            Number between 0 and 100 indicating the current status of the execution
         message : str, optional
             Progress message.
         """
-
         logger = logging.getLogger(__name__)
 
         if not value and not message:
             logger.warning(
-                "No information is available to report the " "progress"
+                "No information is available to report the progress"
             )
             return
 
@@ -185,14 +164,12 @@ class LocalAnalysisContext:
             value = int(value)  # Cast to int to avoid float/string problems
             if value > 100:
                 logger.warning(
-                    "The progress value should be between 0 and 100 (using "
-                    "100 instead)"
+                    "The progress value should be between 0 and 100 (using 100 instead)"
                 )
                 value = 100
             elif value < 0:
                 logger.warning(
-                    "The progress value should be between 0 and 100 "
-                    "(using 0 instead)"
+                    "The progress value should be between 0 and 100 (using 0 instead)"
                 )
                 value = 0
 
@@ -207,7 +184,6 @@ class LocalAnalysisContext:
         dict
             Settings for the current analysis.
         """
-
         return self.__settings
 
     def get_files(
@@ -218,11 +194,9 @@ class LocalAnalysisContext:
         reg_expression=None,
         file_filter_condition_name=None,
         subject_container_id=None,
-        unpack=True,
     ):
         """
-         Returns the files in the input container specified by `input_id`
-         that match the modality, tags
+         Returns the files in the input container specified by `input_id` that match the modality, tags
          and regular expression, if any.
 
          Parameters
@@ -233,13 +207,11 @@ class LocalAnalysisContext:
              Optional modality, will allow any modalities if None given.
              Default is None.
          tags : set, optional
-             Optional set of tags, will allow any tags if None given,
-             and will match any set of tags (including
+             Optional set of tags, will allow any tags if None given, and will match any set of tags (including
              the empty set) otherwise.
              Default is None.
          reg_expression : str, optional
-             Regular expression to match with the file names in the
-             specified container, will allow any file names
+             Regular expression to match with the file names in the specified container, will allow any file names
              if None given.
              Default is None.
          file_filter_condition_name : str, optional
@@ -251,7 +223,6 @@ class LocalAnalysisContext:
          list of File
              List of selected file handlers from the container.
         """
-
         logger = logging.getLogger(__name__)
         logger.info(
             "Get files: {} [modality={} / tags={} / regex={}]".format(
@@ -262,18 +233,15 @@ class LocalAnalysisContext:
         file_handlers = []
 
         # Create File
-
         for file_description in self.__settings[input_id]:
             if "path" not in file_description:
-                msg = (
-                    'Cannot find the key "path" for the input container'
-                    " {}".format(input_id)
+                msg = 'Cannot find the key "path" for the input container {}'.format(
+                    input_id
                 )
                 logger.error(msg)
                 raise RuntimeError(msg)
 
             # Use file_filter_condition_name if available
-
             if file_filter_condition_name:
                 if "file_filter_condition_name" not in file_description:
                     continue  # Skip
@@ -340,7 +308,6 @@ class LocalAnalysisContext:
         protocol : None
         container_id : None
         """
-
         logger = logging.getLogger(__name__)
         if tags:
             logger.warning("Tags ignored (local execution): {}".format(tags))
@@ -376,8 +343,7 @@ class LocalAnalysisContext:
 
     def download_resource(self, resource_path, destination_path):
         """
-        Downloads a file from the user/group tool resources. The resource
-        path can include subdirectories and must
+        Downloads a file from the user/group tool resources. The resource path can include subdirectories and must
         be relative:
         Downloads a resource file to the container.
 
@@ -388,7 +354,6 @@ class LocalAnalysisContext:
         destination_path : str
             Path where the file will be downloaded to
         """
-
         logger = logging.getLogger(__name__)
         logger.info(self.__res_folder)
         if not self.__res_folder:  # Default keyword for external users
@@ -396,12 +361,14 @@ class LocalAnalysisContext:
             return
         else:
             logger.info(
-                "Mocking resources from directory:"
-                " {}".format(self.__res_folder)
+                "Mocking resources from directory: {}".format(
+                    self.__res_folder
+                )
             )
             logger.info(
-                "The selected mode ({}) is ignored in local "
-                "execution.".format(type)
+                "The selected mode ({}) is ignored in local execution.".format(
+                    type
+                )
             )
 
         logger.info(
@@ -422,20 +389,17 @@ class LocalAnalysisContext:
 
     def _get_manual_analysis_data(self):
         """
-        Returns a dictionary with the manual analysis data generated during
-        the manual step (user interaction)
+        Returns a dictionary with the manual analysis data generated during the manual step (user interaction)
 
         Returns
         -------
         dict
             The values generated during the manual step.
         """
-
         logger = logging.getLogger(__name__)
         logger.info("Getting manual analysis data")
         logger.warning(
-            "Getting manual analysis data is not supported locally. "
-            "Skipping..."
+            "Getting manual analysis data is not supported locally. Skipping..."
         )
         return {}
 
@@ -460,10 +424,8 @@ class LocalAnalysisContext:
         title : str, optional
             How the metadata field should be presented
         readonly : bool, optional
-            Whether the user should be able to edit the value on the platform
-              or not (only by analyses)
+            Whether the user should be able to edit the value on the platform or not (only by analyses)
         """
-
         logger = logging.getLogger(__name__)
 
         assert isinstance(key, str)
@@ -482,20 +444,13 @@ class LocalAnalysisContext:
                 "Invalid type for the metadata value: {!r}".format(type(value))
             )
 
