qmenta-client 1.1.dev1324__py3-none-any.whl → 1.1.dev1337__py3-none-any.whl

qmenta/client/Project.py

@@ -200,14 +200,45 @@ def wrap_search_criteria(search_criteria={}):
     return modality, tags, file_metadata
 
 
+def convert_qc_value_to_qcstatus(value):
+    """
+    Convert input string to QCStatus class.
+
+    Parameters
+    ----------
+    value : str
+        Value to convert.
+
+    Returns
+    -------
+    QCStatus or Bool
+        QCStatus.PASS, QCStatus.FAIL or QCStatus.UNDETERMINED
+        False if the Value cannot be convered.
+    """
+    logger = logging.getLogger(logger_name)
+    if value == "pass":
+        return QCStatus.PASS
+    elif value == "fail":
+        return QCStatus.FAIL
+    elif value == "":
+        return QCStatus.UNDERTERMINED
+    else:
+        logger.error(f"The input value '{value}' cannot be converted "
+                     f"to class QCStatus.")
+        return False
+
+
 class QCStatus(Enum):
     """
     Enum with the following options:
-    FAIL, PASS
+    FAIL, PASS, UNDERTERMINED
+    that are the possible options for the QA/QC status of both
+    analysis and session.
     """
 
     PASS = "pass"
     FAIL = "fail"
+    UNDERTERMINED = ""
 
 
 class Project:
@@ -1841,7 +1872,8 @@ class Project:
                 modalities.append(modality)
         return modalities
 
-    def set_qc_status(self, analysis_id, status=QCStatus.PASS, comments=""):
+    def set_qc_status_analysis(self, analysis_id,
+                               status=QCStatus.UNDERTERMINED, comments=""):
         """
         Changes the analysis QC status.
 
@@ -1850,150 +1882,257 @@ class Project:
         analysis_id : int
             Analysis ID number
         status : QCStatus
-            QCStatus.PASS or QCStatus.FAIL
+            QCStatus.PASS, QCStatus.FAIL or QCStatus.UNDETERMINED
         comments : str, optional
-            Additional comments explaining why the QC status has been
-            set to pass or fail.
+            Additional comments explaining why the reasoning of setting the
+            QC status to such state.
+
+        Returns
+        -------
+        bool
+            True if the QC status was correctly changed, False otherwise.
         """
+
         logger = logging.getLogger(__name__)
         logger.info(f"Setting QC status to {status}: {comments}")
 
-        platform.parse_response(
-            platform.post(
-                auth=self._account.auth,
-                endpoint="projectset_manager/set_qa_status",
-                data={"item_ids": analysis_id, "status": status.value, "comments": comments, "entity": "analysis"},
+        if not isinstance(status, QCStatus):
+            raise ValueError("Status should be type 'QCStatus'.")
+
+        try:
+            analysis_id = str(int(analysis_id))
+        except ValueError:
+            raise ValueError(f"analysis_id: '{analysis_id}' not valid. " f"Must be convertible to int.")
+
+        try:
+            platform.parse_response(
+                platform.post(
+                    auth=self._account.auth,
+                    endpoint="projectset_manager/set_qa_status",
+                    data={"item_ids": analysis_id, "status": status.value,
+                          "comments": str(comments), "entity": "analysis"},
+                )
             )
-        )
+        except Exception:
+            logger.error(f"It was not possible to change the QC status of"
+                         f"Analysis ID: {analysis_id}")
+            return False
+        return True
 
-    def get_qc_status(self, patient_secret_name=None, ssid=None, analysis_id=None):
+    def set_qc_status_subject(self, patient_id,
+                              status=QCStatus.UNDERTERMINED, comments=""):
         """
-        Gets the session QC status of a session. If the analysis_id is
-        specified, it returns the QC of the
-        analysis instead.
+        Changes the QC status of a Patient ID (equivalent to a
+        Subject ID/Session ID).
+
+        Parameters
+        ----------
+        patient_id : int
+            Patient ID number of the session.
+        status : QCStatus
+            QCStatus.PASS, QCStatus.FAIL or QCStatus.UNDETERMINED
+        comments : str, optional
+            Additional comments explaining why the reasoning of setting the
+            QC status to such state.
 
+        Returns
+        -------
+        bool
+            True if the QC status was correctly changed, False otherwise.
         """
-        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}",
-                }
+        logger = logging.getLogger(__name__)
+        logger.info(f"Setting QC status to {status}: {comments}")
+
+        if not isinstance(status, QCStatus):
+            raise ValueError("Status should be type 'QCStatus'.")
+
+        try:
+            patient_id = str(int(patient_id))
+        except ValueError:
+            raise ValueError(f"'patient_id': '{patient_id}' not valid. " f"Must be convertible to int.")
+
+        try:
+            platform.parse_response(
+                platform.post(
+                    auth=self._account.auth,
+                    endpoint="projectset_manager/set_qa_status",
+                    data={"item_ids": patient_id, "status": status.value,
+                          "comments": str(comments), "entity": "patients"},
+                )
             )
-            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 {ssid} or {analysis_id}.")
-        return to_return
+        except Exception:
+            logger.error(f"It was not possible to change the QC status of"
+                         f"Patient ID: {patient_id}")
+            return False
+        return True
 
-    def start_multiple_analyses(
-        self,
-        script_name,
-        version,
-        n_times,
-        in_container_id=None,
-        analysis_name=None,
-        analysis_description=None,
-        ignore_warnings=False,
-        settings=None,
-        tags=None,
-        preferred_destination=None,
-    ):
+    def get_qc_status_analysis(self, analysis_id):
         """
-        Starts multiple times the same analysis on a subject with the same
-        settings.
+        Gets the QC status of an anlaysis provided its Analysis ID.
 
         Parameters
         ----------
-        script_name : str
-            ID of the script to be run.
-        version: str
-            Version of the script to be run, examples: 1.0, 5.3.4
-        n_times: int
-            Number of analyses to be scheduled
-        in_container_id : int or dict
-            The ID of the container to get the data from, or a dictionary with
-            one or more container names as keys, and IDs as values.
-            Input container names are generally prefixed with "input\\_".
-            If not, the prefix will be automatically added.
-        analysis_name : str
-            Name of the analysis (optional)
-        analysis_description : str
-            Description of the analysis (optional)
-        ignore_warnings : bool
-            If False, warnings by server cause failure.
-        settings : dict
-            The input settings used to run the analysis.
-            Use either settings or in_container_id. Input specification
-            in the settings dict can be done by using the key "input".
-        tags : list[str]
-            The tags of the analysis.
-        preferred_destination : str
-            The machine on which to run the analysis
+        analysis_id : int
+            Analysis ID number
 
-        Yields
+        Returns
         -------
-        int
-            The analysis ID if correctly started, None otherwise.
+        status : QCStatus or False
+            QCStatus.PASS, QCStatus.FAIL or QCStatus.UNDETERMINED
+            False if the status cannot be extracted.
+        comments : str or False
+            Comments defined in the QC Status.
+            False if the comments cannot be extracted.
         """
-        logger = logging.getLogger(logger_name)
-        for n in range(n_times):
-            logger.info(f"Running tool {script_name}:{version} {n + 1}/{n_times}")
-            yield self.start_analysis(
-                script_name,
-                version,
-                in_container_id=in_container_id,
-                analysis_name=analysis_name,
-                analysis_description=analysis_description,
-                ignore_warnings=ignore_warnings,
-                settings=settings,
-                tags=tags,
-                preferred_destination=preferred_destination,
+        try:
+            search_criteria = {"id": analysis_id}
+            to_return = self.list_analysis(search_criteria)
+            return convert_qc_value_to_qcstatus(to_return[0]["qa_status"]), to_return[0]["qa_comments"]
+        except IndexError:
+            # Handle the case where no matching analysis is found
+            logging.error(f"No analysis was found with such Analysis ID: '{analysis_id}'.")
+            return False, False
+        except Exception:
+            # Handle other potential exceptions
+            logging.error(f"It was not possible to extract the QC status"
+                          f"from Analysis ID: {analysis_id}")
+            return False, False
+
+    def get_qc_status_subject(self, patient_id=None, subject_name=None,
+                              ssid=None):
+        """
+        Gets the session QC status via the patient ID or the Subject ID
+        and the Session ID.
+
+        Parameters
+        ----------
+        patient_id : int
+            Patient ID number of the session
+        subject_name : string
+            Subject ID of the session
+        ssid : string
+            Session ID
+
+        Returns
+        -------
+        status : QCStatus or False
+            QCStatus.PASS, QCStatus.FAIL or QCStatus.UNDETERMINED
+            False if the status cannot be extracted.
+        comments : str or False
+            Comments defined in the QC Status.
+            False if the comments cannot be extracted.
+        """
+
+        if patient_id:
+            try:
+                patient_id = int(patient_id)
+            except ValueError:
+                raise ValueError(f"patient_id '{patient_id}' should be an "
+                                 f"integer.")
+            sessions = self.get_subjects_metadata(search_criteria={})
+            session = [session for session in sessions if int(session["_id"]) == patient_id]
+            if len(session) < 1:
+                logging.error(f"No session was found with Patient ID: "
+                              f"'{patient_id}'.")
+                return False, False
+            return convert_qc_value_to_qcstatus(session[0]["qa_status"]), session[0]["qa_comments"]
+        elif subject_name and ssid:
+            session = self.get_subjects_metadata(
+                search_criteria={
+                    "pars_patient_secret_name": f"string;{subject_name}",
+                    "pars_ssid": f"integer;eq|{ssid}",
+                }
             )
+            if len(session) < 1:
+                logging.error(f"No session was found with Subject ID: "
+                              f"'{subject_name}' and Session ID: '{ssid}'.")
+                return False, False
+            return convert_qc_value_to_qcstatus(session[0]["qa_status"]), session[0]["qa_comments"]
+        else:
+            raise ValueError("Either 'patient_id' or 'subject_name' and 'ssid'"
+                             " must not be empty.")
 
