qmenta-client 2.0__py3-none-any.whl → 2.1.dev1508__py3-none-any.whl

qmenta/client/Project.py

@@ -231,7 +231,7 @@ class Project:
         name="",
         input_data_type="qmenta_medical_image_data:3.10",
         add_to_container_id=0,
-        chunk_size=2 ** 9,
+        chunk_size=2**9,
         split_data=False,
     ):
         """
@@ -262,14 +262,14 @@ class Project:
             a power of 2: 2**x. Default value of x is 9 (chunk_size = 512 kB)
         split_data : bool
             If True, the platform will try to split the uploaded file into
-            different sessions. It will be ignored when the ssid is given.
+            different sessions. It will be ignored when the ssid or a
+            add_to_container_id are given.
 
         Returns
         -------
         bool
             True if correctly uploaded, False otherwise.
         """
-
         filename = os.path.split(file_path)[1]
         input_data_type = "offline_analysis:1.0" if result else input_data_type
 
@@ -280,6 +280,8 @@ class Project:
 
         total_bytes = os.path.getsize(file_path)
 
+        split_data = self.__assert_split_data(split_data, ssid, add_to_container_id)
+
         # making chunks of the file and sending one by one
         logger = logging.getLogger(logger_name)
         with open(file_path, "rb") as file_object:
@@ -296,10 +298,6 @@ class Project:
             response = None
             last_chunk = False
 
-            if ssid and split_data:
-                logger.warning("split-data argument will be ignored because" + " ssid has been specified")
-                split_data = False
-
             while True:
                 data = file_object.read(chunk_size)
                 if not data:
@@ -374,11 +372,33 @@ class Project:
             logger.error(error)
             return False
 
-        message = "Your data was successfully uploaded."
-        message += "The uploaded file will be soon processed !"
+        message = "Your data was successfully uploaded. The uploaded file will be soon processed !"
         logger.info(message)
         return True
 
+    def delete_file(self, container_id, filenames):
+        """
+        Delete a file or files from a container.
+        Can be an input or an output container
+
+        Parameters
+        ----------
+        container_id : int
+        filenames : str or list of str
+
+        """
+        if not isinstance(filenames, str):
+            if isinstance(filenames, list):
+                if not all([isinstance(f, str) for f in filenames]):
+                    raise TypeError("Elements of `filenames` must be str")
+                filenames = ";".join(filenames)
+            else:
+                raise TypeError("`filenames` must be str or list of str")
+
+        platform.post(
+            self._account.auth, "file_manager/delete_files", data={"container_id": container_id, "files": filenames}
+        )
+
     def upload_mri(self, file_path, subject_name):
         """
         Upload new MRI data to the subject.
@@ -477,7 +497,7 @@ class Project:
             self._account.auth, "file_manager/download_file", data=params, stream=True
         ) as response, open(local_filename, "wb") as f:
 
-            for chunk in response.iter_content(chunk_size=2 ** 9 * 1024):
+            for chunk in response.iter_content(chunk_size=2**9 * 1024):
                 f.write(chunk)
             f.flush()
 
@@ -523,7 +543,7 @@ class Project:
             self._account.auth, "file_manager/download_file", data=params, stream=True
         ) as response, open(zip_name, "wb") as f:
 
-            for chunk in response.iter_content(chunk_size=2 ** 9 * 1024):
+            for chunk in response.iter_content(chunk_size=2**9 * 1024):
                 f.write(chunk)
             f.flush()
 
@@ -2045,7 +2065,7 @@ class Project:
         """
         Parse QC (Quality Control) text output into a structured dictionary format.
 
-        This function takes raw QC text output (typically from medical imaging quality checks)
+        This function takes raw QC text output (from the Protocol Adherence analysis)
         and parses it into a structured format that separates passed and failed rules,
         along with their associated files and conditions.
 
