qmenta-client 1.1.dev1217__py3-none-any.whl → 1.1.dev1230__py3-none-any.whl

qmenta/client/Project.py

@@ -23,7 +23,7 @@ logger_name = "qmenta.client"
 def show_progress(done, total, finish=False):
     bytes_in_mb = 1024 * 1024
     progress_message = "\r[{:.2f} %] Uploaded {:.2f} of {:.2f} Mb".format(
-        done / float(total) * 100, done / (bytes_in_mb), total / (bytes_in_mb))
+        done / float(total) * 100, done / bytes_in_mb, total / bytes_in_mb)
     sys.stdout.write(progress_message)
     sys.stdout.flush()
     if not finish:
@@ -91,15 +91,16 @@ class Project:
     """
 
     def __init__(self, account: Account, project_id, max_upload_retries=5):
-
         # if project_id is a string (the name of the project), get the
         # project id (int)
-        if type(project_id) == str:
+        if isinstance(project_id, str):
             project_name = project_id
             project_id = next(iter(filter(
                 lambda proj: proj["name"] == project_id, account.projects)
             ))["id"]
         else:
+            if isinstance(project_id, float):
+                project_id = int(project_id)
             project_name = next(iter(filter(
                 lambda proj: proj["id"] == project_id, account.projects)
             ))["name"]
@@ -162,9 +163,21 @@ class Project:
         """
         return self.get_subjects_metadata(cache=False)
 
-    def get_subjects_metadata(self, cache=True):
+    def get_subjects_metadata(self, cache=True, search_criteria=None):
         """
         List all subject data from the selected project.
+        Parameters
+        ----------
+        cache: bool
+            Whether to use the cached metadata or not
+
+        search_criteria: dict
+            Each element is a string and is built using the formatting
+        "type;value", or "type;operation|value"
+
+        Example:
+        search_criteria = {"pars_patient_secret_name": "string;abide",
+        "pars_ssid": "integer;eq|2"}
 
         Returns
         -------
@@ -175,6 +188,7 @@ class Project:
         if not cache or not self._subjects_metadata:
             content = platform.parse_response(platform.post(
                 self._account.auth, "patient_manager/get_patient_list",
+                data=search_criteria,
                 headers={"X-Range": "items=0-9999"}
             ))
             self._subjects_metadata = content
@@ -218,7 +232,7 @@ class Project:
         List all the parameters in the subject metadata.
 
         Each project has a set of parameters that define the subjects metadata.
-        This function returns all this parameters and its properties.
+        This function returns all these parameters and its properties.
 
         Returns
         -------
@@ -284,7 +298,7 @@ class Project:
             answer = {}
 
         if title not in answer:
-            logger.error("Could not add new parameter: {}".format(title))
+            logger.error(f"Could not add new parameter: {title}")
             return False
 
         logger.info("New parameter added:", title, param_properties)
@@ -296,9 +310,8 @@ class Project:
         elif isinstance(analysis_name_or_id, str):
             search_tag = "p_n"
         else:
-            raise Exception(
-                "The analysis identifier must be its name or an integer"
-            )
+            raise Exception("The analysis identifier must be its name or an "
+                            "integer")
 
         search_condition = {
             search_tag: analysis_name_or_id,
@@ -309,10 +322,8 @@ class Project:
         ))
 
         if len(response) > 1:
-            raise Exception(
-                "multiple analyses with name {!r} found".format(
-                    analysis_name_or_id)
-            )
+            raise Exception(f"multiple analyses with name "
+                            f"{analysis_name_or_id} found")
         elif len(response) == 1:
             return response[0]
         else:
@@ -348,9 +359,8 @@ class Project:
         )
 
         if len(response) > 1:
-            raise Exception(
-                "multiple containers for subject {!r} found".format(
-                    subject_name))
+            raise Exception(f"multiple containers for subject {subject_name} "
+                            f"found")
         elif len(response) == 1:
             return response[0]
         else:
@@ -500,10 +510,10 @@ class Project:
         filename : str
             Name of the file to be edited.
         modality : str or None
-            Modality identifier, or None if the file shouldn"t have
+            Modality identifier, or None if the file shouldn't have
             any modality
         tags : list[str] or None
-            List of tags, or None if the filename shouldn"t have any tags
+            List of tags, or None if the filename shouldn't have any tags
         """
 
         tags_str = "" if tags is None else ";".join(tags)
@@ -580,15 +590,14 @@ class Project:
             Name of the zip where the downloaded files are stored.
         """
         logger = logging.getLogger(logger_name)
-
-        files_in_container = self.list_container_files(container_id)
-        files_not_in_container = filter(lambda f: f not in files_in_container,
-                                        filenames)
-        files_not_in_container = list(files_not_in_container)
+        files_not_in_container = list(
+            filter(lambda f: f not in self.list_container_files(container_id),
+                   filenames)
+        )
 
         if files_not_in_container:
-            msg = "The following files are missing in container {}: {}".format(
-                container_id, ", ".join(files_not_in_container))
+            msg = (f"The following files are missing in container "
+                   f"{container_id}: {', '.join(files_not_in_container)}")
             logger.error(msg)
             return False
 