-    def set_project_qa_rules(self, rules_file_path, guidance_text=""):
+    def set_project_pa_rules(self, rules_file_path, guidance_text=""):
         """
-        Logs in to the Qmenta platform, retrieves the project ID based on the project name,
-        and updates the project's QA rules using the provided rules file.
+        Updates the active project's protocol adherence rules using the
+        provided rules file.
 
-        Args:
-            rules_file_path (str): The file path to the JSON file containing the QA rules.
-            guidance_text (str): Description of the rules. Only visible for Platform admins.
+        Parameters
+        ----------
+            rules_file_path : str
+                The file path to the JSON file containing the protocol
+                 adherence rules.
+            guidance_text : str
+                Description of the protocol adherence rules.
 
-        Returns:
-            bool: True if the rules were set successfully, False otherwise.
+        Returns
+        -------
+            bool: True if the protocol adherence rules were set successfully,
+            False otherwise.
         """
+        logger = logging.getLogger(logger_name)
         # Read the rules from the JSON file
         try:
             with open(rules_file_path, "r") as fr:
                 rules = json.load(fr)
         except FileNotFoundError:
-            print(f"ERROR: Rules file '{rules_file_path}' not found.")
+            logger.error(f"Pprotocol adherence rule file '{rules_file_path}' "
+                         f"not found.")
             return False
 
         # Update the project's QA rules
-        res = platform.post(
+        res = platform.parse_response(platform.post(
             auth=self._account.auth,
             endpoint="projectset_manager/set_session_qa_requirements",
             data={"project_id": self._project_id, "rules": json.dumps(rules), "guidance_text": guidance_text},
-        )
+        ))
 
-        if res.json().get("success") == 1:
-            print("Rules set up successfully!")
-            return True
-        else:
-            print("ERROR setting the rules")
-            print(res.json())
+        if not res.get("success") == 1:
+            logger.error("There was an error setting up the protocol "
+                         "adherence rules.")
+            logger.error(platform.parse_response(res))
+            return False
+
+        return True
+
+    def get_project_pa_rules(self, rules_file_path):
+        """
+        Retrive the active project's protocol adherence rules
+
+        Parameters
+        ----------
+            rules_file_path : str
+                The file path to the JSON file to store the protocol adherence
+                rules.
+
+        Returns
+        -------
+            guidance_text : str
+                Description of the protocol adherence rules,
+                False if extraction of the protocol adhernece rules is not
+                possible.
+        """
+        logger = logging.getLogger(logger_name)
+
+        # Update the project's QA rules
+        res = platform.parse_response(platform.post(
+            auth=self._account.auth,
+            endpoint="projectset_manager/get_session_qa_requirements",
+            data={"project_id": self._project_id},
+        ))
+
+        if "rules" not in res:
+            logger.error(f"There was an error extracting the protocol "
+                         f"adherence rules from {self._project_name}.")
+            logger.error(platform.parse_response(res))
             return False
+
+        try:
+            with open(rules_file_path, "w") as fr:
+                json.dump(res["rules"], fr, indent=4)
+        except FileNotFoundError:
+            logger.error(f"Protocol adherence rules could not be exported"
+                         f"to file: '{rules_file_path}'.")
+            return False
+
+        return res["guidance_text"]

{qmenta_client-1.1.dev1324.dist-info → qmenta_client-1.1.dev1337.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta-client
-Version: 1.1.dev1324
+Version: 1.1.dev1337
 Summary: Python client lib to interact with the QMENTA platform.
 Author: QMENTA
 Author-email: dev@qmenta.com

{qmenta_client-1.1.dev1324.dist-info → qmenta_client-1.1.dev1337.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=9a6v7-H6BxU-2EykaWnFhW61GZijDB-XWsYzPdzWxz4,70398
+qmenta/client/Project.py,sha256=XzolIEPQzUWPelWtv67fiYvLGXp7bLRfH2-Ckvgl8Ao,75153
 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.dev1324.dist-info/METADATA,sha256=yDhr3jCEwhPFFSWqIdJUeaZtj10Y3GXyEbAq7fDj7UQ,672
-qmenta_client-1.1.dev1324.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-qmenta_client-1.1.dev1324.dist-info/RECORD,,
+qmenta_client-1.1.dev1337.dist-info/METADATA,sha256=Epl4svIqv_lvXPjjfBh5zAU02b5i_sq1z-ZptA0c58o,672
+qmenta_client-1.1.dev1337.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+qmenta_client-1.1.dev1337.dist-info/RECORD,,