@@ -2104,18 +2124,15 @@ class Project:
 
         _, text = self.get_qc_status_subject(patient_id=patient_id, subject_name=subject_name, ssid=ssid)
 
-        result = {
-            "passed": [],
-            "failed": []
-        }
+        result = {"passed": [], "failed": []}
 
         # Split into failed and passed sections
-        sections = re.split(r'={10,}\n\n', text)
+        sections = re.split(r"={10,}\n\n", text)
         if len(sections) == 3:
-            failed_section = sections[1].split('=' * 10)[0].strip()
+            failed_section = sections[1].split("=" * 10)[0].strip()
             passed_section = sections[2].strip()
         else:
-            section = sections[1].split('=' * 10)[0].strip()
+            section = sections[1].split("=" * 10)[0].strip()
             if "PASSED QC MESSAGES" in section:
                 passed_section = section
                 failed_section = ""
@@ -2123,85 +2140,13 @@ class Project:
                 failed_section = section
                 passed_section = ""
 
-                # Parse failed rules
-        failed_rules = re.split(r'\n ❌ ', failed_section)
-        for rule_text in failed_rules[1:]:  # Skip first empty part
-            rule_name = rule_text.split(' ❌')[0].strip()
-            rule_data = {
-                "rule": rule_name,
-                "files": [],
-                "failed_conditions": {}
-            }
-
-            # Extract all file comparisons for this rule
-            file_comparisons = re.split(r'\t- Comparison with file:', rule_text)
-            for comp in file_comparisons[1:]:  # Skip first part
-                file_name = comp.split('\n')[0].strip()
-                conditions_match = re.search(
-                    r'Conditions:(.*?)(?=\n\t- Comparison|\n\n|$)',
-                    comp,
-                    re.DOTALL
-                )
-                if not conditions_match:
-                    continue
-
-                conditions_text = conditions_match.group(1).strip()
-                # Parse conditions
-                conditions = []
-                for line in conditions_text.split('\n'):
-                    line = line.strip()
-                    if line.startswith('·'):
-                        status = '✔' if '✔' in line else '🚫'
-                        condition = re.sub(r'^· [✔🚫]\s*', '', line)
-                        conditions.append({
-                            "status": "passed" if status == '✔' else "failed",
-                            "condition": condition
-                        })
-
-                # Add to failed conditions summary
-                for cond in conditions:
-                    if cond['status'] == 'failed':
-                        cond_text = cond['condition']
-                        if cond_text not in rule_data['failed_conditions']:
-                            rule_data['failed_conditions'][cond_text] = 0
-                        rule_data['failed_conditions'][cond_text] += 1
-
-                rule_data['files'].append({
-                    "file": file_name,
-                    "conditions": conditions
-                })
-
-            result['failed'].append(rule_data)
+        # Parse failed rules
+        failed_rules = re.split(r"\n ❌ ", failed_section)
+        result = self.__parse_fail_rules(failed_rules, result)
 
         # Parse passed rules
-        passed_rules = re.split(r'\n ✅ ', passed_section)
-        for rule_text in passed_rules[1:]:  # Skip first empty part
-            rule_name = rule_text.split(' ✅')[0].strip()
-            rule_data = {
-                "rule": rule_name,
-                "sub_rule": None,
-                "files": []
-            }
-
-            # Get sub-rule
-            sub_rule_match = re.search(r'Sub-rule: (.*?)\n', rule_text)
-            if sub_rule_match:
-                rule_data['sub_rule'] = sub_rule_match.group(1).strip()
-
-            # Get files passed
-            files_passed = re.search(r'List of files passed:(.*?)(?=\n\n|\Z)', rule_text, re.DOTALL)
-            if files_passed:
-                for line in files_passed.group(1).split('\n'):
-                    line = line.strip()
-                    if line.startswith('·'):
-                        file_match = re.match(r'· (.*?) \((\d+)/(\d+)\)', line)
-                        if file_match:
-                            rule_data['files'].append({
-                                "file": file_match.group(1).strip(),
-                                "passed_conditions": int(file_match.group(2)),
-                            })
-
-            result['passed'].append(rule_data)
+        passed_rules = re.split(r"\n ✅ ", passed_section)
+        result = self.__parse_pass_rules(passed_rules, result)
 
         return result
 
@@ -2272,19 +2217,15 @@ class Project:
 
         # Initialize statistics
         stats = {
-            'passed_rules': 0,
-            'failed_rules': 0,
+            "passed_rules": 0,
+            "failed_rules": 0,
             "subjects_passed": 0,
             "subjects_with_failed": 0,
-            'num_passed_files_distribution': defaultdict(int),  # How many rules have N passed files
-            'file_stats': {
-                'total': 0,
-                'passed': 0,
-                'failed': 0,
-                'pass_percentage': 0.0
-            },
-            'condition_failure_rates': defaultdict(lambda: {'count': 0, 'percentage': 0.0}),
-            'rule_success_rates': defaultdict(lambda: {'passed': 0, 'failed': 0, 'success_rate': 0.0}),
+            "num_passed_files_distribution": defaultdict(int),
+            # How many rules have N passed files
+            "file_stats": {"total": 0, "passed": 0, "failed": 0, "pass_percentage": 0.0},
+            "condition_failure_rates": defaultdict(lambda: {"count": 0, "percentage": 0.0}),
+            "rule_success_rates": defaultdict(lambda: {"passed": 0, "failed": 0, "success_rate": 0.0}),
         }
 
         total_failures = 0
@@ -2294,56 +2235,56 @@ class Project:
         # sum subjects with some failed qc message
         stats["subjects_with_failed"] = sum([1 for rules in qc_results_list if rules["failed"]])
         # sum rules that have passed
-        stats["passed_rules"] = sum([len(rules['passed']) for rules in qc_results_list if rules["failed"]])
+        stats["passed_rules"] = sum([len(rules["passed"]) for rules in qc_results_list if rules["failed"]])
         # sum rules that have failed
-        stats["failed_rules"] = sum([len(rules['failed']) for rules in qc_results_list if rules["failed"]])
+        stats["failed_rules"] = sum([len(rules["failed"]) for rules in qc_results_list if rules["failed"]])
 
         for qc_results in qc_results_list:
 
             # Count passed files distribution
-            for rule in qc_results['passed']:
-                num_files = len(rule['files'])
-                stats['num_passed_files_distribution'][num_files] += 1
-                stats['file_stats']['passed'] += len(rule['files'])
-                stats['file_stats']['total'] += len(rule['files'])
-                rule_name = rule['rule']
-                stats['rule_success_rates'][rule_name]['passed'] += 1
-
-            for rule in qc_results['failed']:
-                stats['file_stats']['total'] += len(rule['files'])
-                stats['file_stats']['failed'] += len(rule['files'])
-                for condition, count in rule['failed_conditions'].items():
+            for rule in qc_results["passed"]:
+                num_files = len(rule["files"])
+                stats["num_passed_files_distribution"][num_files] += 1
+                stats["file_stats"]["passed"] += len(rule["files"])
+                stats["file_stats"]["total"] += len(rule["files"])
+                rule_name = rule["rule"]
+                stats["rule_success_rates"][rule_name]["passed"] += 1
+
+            for rule in qc_results["failed"]:
+                stats["file_stats"]["total"] += len(rule["files"])
+                stats["file_stats"]["failed"] += len(rule["files"])
+                for condition, count in rule["failed_conditions"].items():
                     # Extract just the condition text without actual value
-                    clean_condition = re.sub(r'\.\s*Actual value:.*$', '', condition)
-                    stats['condition_failure_rates'][clean_condition]['count'] += count
+                    clean_condition = re.sub(r"\.\s*Actual value:.*$", "", condition)
+                    stats["condition_failure_rates"][clean_condition]["count"] += count
                     total_failures += count
-                rule_name = rule['rule']
-                stats['rule_success_rates'][rule_name]['failed'] += 1
+                rule_name = rule["rule"]
+                stats["rule_success_rates"][rule_name]["failed"] += 1
 
-        if stats['file_stats']['total'] > 0:
-            stats['file_stats']['pass_percentage'] = round(
-                (stats['file_stats']['passed'] / stats['file_stats']['total']) * 100, 2
+        if stats["file_stats"]["total"] > 0:
+            stats["file_stats"]["pass_percentage"] = round(
+                (stats["file_stats"]["passed"] / stats["file_stats"]["total"]) * 100, 2
             )
 
         # Calculate condition failure percentages
-        for condition in stats['condition_failure_rates']:
+        for condition in stats["condition_failure_rates"]:
             if total_failures > 0:
-                stats['condition_failure_rates'][condition]['percentage'] = round(
-                    (stats['condition_failure_rates'][condition]['count'] / total_failures) * 100, 2
+                stats["condition_failure_rates"][condition]["percentage"] = round(
+                    (stats["condition_failure_rates"][condition]["count"] / total_failures) * 100, 2
                 )
 
         # Calculate rule success rates
-        for rule in stats['rule_success_rates']:
-            total = stats['rule_success_rates'][rule]['passed'] + stats['rule_success_rates'][rule]['failed']
+        for rule in stats["rule_success_rates"]:
+            total = stats["rule_success_rates"][rule]["passed"] + stats["rule_success_rates"][rule]["failed"]
             if total > 0:
-                stats['rule_success_rates'][rule]['success_rate'] = round(
-                    (stats['rule_success_rates'][rule]['passed'] / total) * 100, 2
+                stats["rule_success_rates"][rule]["success_rate"] = round(
+                    (stats["rule_success_rates"][rule]["passed"] / total) * 100, 2
                 )
 
         # Convert defaultdict to regular dict for cleaner JSON output
-        stats['num_passed_files_distribution'] = dict(stats['num_passed_files_distribution'])
-        stats['condition_failure_rates'] = dict(stats['condition_failure_rates'])
-        stats['rule_success_rates'] = dict(stats['rule_success_rates'])
+        stats["num_passed_files_distribution"] = dict(stats["num_passed_files_distribution"])
+        stats["condition_failure_rates"] = dict(stats["condition_failure_rates"])
+        stats["rule_success_rates"] = dict(stats["rule_success_rates"])
 
         return stats
 
@@ -2673,3 +2614,107 @@ class Project:
                     value.replace(d_type + ";", "")
                     file_metadata[d_tag] = {"operation": "in-list", "value": value.replace(d_type + ";", "").split(";")}
         return modality, tags, file_metadata
+
+    def __assert_split_data(self, split_data, ssid, add_to_container_id):
+        """
+        Assert if the split_data parameter is possible to use in regards
+        to the ssid and add_to_container_id parameters during upload.
+        Changes its status to False if needed.
+
+        Parameters
+        ----------
+        split_data : Bool
+            split_data parameter from method 'upload_file'.
+        ssid : str
+            Session ID.
+        add_to_container_id : int or bool
+            Container ID or False
+
+        Returns
+        -------
+        split_data : Bool
+
+        """
+
+        logger = logging.getLogger(logger_name)
+        if ssid and split_data:
+            logger.warning("split-data argument will be ignored because ssid has been specified")
+            split_data = False
+
+        if add_to_container_id and split_data:
+            logger.warning("split-data argument will be ignored because add_to_container_id has been specified")
+            split_data = False
+
+        return split_data
+
+    def __parse_fail_rules(self, failed_rules, result):
+        """
+        Parse fail rules.
+        """
+
+        for rule_text in failed_rules[1:]:  # Skip first empty part
+            rule_name = rule_text.split(" ❌")[0].strip()
+            rule_data = {"rule": rule_name, "files": [], "failed_conditions": {}}
+
+            # Extract all file comparisons for this rule
+            file_comparisons = re.split(r"\t- Comparison with file:", rule_text)
+            for comp in file_comparisons[1:]:  # Skip first part
+                file_name = comp.split("\n")[0].strip()
+                conditions_match = re.search(r"Conditions:(.*?)(?=\n\t- Comparison|\n\n|$)", comp, re.DOTALL)
+                if not conditions_match:
+                    continue
+
+                conditions_text = conditions_match.group(1).strip()
+                # Parse conditions
+                conditions = []
+                for line in conditions_text.split("\n"):
+                    line = line.strip()
+                    if line.startswith("·"):
+                        status = "✔" if "✔" in line else "🚫"
+                        condition = re.sub(r"^· [✔🚫]\s*", "", line)
+                        conditions.append({"status": "passed" if status == "✔" else "failed", "condition": condition})
+
+                # Add to failed conditions summary
+                for cond in conditions:
+                    if cond["status"] == "failed":
+                        cond_text = cond["condition"]
+                        if cond_text not in rule_data["failed_conditions"]:
+                            rule_data["failed_conditions"][cond_text] = 0
+                        rule_data["failed_conditions"][cond_text] += 1
+
+                rule_data["files"].append({"file": file_name, "conditions": conditions})
+
+            result["failed"].append(rule_data)
+        return result
+
+    def __parse_pass_rules(self, passed_rules, result):
+        """
+        Parse pass rules.
+        """
+
+        for rule_text in passed_rules[1:]:  # Skip first empty part
+            rule_name = rule_text.split(" ✅")[0].strip()
+            rule_data = {"rule": rule_name, "sub_rule": None, "files": []}
+
+            # Get sub-rule
+            sub_rule_match = re.search(r"Sub-rule: (.*?)\n", rule_text)
+            if sub_rule_match:
+                rule_data["sub_rule"] = sub_rule_match.group(1).strip()
+
+            # Get files passed
+            files_passed = re.search(r"List of files passed:(.*?)(?=\n\n|\Z)", rule_text, re.DOTALL)
+            if files_passed:
+                for line in files_passed.group(1).split("\n"):
+                    line = line.strip()
+                    if line.startswith("·"):
+                        file_match = re.match(r"· (.*?) \((\d+)/(\d+)\)", line)
+                        if file_match:
+                            rule_data["files"].append(
+                                {
+                                    "file": file_match.group(1).strip(),
+                                    "passed_conditions": int(file_match.group(2)),
+                                }
+                            )
+
+            result["passed"].append(rule_data)
+        return result