@@ -642,6 +651,8 @@ class Project:
         ----------
         subject_name : str
             Name of the subject.
+        cache: bool
+            Whether to use the cached metadata or not
 
         Returns
         -------
@@ -674,9 +685,8 @@ class Project:
         """
         logger = logging.getLogger(logger_name)
         if self.check_subject_name(subject.name):
-            logger.error(
-                "Subject with name {} already exists in project!".format(
-                    subject.name))
+            logger.error(f"Subject with name {subject.name} already exists in "
+                         f"project!")
             return False
 
         try:
@@ -685,8 +695,7 @@ class Project:
                 data={"secret_name": subject.name}
             ))
         except errors.PlatformError:
-            logger.error(
-                "Subject {} could not be created.".format(subject.name))
+            logger.error(f"Subject {subject.name} could not be created.")
             return False
 
         subject.subject_id = self.get_subject_id(subject.name)
@@ -764,7 +773,7 @@ class Project:
 
         Parameters
         ----------
-        name : str
+        subject_name : str
             Name of the subject to be deleted.
 
         Returns
@@ -828,12 +837,12 @@ class Project:
             the uploaded file into multiple sessions.
         """
 
-        request_headers = {}
-        request_headers["Content-Type"] = "application/zip"
-        request_headers["Content-Range"] = range_str
-        request_headers["Session-ID"] = str(session_id)
-        request_headers["Content-Length"] = str(length)
-        request_headers["Content-Disposition"] = disposition
+        request_headers = {
+            "Content-Type": "application/zip", "Content-Range":
+                range_str, "Session-ID": str(session_id),
+            "Content-Length": str(length),
+            "Content-Disposition": disposition
+        }
 
         if last_chunk:
             request_headers["X-Mint-Name"] = name
@@ -885,7 +894,7 @@ class Project:
             Subject to which this file will belong
         ssid : str
             The ID of the timepoint
-        data_of_scan : str
+        date_of_scan : str
             Date of scan/creation of the file
         description : str
             Description of the file
@@ -932,7 +941,6 @@ class Project:
             session_id = get_session_id(file_path)
             chunk_num = 0
             retries_count = 0
-            error_message = ""
             uploaded_bytes = 0
             response = None
             last_chunk = False
@@ -959,7 +967,7 @@ class Project:
                 bytes_range = "bytes " + str(start_position) + "-" + \
                               str(end_position) + "/" + str(total_bytes)
 
-                dispstr = "attachment; filename=%s" % filename
+                dispstr = f"attachment; filename={filename}"
                 response = self._upload_chunk(
                     data, bytes_range, bytes_to_send, session_id, dispstr,
                     last_chunk,
@@ -972,6 +980,7 @@ class Project:
                     time.sleep(retries_count * 5)
                     if retries_count > max_retries:
                         error_message = "HTTP Connection Problem"
+                        logger.error(error_message)
                         break
                 elif int(response.status_code) == 201:
                     chunk_num += 1
@@ -987,6 +996,7 @@ class Project:
                         error_message = (
                             "Error Code: 416; "
                             "Requested Range Not Satisfiable (NGINX)")
+                        logger.error(error_message)
                         break
                 else:
                     retries_count += 1
@@ -1019,6 +1029,7 @@ class Project:
         ----------
         file_path : str
             Path to the file to upload
+        subject_name: str
 
         Returns
         -------
@@ -1037,6 +1048,7 @@ class Project:
         ----------
         file_path : str
             Path to the file to upload
+        subject_name: str
 
         Returns
         -------
@@ -1058,6 +1070,7 @@ class Project:
         ----------
         file_path : str
             Path to the file to upload
+        subject_name: str
 
         Returns
         -------
@@ -1078,7 +1091,7 @@ class Project:
         container_id : int
             ID of the container to copy.
         project_id : int or str
-            ID of the project to retireve, either the numeric ID or the name
+            ID of the project to retrieve, either the numeric ID or the name
 
         Returns
         -------
@@ -1094,7 +1107,7 @@ class Project:
                               if proj["name"] == project_id]
             if not projects_match:
                 raise Exception(
-                    "Project {}".format(project_id) +
+                    f"Project {project_id}" +
                     " does not exist or is not available for this user."
                 )
             p_id = int(projects_match[0]["id"])
@@ -1203,7 +1216,7 @@ class Project:
         if preferred_destination:
             post_data["preferred_destination"] = preferred_destination
 
