qmenta-sdk-lib 2.0.1.dev3468__tar.gz → 2.0.1.dev3469__tar.gz

{qmenta_sdk_lib-2.0.1.dev3468 → qmenta_sdk_lib-2.0.1.dev3469}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta_sdk_lib
-Version: 2.0.1.dev3468
+Version: 2.0.1.dev3469
 Summary: QMENTA SDK for tool development.
 Author: QMENTA
 Maintainer: Marc Ramos

{qmenta_sdk_lib-2.0.1.dev3468 → qmenta_sdk_lib-2.0.1.dev3469}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "qmenta_sdk_lib"
-version = "2.0.1.dev3468"
+version = "2.0.1.dev3469"
 description = "QMENTA SDK for tool development."
 authors = ["QMENTA"]
 packages = [

{qmenta_sdk_lib-2.0.1.dev3468 → qmenta_sdk_lib-2.0.1.dev3469}/python/qmenta/sdk/context.py

@@ -51,7 +51,8 @@ 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
@@ -73,15 +74,19 @@ 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
         """
@@ -105,14 +110,17 @@ 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
         """
@@ -154,7 +162,8 @@ 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
         -------
@@ -178,11 +187,13 @@ 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
@@ -232,7 +243,8 @@ class AnalysisContext:
                 "patient_manager/get_patient_list",
                 req_headers={"X-Range": "items=0-9999"},
                 req_data={
-                    "pars_patient_secret_name": f"string;{self.analysis_data['patient_secret_name']}"
+                    "pars_patient_secret_name": "string;"
+                    f"{self.analysis_data['patient_secret_name']}"
                 },
             )
             self.logger.info(data_sessions[0])
@@ -349,7 +361,8 @@ 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.
         """
@@ -366,12 +379,14 @@ 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
@@ -391,8 +406,10 @@ 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"]
 
@@ -404,10 +421,13 @@ 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
@@ -418,38 +438,47 @@ 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')
 
@@ -475,7 +504,10 @@ 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)
 
@@ -525,7 +557,8 @@ 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 = []
 
@@ -535,9 +568,8 @@ class AnalysisContext:
                         file_filter_condition_name
                     ]
                 except KeyError:
-                    msg = "File filter condition {} not specified in the container {} settings !".format(
-                        file_filter_condition_name, input_id
-                    )
+                    msg = f"File filter condition {file_filter_condition_name}"
+                    f"not specified in the container {input_id} settings !"
                     self.logger.error(msg)
                     raise Exception(msg)
 
@@ -575,7 +607,8 @@ 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
@@ -607,7 +640,8 @@ 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"],
@@ -651,13 +685,15 @@ 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
@@ -671,13 +707,15 @@ 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 = {
@@ -732,9 +770,8 @@ class AnalysisContext:
                     return True
                 else:
                     raise RuntimeError(
-                        "Intermediate chunk upload failed: {!r} != {!r}".format(
-                            response.text, expected_response
-                        )
+                        "Intermediate chunk upload "
+                        f"failed: {response.text} != {expected_response}"
                     )
         except Exception as e:
             logger.error(
@@ -813,7 +850,8 @@ 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
@@ -862,7 +900,7 @@ class AnalysisContext:
                 ) and chunk_retry_count <= self.__max_chunk_retries:
                     start_position = chunk_num * self.__comm.chunk_size
                     self.logger.debug(
-                        "Chunk size is {}".format(self.__comm.chunk_size)
+                        "Chunk size " f"is {self.__comm.chunk_size}"
                     )
                     end_position = start_position + self.__comm.chunk_size - 1
                     bytes_to_send = self.__comm.chunk_size
@@ -883,9 +921,8 @@ class AnalysisContext:
                         "Content-Range": bytes_range,
                         "Session-ID": str(session_id),
                         "Content-Length": str(bytes_to_send),
-                        "Content-Disposition": "attachment; filename={}".format(
-                            file_name
-                        ),
+                        "Content-Disposition": "attachment; "
+                        f"filename={file_name}",
                     }
 