{qmenta_client-2.0.dist-info → qmenta_client-2.1.dev1508.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: qmenta-client
-Version: 2.0
+Version: 2.1.dev1508
 Summary: Python client lib to interact with the QMENTA platform.
 Author: QMENTA
 Author-email: dev@qmenta.com

{qmenta_client-2.0.dist-info → qmenta_client-2.1.dev1508.dist-info}/RECORD

@@ -1,10 +1,10 @@
 qmenta/__init__.py,sha256=ED6jHcYiuYpr_0vjGz0zx2lrrmJT9sDJCzIljoDfmlM,65
 qmenta/client/Account.py,sha256=7BOWHtRbHdfpBYQqv9v2m2Fag13pExZSxFsjDA7UsW0,9500
 qmenta/client/File.py,sha256=iCrzrd7rIfjjW2AgMgUoK-ZF2wf-95wCcPKxKw6PGyg,4816
-qmenta/client/Project.py,sha256=vx1GabCiVG7gYqnkNmqhqRyzy7ml7eT4jjnUciBq_Gw,99565
+qmenta/client/Project.py,sha256=TP_CHoyKQsqlQ7AALnjx2kwcgQ-5os26lJGH5XW--5E,101305
 qmenta/client/Subject.py,sha256=b5sg9UFtn11bmPM-xFXP8aehOm_HGxnhgT7IPKbrZnE,8688
 qmenta/client/__init__.py,sha256=Mtqe4zf8n3wuwMXSALENQgp5atQY5VcsyXWs2hjBs28,133
 qmenta/client/utils.py,sha256=vWUAW0r9yDetdlwNo86sdzKn03FNGvwa7D9UtOA3TEc,2419
-qmenta_client-2.0.dist-info/METADATA,sha256=niv_y8-oKl7puOvmGkjnci_11YuMgUN7Qv2iO8umNOI,664
-qmenta_client-2.0.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-qmenta_client-2.0.dist-info/RECORD,,
+qmenta_client-2.1.dev1508.dist-info/METADATA,sha256=zV7x_6f673FhaUoFQ8f_5f42D4VGxojIx0mCwuQP8cg,672
+qmenta_client-2.1.dev1508.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+qmenta_client-2.1.dev1508.dist-info/RECORD,,