-        logger.info(
-            "Setting metadata parameter: {} =" "{!r}".format(key, value)
-        )
+        logger.info("Setting metadata parameter: {} = {!r}".format(key, value))
         logger.warning(
-            "Setting metadata values is not supported locally. " "Skipping..."
+            "Setting metadata values is not supported locally. Skipping..."
         )
         return None
 
-    def get_metadata_value(
-        self,
-        key,
-        patient_secret_name=None,
-        ssid=None,
-    ):
+    def get_metadata_value(self, key, patient_secret_name=None, ssid=None):
         """
         Gets the value of a metadata parameter for the current session
 
@@ -512,30 +467,26 @@ class LocalAnalysisContext:
         -------
         The value of the parameter if it exists, None otherwise
         """
-
         logger = logging.getLogger(__name__)
         logger.info("Getting metadata value: {}".format(key))
         logger.warning(
-            "Getting metadata values is not supported locally. " "Skipping..."
+            "Getting metadata values is not supported locally. Skipping..."
         )
         return None
 
     def _assure_metadata_parameters(self, params):
         """
-        Check whether a metadata parameter exists, creating it if not.
-        Not supported for local testing.
+        Check whether a metadata parameter exists, creating it if not. Not supported for local testing.
 
         Parameters
         ----------
         params : dict
-            The definition of the parameter. It may contain "title", "type",
-            "visible", "readonly" or "order".
+            The definition of the parameter. It may contain "title", "type", "visible", "readonly" or "order".
         """
-
         logger = logging.getLogger(__name__)
         logger.info("Setting metadata param (ckeck): {}".format(params))
         logger.warning(
-            "Assuring metadata params is not supported locally. " "Skipping..."
+            "Assuring metadata params is not supported locally. Skipping..."
         )
 
     def set_analysis_output_variables(
@@ -551,26 +502,15 @@ class LocalAnalysisContext:
         clear_previous : bool, optional
             Whether the previous output variables should be cleared or not
         """
-
         logger = logging.getLogger(__name__)
         logger.warning("Output variables not supported locally. Skipping...")
 
 
 class LocalFile:
-
-    def __init__(
-        self,
-        name,
-        input_container_path,
-        modality,
-        tags,
-        file_info,
-    ):
+    def __init__(self, name, input_container_path, modality, tags, file_info):
         """
-        Object that represents a file and all its metadata in the platform.
-        Should not be created directly.
+        Object that represents a file and all its metadata in the platform. Should not be created directly.
         """
-
         self.name = name
         self.__input_container_path = input_container_path
         self.__download_path = None
@@ -587,7 +527,6 @@ class LocalFile:
         str or None
             Modality of the file or None if not known.
         """
-
         return self.__modality
 
     @staticmethod
@@ -600,23 +539,18 @@ class LocalFile:
         str or None
             File format or None if not known.
         """
-
         return None
 
     def get_file_info(self):
         """
-        Get the file information. The type of information depends on the type
-        of file
-        (e.g. nifti files include information such as 'Data strides',
-        'Data type', 'Dimensions' or 'Voxel size').
+        Get the file information. The type of information depends on the type of file
+        (e.g. nifti files include information such as 'Data strides', 'Data type', 'Dimensions' or 'Voxel size').
 
         Returns
         -------
         dict
-            Dictionary of key-value pairs that depend on the format of the
-            file.
+            Dictionary of key-value pairs that depend on the format of the file.
         """
-
         return self.__file_info
 
     def get_file_tags(self):
@@ -628,7 +562,6 @@ class LocalFile:
         set
             Set of tags associated to this file
         """
-
         return self.__tags
 
     def get_file_path(self):
@@ -645,11 +578,9 @@ class LocalFile:
         RuntimeError
             If `get_file_path` is called before the file has been downloaded
         """
-
         if self.__download_path is None:
-            err_msg = (
-                "File {!r} has no path because it has not been "
-                "downloaded".format(self.name)
+            err_msg = "File {!r} has no path because it has not been downloaded".format(
+                self.name
             )
             logging.getLogger(__name__).error(err_msg)
             raise RuntimeError(err_msg)
@@ -665,7 +596,6 @@ class LocalFile:
         destination_file_path : str
             Path where the file should be downloaded.
         """
-
         logger = logging.getLogger(__name__)
         logger.info(
             "Downloading {!r} to {!r}".format(self.name, destination_file_path)
@@ -677,37 +607,30 @@ class LocalFile:
 
     def download(self, dest_path, unpack=True):
         """
-        Downloads a file or the contents of a packed file to to the specified
-        `path`.
+        Downloads a file or the contents of a packed file to to the specified `path`.
 
         Parameters
         ----------
         dest_path:
             Path where the file should be downloaded to.
         unpack:
-            Tells the function whether the file should be unpacked to the
-            given folder.
+            Tells the function whether the file should be unpacked to the given folder.
 
         Returns
         -------
         str:
             The full path of the file or the folder with the unpacked files.
         """
-
         logger = logging.getLogger(__name__)
         source_file = self.name
 
         # Normalize path
-
         dest_path = os.path.abspath(dest_path)
 
         logger.debug("Using path {!r}".format(dest_path))
 
         if source_file.endswith(".zip") and unpack:
-
-            # Download the zip to a temporary directory and unpack its
-            # contents to the user dir path
-
+            # Download the zip to a temporary directory and unpack its contents to the user dir path
             with TemporaryDirectory() as temp_dir:
                 temp_path = os.path.join(temp_dir, source_file)
                 self.__download_file(temp_path)