qmenta-client 1.1.dev1507__py3-none-any.whl → 2.1__py3-none-any.whl

qmenta/client/Account.py

@@ -1,10 +1,9 @@
 from __future__ import print_function
 
 import logging
-from urllib3.exceptions import HTTPError
-
-from qmenta.core import platform
 from qmenta.core import errors
+from qmenta.core import platform
+from urllib3.exceptions import HTTPError
 
 from .Project import Project
 from .utils import load_json
@@ -35,7 +34,13 @@ class Account:
         The Auth object used for communication with the platform
     """
 
-    def __init__(self, username, password, base_url="https://platform.qmenta.com", verify_certificates=True):
+    def __init__(
+        self,
+        username,
+        password,
+        base_url="https://platform.qmenta.com",
+        verify_certificates=True,
+    ):
 
         self._cookie = None
         self.username = username
@@ -62,7 +67,12 @@ class Account:
         """
         logger = logging.getLogger(logger_name)
         try:
-            auth = platform.Auth.login(self.username, self.password, base_url=self.baseurl, ask_for_2fa_input=True)
+            auth = platform.Auth.login(
+                self.username,
+                self.password,
+                base_url=self.baseurl,
+                ask_for_2fa_input=True,
+            )
         except errors.PlatformError as e:
             logger.error("Failed to log in: {}".format(e))
             self.auth = None
@@ -109,10 +119,16 @@ class Account:
             return Project(self, int(project_id))
         elif type(project_id) is str:
             projects = self.projects
-            projects_match = [proj for proj in projects if proj["name"] == project_id]
+            projects_match = [
+                proj for proj in projects if proj["name"] == project_id
+            ]
             if not projects_match:
-                raise Exception(f"Project {project_id} does not exist or is not available for this user.")
+                raise Exception(
+                    f"Project {project_id} does not exist or is not available "
+                    f"for this user."
+                )
             return Project(self, int(projects_match[0]["id"]))
+        return None
 
     @property
     def projects(self):
@@ -127,7 +143,11 @@ class Account:
         logger = logging.getLogger(logger_name)
 
         try:
-            data = platform.parse_response(platform.post(self.auth, "projectset_manager/get_projectset_list"))
+            data = platform.parse_response(
+                platform.post(
+                    self.auth, "projectset_manager/get_projectset_list"
+                )
+            )
         except errors.PlatformError as e:
             logger.error("Failed to get project list: {}".format(e))
             raise
@@ -137,7 +157,15 @@ class Account:
             titles.append({"name": project["name"], "id": project["_id"]})
         return titles
 
-    def add_project(self, project_abbreviation, project_name, description="", users=None, from_date="", to_date=""):
+    def add_project(
+        self,
+        project_abbreviation,
+        project_name,
+        description="",
+        users=None,
+        from_date="",
+        to_date="",
+    ):
         """
         Add a new project to the user account.
 
@@ -256,7 +284,9 @@ class Account:
                     preload_content=not stream,
                 )
             if response.status >= 400:
-                raise HTTPError("STATUS {}: {}".format(response.status, response.reason))
+                raise HTTPError(
+                    "STATUS {}: {}".format(response.status, response.reason)
+                )
         except Exception as e:
             error = "Could not send request. ERROR: {0}".format(e)
             logger.error(error)
@@ -278,7 +308,9 @@ class Account:
         try:
             parsed_content = load_json(response.data)
         except Exception:
-            error = "Could not parse the response as JSON data: {}".format(response.data)
+            error = "Could not parse the response as JSON data: {}".format(
+                response.data
+            )
             logger.error(error)
             raise
 

qmenta/client/File.py

@@ -32,12 +32,21 @@ class File:
     `ff_container = File(project, "MRB", "1", "gre_field_mapping_3.zip")`
     """
 
-    def __init__(self, project: qmenta.client.Project, subject_name: str, ssid: str, file_name: str):
+    def __init__(
+        self,
+        project: qmenta.client.Project,
+        subject_name: str,
+        ssid: str,
+        file_name: str,
+    ):
         self.file_name = file_name
         self.project = project
         self._container_id = None
         for cont in self.project.list_input_containers():
-            if cont["patient_secret_name"] == subject_name and cont["ssid"] == ssid:
+            if (
+                cont["patient_secret_name"] == subject_name
+                and cont["ssid"] == ssid
+            ):
                 self._container_id = cont["container_id"]
                 break
         if self.file_name.endswith(".zip"):
@@ -50,7 +59,9 @@ class File:
     def __str__(self):
         return self.file_name
 
-    def pull_scan_sequence_info(self, specify_dicom_tags=None, output_format: str = "csv"):
+    def pull_scan_sequence_info(
+        self, specify_dicom_tags=None, output_format: str = "csv"
+    ):
         """
         Pulling scan sequence information (e.g. series number, series type,
         series description, number of files, file formats available)
@@ -74,11 +85,18 @@ class File:
         if specify_dicom_tags is None:
             specify_dicom_tags = list()
         valid_output_formats = ["csv", "tsv", "json", "dict"]
-        assert output_format in valid_output_formats, f"Output format not valid. Choose one of {valid_output_formats}"
+        assert (
+            output_format in valid_output_formats
+        ), f"Output format not valid. Choose one of {valid_output_formats}"
 
         with TemporaryDirectory() as temp_dir:
             local_file_name = mkstemp(dir=temp_dir) + ".zip"
-            self.project.download_file(self._container_id, self.file_name, local_file_name, overwrite=False)
+            self.project.download_file(
+                self._container_id,
+                self.file_name,
+                local_file_name,
+                overwrite=False,
+            )
             if self._file_type == "DICOM":
                 unzip_dicoms(local_file_name, temp_dir, exclude_members=None)
                 dicoms = glob.glob(os.path.join(temp_dir, "*"))
@@ -92,11 +110,21 @@ class File:
                             # only needed for one file, all have the same data.
                             for attribute in specify_dicom_tags:
                                 # error handling of attributes send by the user
-                                assert len(attribute) == 2, "Invalid length of DICOM Attribute"
-                                assert isinstance(attribute[0], int), "Invalid type of DICOM Attribute"
-                                output_data["dicom tag"].append(open_file[attribute].tag)
-                                output_data["attribute"].append(open_file[attribute].name)
-                                output_data["value"].append(open_file[attribute].value)
+                                assert (
+                                    len(attribute) == 2
+                                ), "Invalid length of DICOM Attribute"
+                                assert isinstance(
+                                    attribute[0], int
+                                ), "Invalid type of DICOM Attribute"
+                                output_data["dicom tag"].append(
+                                    open_file[attribute].tag
+                                )
+                                output_data["attribute"].append(
+                                    open_file[attribute].name
+                                )
+                                output_data["value"].append(
+                                    open_file[attribute].value
+                                )
                     except Exception as e:
                         print(str(e))
                         pass
@@ -106,10 +134,14 @@ class File:
         output_data["value"].append(number_files)
 
         if output_format == "csv":
-            pd.DataFrame(output_data).to_csv(f"scan_sequence_info.{output_format}", index=False)
+            pd.DataFrame(output_data).to_csv(
+                f"scan_sequence_info.{output_format}", index=False
+            )
 
         elif output_format == "tsv":
-            pd.DataFrame(output_data).to_csv(f"scan_sequence_info.{output_format}", sep="\t", index=False)
+            pd.DataFrame(output_data).to_csv(
+                f"scan_sequence_info.{output_format}", sep="\t", index=False
+            )
 
         elif output_format == "json":
             with open(f"scan_sequence_info.{output_format}", "w") as fp: