qmenta-client 1.1.dev1373__py3-none-any.whl → 1.1.dev1382__py3-none-any.whl

qmenta/client/Project.py

@@ -20,186 +20,6 @@ logger_name = "qmenta.client"
 OPERATOR_LIST = ["eq", "ne", "gt", "gte", "lt", "lte"]
 
 
-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
-    )
-    sys.stdout.write(progress_message)
-    sys.stdout.flush()
-    if not finish:
-        pass
-        # sys.stdout.write("")
-        # sys.stdout.flush()
-    else:
-        sys.stdout.write("\n")
-
-
-def get_session_id(file_path):
-    m = hashlib.md5()
-    m.update(file_path.encode("utf-8"))
-    return str(time.time()).replace(".", "") + "_" + m.hexdigest()
-
-
-def check_upload_file(file_path):
-    """
-    Check whether a file has the correct extension to upload.
-
-    Parameters
-    ----------
-    file_path : str
-        Path to the file
-
-    Returns
-    -------
-    bool
-        True if correct extension, False otherwise.
-    """
-
-    # TODO: Add a file zipper here so zips files in a folder
-
-    file_parts = file_path.split(".")
-    extension = file_parts[-1]
-
-    if extension != "zip":
-        logging.getLogger(logger_name).error("You must upload a zip.")
-        return False
-    else:
-        return True
-
-
-def operation(reference_value, operator, input_value):
-    """
-    The method performs an operation by comparing the two input values.
-    The Operation is applied to the Input Value in comparison to the Reference
-    Value.
-
-    Parameters
-    ----------
-    reference_value : str, list, or int
-        Reference value.
-    operator : str
-        Operation.
-    input_value : str, list, or int
-        Input value.
-
-    Returns
-    -------
-    bool
-        True if the operation is satisfied, False otherwise.
-    """
-    if input_value is None or input_value == "":
-        return False
-
-    if operator == "in":
-        return reference_value in input_value
-
-    elif operator == "in-list":
-        return all([el in input_value for el in reference_value])
-
-    elif operator == "eq":
-        return input_value == reference_value
-
-    elif operator == "gt":
-        return input_value > reference_value
-
-    elif operator == "gte":
-        return input_value >= reference_value
-
-    elif operator == "lt":
-        return input_value < reference_value
-
-    elif operator == "lte":
-        return input_value <= reference_value
-    else:
-        return False
-
-
-def wrap_search_criteria(search_criteria={}):
-    """
-    Wraps the conditions specified within the Search Criteria in order for
-    other methods to handle it easily. The conditions are grouped only into
-    three groups: Modality, Tags and the File Metadata (if DICOM it corresponds
-    to the DICOM information), and each of them is output in a different
-    variable.
-
-    Parameters
-    ----------
-    search_criteria : dict
-        Each element is a string and is built using the formatting
-            "KEYTYPE;VALUE", or "KEYTYPE;OPERATOR|VALUE".
-
-            Full list of keys avaiable for the dictionary:
-
-            search_criteria = {
-                "pars_patient_secret_name": "string;SUBJECTID",
-                "pars_ssid": "integer;OPERATOR|SSID",
-                "pars_modalities": "string;MODALITY",
-                "pars_tags": "tags;TAGS",
-                "pars_age_at_scan": "integer;OPERATOR|AGE_AT_SCAN",
-                "pars_[dicom]_KEY": "KEYTYPE;KEYVALUE",
-                "pars_PROJECTMETADATA": "METADATATYPE;METADATAVALUE",
-                }
-
-            See documentation for a complete definition.
-
-    Returns
-    -------
-    modality : str
-        String containing the modality of the search criteria extracted from
-        'pars_modalities'
-
-    tags : list of str
-        List of strings containing the tags of the search criteria extracted
-        'from pars_tags'
-
-    file_metadata : Dict
-        Dictionary containing the file metadata of the search criteria
-        extracted from 'pars_[dicom]_KEY'
-    """
-
-    # The keys not included bellow apply to the whole session.
-    modality, tags, file_metadata = "", list(), dict()
-    for key, value in search_criteria.items():
-        if key == "pars_modalities":
-            modalities = value.split(";")[1].split(",")
-            if len(modalities) != 1:
-                raise ValueError(f"A file can only have one modality. "
-                                 f"Provided Modalities: "
-                                 f"{', '.join(modalities)}.")
-            modality = modalities[0]
-        elif key == "pars_tags":
-            tags = value.split(";")[1].split(",")
-        elif "pars_[dicom]_" in key:
-            d_tag = key.split("pars_[dicom]_")[1]
-            d_type = value.split(";")[0]
-            if d_type == "string":
-                file_metadata[d_tag] = {
-                    "operation": "in",
-                    "value": value.replace(d_type + ";", "")
-                }
-            elif d_type == "integer":
-                d_operator = value.split(";")[1].split("|")[0]
-                d_value = value.split(";")[1].split("|")[1]
-                file_metadata[d_tag] = {
-                    "operation": d_operator,
-                    "value": int(d_value)}
-            elif d_type == "decimal":
-                d_operator = value.split(";")[1].split("|")[0]
-                d_value = value.split(";")[1].split("|")[1]
-                file_metadata[d_tag] = {
-                    "operation": d_operator,
-                    "value": float(d_value)
-                }
-            elif d_type == "list":
-                value.replace(d_type + ";", "")
-                file_metadata[d_tag] = {
-                    "operation": "in-list",
-                    "value": value.replace(d_type + ";", "").split(";")
-                }
-    return modality, tags, file_metadata
-
-
 def convert_qc_value_to_qcstatus(value):
     """
     Convert input string to QCStatus class.
@@ -577,7 +397,7 @@ class Project:
         content = self.get_subjects_metadata(search_criteria, items=(0, 9999))
 
         # Wrap search criteria.
-        modality, tags, dicoms = wrap_search_criteria(search_criteria)
+        modality, tags, dicoms = self.__wrap_search_criteria(search_criteria)
 
         # Iterate over the files of each subject selected to include/exclude
         # them from the results.
@@ -602,7 +422,7 @@ class Project:
                         d_operator = dict_value["operation"]
                         d_value = dict_value["value"]
                         result_values.append(
-                            operation(d_value, d_operator, f_value)
+                            self.__operation(d_value, d_operator, f_value)
                         )
 
                     if not all(result_values):
@@ -731,17 +551,17 @@ class Project:
         Parameters
         ----------
         search_condition : dict
-            - p_n: str Analysis name
-            - type: str Type
-            - from_d: str  dd.mm.yyyy Date from
-            - to_d: str dd.mm.yyyy Date to
-            - qa_status: str pass/fail/nd QC status
-            - secret_name: str Subject ID
-            - tags: str
-            - with_child_analysis: 1 if 1, child analysis of workflows will appear
-            - id: str ID
-            - state: running, completed, pending, exception
-            - username: str
+            - p_n: str or None Analysis name
+            - type: str or None Type
+            - from_d: str or None dd.mm.yyyy Date from
+            - to_d: str or None dd.mm.yyyy Date to
+            - qa_status: str or None pass/fail/nd QC status
+            - secret_name: str or None Subject ID
+            - tags: str or None
+            - with_child_analysis: 1 or None if 1, child analysis of workflows will appear
+            - id: str or None ID
+            - state: running, completed, pending, exception or None
+            - username: str or None
 
         items : List[int]
             list containing two elements [min, max] that correspond to the
@@ -770,7 +590,7 @@ class Project:
         for key in search_condition.keys():
             if key not in search_keys.keys():
                 raise Exception((f"This key '{key}' is not accepted by this" "search condition"))
-            if not isinstance(search_condition[key], search_keys[key]):
+            if not isinstance(search_condition[key], search_keys[key]) and search_condition[key] is not None:
                 raise Exception((f"The key {key} in the search condition" f"is not type {search_keys[key]}"))
         req_headers = {"X-Range": f"items={items[0]}-{items[1] - 1}"}
         return platform.parse_response(
@@ -881,17 +701,17 @@ class Project:
         Parameters
         ----------
         search_condition : dict
-            - p_n: str Analysis name
-            - type: str Type
-            - from_d: str  dd.mm.yyyy Date from
-            - to_d: str dd.mm.yyyy Date to
-            - qa_status: str pass/fail/nd QC status
-            - secret_name: str Subject ID
-            - tags: str
-            - with_child_analysis: 1 if 1, child analysis of workflows will appear
-            - id: str ID
-            - state: running, completed, pending, exception
-            - username: str
+            - p_n: str or None Analysis name
+            - type: str or None Type
+            - from_d: str or None dd.mm.yyyy Date from
+            - to_d: str or None dd.mm.yyyy Date to
+            - qa_status: str or None pass/fail/nd QC status
+            - secret_name: str or None Subject ID
+            - tags: str or None
+            - with_child_analysis: 1 or None if 1, child analysis of workflows will appear
+            - id: str or None ID
+            - state: running, completed, pending, exception or None
+            - username: str or None
         items : List[int]
             list containing two elements [min, max] that correspond to the
             mininum and maximum range of analysis listed
@@ -1533,7 +1353,7 @@ class Project:
                 logger.error("Cannot upload empty file {}".format(file_path))
                 return False
             uploaded = 0
-            session_id = get_session_id(file_path)
+            session_id = self.__get_session_id(file_path)
             chunk_num = 0
             retries_count = 0
             uploaded_bytes = 0
@@ -1592,7 +1412,7 @@ class Project:
                     retries_count = 0
                     uploaded_bytes += chunk_size
                 elif int(response.status_code) == 200:
-                    show_progress(file_size, file_size, finish=True)
+                    self.__show_progress(file_size, file_size, finish=True)
                     break
                 elif int(response.status_code) == 416:
                     retries_count += 1
@@ -1610,7 +1430,7 @@ class Project:
                         break
 
                 uploaded += chunk_size
-                show_progress(uploaded, file_size)
+                self.__show_progress(uploaded, file_size)
 
         try:
             platform.parse_response(response)
@@ -1639,7 +1459,7 @@ class Project:
             True if upload was correctly done, False otherwise.
         """
 
-        if check_upload_file(file_path):
+        if self.__check_upload_file(file_path):
             return self.upload_file(file_path, subject_name)
 
     def upload_gametection(self, file_path, subject_name):
@@ -1658,7 +1478,7 @@ class Project:
             True if upload was correctly done, False otherwise.
         """
 
-        if check_upload_file(file_path):
+        if self.__check_upload_file(file_path):
             return self.upload_file(file_path, subject_name, input_data_type="parkinson_gametection")
         return False
 
@@ -1678,7 +1498,7 @@ class Project:
             True if upload was correctly done, False otherwise.
         """
 
-        if check_upload_file(file_path):
+        if self.__check_upload_file(file_path):
             return self.upload_file(file_path, subject_name, result=True)
         return False
 
@@ -2183,3 +2003,178 @@ class Project:
             return False
 
         return res["guidance_text"]
+
+    def __show_progress(self, 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
+        )
+        sys.stdout.write(progress_message)
+        sys.stdout.flush()
+        if not finish:
+            pass
+            # sys.stdout.write("")
+            # sys.stdout.flush()
+        else:
+            sys.stdout.write("\n")
+
+    def __get_session_id(self, file_path):
+        m = hashlib.md5()
+        m.update(file_path.encode("utf-8"))
+        return str(time.time()).replace(".", "") + "_" + m.hexdigest()
+
+    def __check_upload_file(self, file_path):
+        """
+        Check whether a file has the correct extension to upload.
+
+        Parameters
+        ----------
+        file_path : str
+            Path to the file
+
+        Returns
+        -------
+        bool
+            True if correct extension, False otherwise.
+        """
+
+        # TODO: Add a file zipper here so zips files in a folder
+
+        file_parts = file_path.split(".")
+        extension = file_parts[-1]
+
+        if extension != "zip":
+            logging.getLogger(logger_name).error("You must upload a zip.")
+            return False
+        else:
+            return True
+
+    def __operation(self, reference_value, operator, input_value):
+        """
+        The method performs an operation by comparing the two input values.
+        The Operation is applied to the Input Value in comparison to the Reference
+        Value.
+
+        Parameters
+        ----------
+        reference_value : str, list, or int
+            Reference value.
+        operator : str
+            Operation.
+        input_value : str, list, or int
+            Input value.
+
+        Returns
+        -------
+        bool
+            True if the operation is satisfied, False otherwise.
+        """
+        if input_value is None or input_value == "":
+            return False
+
+        if operator == "in":
+            return reference_value in input_value
+
+        elif operator == "in-list":
+            return all([el in input_value for el in reference_value])
+
+        elif operator == "eq":
+            return input_value == reference_value
+
+        elif operator == "gt":
+            return input_value > reference_value
+
+        elif operator == "gte":
+            return input_value >= reference_value
+
+        elif operator == "lt":
+            return input_value < reference_value
+
+        elif operator == "lte":
+            return input_value <= reference_value
+        else:
+            return False
+
+    def __wrap_search_criteria(self, search_criteria={}):
+        """
+        Wraps the conditions specified within the Search Criteria in order for
+        other methods to handle it easily. The conditions are grouped only into
+        three groups: Modality, Tags and the File Metadata (if DICOM it corresponds
+        to the DICOM information), and each of them is output in a different
+        variable.
+
+        Parameters
+        ----------
+        search_criteria : dict