-        logger.debug("post_data = {}".format(post_data))
+        logger.debug(f"post_data = {post_data}")
         return self.__handle_start_analysis(
             post_data, ignore_warnings=ignore_warnings
         )
@@ -1245,8 +1258,8 @@ class Project:
 
         logger = logging.getLogger(logger_name)
         if n_calls > call_limit:
-            logger.error("__handle_start_analysis_response called itself more\
-                          than {} times: aborting.".format(n_calls))
+            logger.error(f"__handle_start_analysis_response called itself more\
+                          than {n_calls} times: aborting.")
             return None
 
         try:
@@ -1319,7 +1332,7 @@ class Project:
                 new_post, ignore_warnings=ignore_warnings, n_calls=n_calls
             )
         except platform.ActionFailedError as e:
-            logger.error("Unable to start the analysis: {}".format(e))
+            logger.error(f"Unable to start the analysis: {e}")
             return None
 
     @staticmethod
@@ -1346,7 +1359,7 @@ class Project:
             set to pass or fail.
         """
         logger = logging.getLogger(__name__)
-        logger.info("Setting QC status to {}: {}".format(status, comments))
+        logger.info(f"Setting QC status to {status}: {comments}")
 
         platform.parse_response(platform.post(
             auth=self._account.auth,
@@ -1359,6 +1372,42 @@ class Project:
             }
         ))
 
+    def get_qc_status(
+            self, patient_secret_name=None, ssid=None, analysis_id=None):
+        """
+        Gets the session QC status of a session. If the analysis_id is
+        specified, it returns the QC of the
+        analysis instead.
+
+        """
+        if patient_secret_name and ssid:
+            session = self.get_subjects_metadata(
+                search_criteria={
+                    "pars_patient_secret_name": f"string;"
+                                                f"{patient_secret_name}",
+                    "pars_ssid": f"integer;eq|{ssid}"
+                }
+            )
+            to_return = session["qa_status"], session["qa_comments"]
+        elif analysis_id:
+            try:
+                to_return = [
+                    analysis["qa_data"] for analysis in self.list_analysis()
+                    if analysis["_id"] == analysis_id
+                ][0]
+                to_return = to_return["qa_status"], to_return["qa_comments"]
+            except IndexError:
+                # Handle the case where no matching analysis is found
+                to_return = None
+            except Exception as e:
+                # Handle other potential exceptions
+                print(f"An error occurred: {e}")
+                to_return = None
+        else:
+            raise Exception(f"Must specify {patient_secret_name} and "
+                            f"{ssid} or {analysis_id}.")
+        return to_return
+
     def start_multiple_analyses(
             self,
             script_name,

{qmenta_client-1.1.dev1217.dist-info → qmenta_client-1.1.dev1230.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: qmenta-client
-Version: 1.1.dev1217
+Version: 1.1.dev1230
 Summary: Python client lib to interact with the QMENTA platform.
 Home-page: https://www.qmenta.com/
 Author: QMENTA

{qmenta_client-1.1.dev1217.dist-info → qmenta_client-1.1.dev1230.dist-info}/RECORD

@@ -1,10 +1,10 @@
 qmenta/__init__.py,sha256=jv2YF__bseklT3OWEzlqJ5qE24c4aWd5F4r0TTjOrWQ,65
 qmenta/client/Account.py,sha256=MEljEy9cmg2uP2FG1d3TZAgfj66EE2_3PQAZ9rvpCXY,9647
 qmenta/client/File.py,sha256=ZgvSqejIosUt4uoX7opUnPnp5XGEaJNMRwFC0mQVB8k,5344
-qmenta/client/Project.py,sha256=ugxLNnfYBojylOTfSlCpaDGA9_8DwSAB2pONOYA3Sbw,46445
+qmenta/client/Project.py,sha256=rxOd03sZXCrZjHbxQlgV7qbEXc2STX-sTSXprBKkIOA,48357
 qmenta/client/Subject.py,sha256=lhxxVdQ6d-GNoQC8mrJwa4L1f44nJc4PcJtDspmKN7I,8756
 qmenta/client/__init__.py,sha256=AjTojBhZeW5nl0i605KS8S1Gl5tPNc1hdzD47BGNfoI,147
 qmenta/client/utils.py,sha256=5DK2T_HQprrCwLS0Ycm2CjseaYmAUKaJkJvYoW-Rqzc,2479
-qmenta_client-1.1.dev1217.dist-info/METADATA,sha256=u1nGnyNgNrpjs3T1kBHOEw7_cQxUdd7Os8Chlqu0Vsw,609
-qmenta_client-1.1.dev1217.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-qmenta_client-1.1.dev1217.dist-info/RECORD,,
+qmenta_client-1.1.dev1230.dist-info/METADATA,sha256=GVsXH4eCCog-jbYRrB-vthtUbOnvsemdnc-yAmeNdak,609
+qmenta_client-1.1.dev1230.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+qmenta_client-1.1.dev1230.dist-info/RECORD,,

{qmenta_client-1.1.dev1217.dist-info → qmenta_client-1.1.dev1230.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any