                     # If it is the last chunk, define more header fields
@@ -893,35 +930,30 @@ 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(
-                            {
-                                "X-Mint-Analysis-Output": str(
-                                    self.analysis_id
-                                ),
-                                "X-Mint-File-Destination-Path": destination_path,
-                                "X-Mint-File-Tags": ",".join(tags),
-                            }
-                        )
+                        req_headers.update(last_data)
 
                         # Conditional headers
-                        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
+                        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)
+                                )
                         req_headers["X-Requested-With"] = "XMLHttpRequest"
 
                     # Send data chunk
@@ -943,9 +975,8 @@ 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"
@@ -977,6 +1008,9 @@ 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
             )
@@ -1038,13 +1072,16 @@ 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={
-                    "container_id": container_id,
-                    "path": destination_path,
-                    "md5": md5_hash,
-                },
+                req_data=req_data,
             )
             if not verification_response.get("success", False):
                 msg = "The upload could not be verified: {}".format(
@@ -1057,7 +1094,8 @@ 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
         ----------
@@ -1108,7 +1146,8 @@ 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
         -------
@@ -1156,11 +1195,13 @@ 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):
@@ -1172,7 +1213,8 @@ 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):
@@ -1241,11 +1283,13 @@ 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
         -------
@@ -1294,7 +1338,8 @@ 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):
@@ -1302,7 +1347,10 @@ 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)
 
@@ -1380,9 +1428,8 @@ 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 !"
@@ -1470,7 +1517,8 @@ 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
@@ -1504,13 +1552,16 @@ 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", {})
 
@@ -1540,8 +1591,9 @@ 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)
@@ -1599,7 +1651,8 @@ 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
@@ -1614,14 +1667,16 @@ 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
         -------
@@ -1636,13 +1691,16 @@ 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)
 
@@ -1669,7 +1727,8 @@ 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.dev3468 → qmenta_sdk_lib-2.0.1.dev3469}/python/qmenta/sdk/local/context.py

@@ -1,3 +1,5 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
 import logging
 import os
 import shutil
@@ -10,6 +12,7 @@ from qmenta.sdk.directory_utils import TemporaryDirectory
 
 
 class LocalAnalysisContext:
+
     class QCEntity(Enum):
         """
         Enum with the following options:
@@ -28,9 +31,16 @@ 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
@@ -45,17 +55,21 @@ 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",
@@ -83,12 +97,15 @@ 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))
@@ -98,6 +115,7 @@ class LocalAnalysisContext:
         Changes the analysis or session QC status.
 
         """
+
         logger = logging.getLogger(__name__)
 
         logger.info("Getting QC status")
@@ -111,17 +129,17 @@ 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):
@@ -135,9 +153,10 @@ 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
@@ -148,15 +167,17 @@ 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
 
@@ -164,12 +185,14 @@ 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
 
@@ -184,6 +207,7 @@ class LocalAnalysisContext:
         dict
             Settings for the current analysis.
         """
+
         return self.__settings
 
     def get_files(
@@ -194,9 +218,11 @@ 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
@@ -207,11 +233,13 @@ 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
@@ -223,6 +251,7 @@ 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(
@@ -233,15 +262,18 @@ 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
@@ -308,6 +340,7 @@ class LocalAnalysisContext:
         protocol : None
         container_id : None
         """
+
         logger = logging.getLogger(__name__)
         if tags:
             logger.warning("Tags ignored (local execution): {}".format(tags))
@@ -343,7 +376,8 @@ 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.
 
@@ -354,6 +388,7 @@ 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
@@ -361,14 +396,12 @@ 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(
@@ -389,17 +422,20 @@ 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 {}
 
@@ -424,8 +460,10 @@ 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)
@@ -444,13 +482,20 @@ 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
 
@@ -467,26 +512,30 @@ 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(
@@ -502,15 +551,26 @@ 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
@@ -527,6 +587,7 @@ class LocalFile:
         str or None
             Modality of the file or None if not known.
         """
+
         return self.__modality
 
     @staticmethod
@@ -539,18 +600,23 @@ 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):
@@ -562,6 +628,7 @@ class LocalFile:
         set
             Set of tags associated to this file
         """
+
         return self.__tags
 
     def get_file_path(self):
@@ -578,9 +645,11 @@ 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)
@@ -596,6 +665,7 @@ 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)
@@ -607,30 +677,37 @@ 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)