+            Each element is a string and is built using the formatting
+                "KEYTYPE;VALUE", or "KEYTYPE;OPERATOR|VALUE".
+
+                Full list of keys avaiable for the dictionary:
+
+                search_criteria = {
+                    "pars_patient_secret_name": "string;SUBJECTID",
+                    "pars_ssid": "integer;OPERATOR|SSID",
+                    "pars_modalities": "string;MODALITY",
+                    "pars_tags": "tags;TAGS",
+                    "pars_age_at_scan": "integer;OPERATOR|AGE_AT_SCAN",
+                    "pars_[dicom]_KEY": "KEYTYPE;KEYVALUE",
+                    "pars_PROJECTMETADATA": "METADATATYPE;METADATAVALUE",
+                    }
+
+                See documentation for a complete definition.
+
+        Returns
+        -------
+        modality : str
+            String containing the modality of the search criteria extracted from
+            'pars_modalities'
+
+        tags : list of str
+            List of strings containing the tags of the search criteria extracted
+            'from pars_tags'
+
+        file_metadata : Dict
+            Dictionary containing the file metadata of the search criteria
+            extracted from 'pars_[dicom]_KEY'
+        """
+
+        # The keys not included bellow apply to the whole session.
+        modality, tags, file_metadata = "", list(), dict()
+        for key, value in search_criteria.items():
+            if key == "pars_modalities":
+                modalities = value.split(";")[1].split(",")
+                if len(modalities) != 1:
+                    raise ValueError(f"A file can only have one modality. "
+                                     f"Provided Modalities: "
+                                     f"{', '.join(modalities)}.")
+                modality = modalities[0]
+            elif key == "pars_tags":
+                tags = value.split(";")[1].split(",")
+            elif "pars_[dicom]_" in key:
+                d_tag = key.split("pars_[dicom]_")[1]
+                d_type = value.split(";")[0]
+                if d_type == "string":
+                    file_metadata[d_tag] = {
+                        "operation": "in",
+                        "value": value.replace(d_type + ";", "")
+                    }
+                elif d_type == "integer":
+                    d_operator = value.split(";")[1].split("|")[0]
+                    d_value = value.split(";")[1].split("|")[1]
+                    file_metadata[d_tag] = {
+                        "operation": d_operator,
+                        "value": int(d_value)}
+                elif d_type == "decimal":
+                    d_operator = value.split(";")[1].split("|")[0]
+                    d_value = value.split(";")[1].split("|")[1]
+                    file_metadata[d_tag] = {
+                        "operation": d_operator,
+                        "value": float(d_value)
+                    }
+                elif d_type == "list":
+                    value.replace(d_type + ";", "")
+                    file_metadata[d_tag] = {
+                        "operation": "in-list",
+                        "value": value.replace(d_type + ";", "").split(";")
+                    }
+        return modality, tags, file_metadata

{qmenta_client-1.1.dev1373.dist-info → qmenta_client-1.1.dev1382.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta-client
-Version: 1.1.dev1373
+Version: 1.1.dev1382
 Summary: Python client lib to interact with the QMENTA platform.
 Author: QMENTA
 Author-email: dev@qmenta.com

{qmenta_client-1.1.dev1373.dist-info → qmenta_client-1.1.dev1382.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=xk-C4kf2i7RLsIp3fiwHQzlEOZpb1sL-KqxGqDex8Mc,76953
+qmenta/client/Project.py,sha256=-Smnh6NCv-N-xF07f1OtTH1VpqVEMLl7fbemwK3Aayk,77848
 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.dev1373.dist-info/METADATA,sha256=TYlTOCDsSr_eH8mjJ8RQ_F91JQQYmlLHVCMbZDkn0r4,672
-qmenta_client-1.1.dev1373.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-qmenta_client-1.1.dev1373.dist-info/RECORD,,
+qmenta_client-1.1.dev1382.dist-info/METADATA,sha256=E0qXlYKpgxu_Uh-1tuvWKs_FHUrbn6Kcy9YqXyCN82Y,672
+qmenta_client-1.1.dev1382.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+qmenta_client-1.1.dev1382.dist-info/RECORD,,