pylantir 0.0.8__tar.gz → 0.1.0__tar.gz

{pylantir-0.0.8 → pylantir-0.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylantir
-Version: 0.0.8
+Version: 0.1.0
 Summary: Python - DICOM Modality WorkList
 Author-email: Milton Camacho <miltoncamachoicc@gmail.com>
 Requires-Python: >=3.11.1
@@ -31,7 +31,7 @@ Requires-Dist: flake8-formatter_junit_xml ; extra == "test"
 Requires-Dist: flake8 ; extra == "test"
 Requires-Dist: flake8-pyproject ; extra == "test"
 Requires-Dist: pre-commit==3.3.1 ; extra == "test"
-Requires-Dist: pylint==2.17.4 ; extra == "test"
+Requires-Dist: pylint==3.3.6 ; extra == "test"
 Requires-Dist: pylint_junit ; extra == "test"
 Requires-Dist: pytest-cov==4.0.0 ; extra == "test"
 Requires-Dist: pytest-mock<3.10.1 ; extra == "test"
@@ -82,12 +82,19 @@ pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config
 
 ## Tests
 
-Once your modality worklist server is running you can test it running the following:
+If you want to run the tests make sure to clone the repository and run them from there.
+
+Git clone the repository:
+
+```bash
+git clone https://github.com/miltoncamacho/pylantir
+cd pylantir/tests
+```
 
 Query the worklist database to check that you have some entries using:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 Then, you can get a StudyUID from one of the entries to test the MPPS workflow. For example: 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
@@ -95,19 +102,19 @@ Then, you can get a StudyUID from one of the entries to test the MPPS workflow.
 Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
 
 ```bash
-pylantir test-mpps --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
+python test-mpps.py --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
 ```
 
 You can verify that this in fact modified your database re-running:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
 
 ```bash
-pylantir test-mpps --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
+python test-mpps.py --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
 ```
 
 ## Usage
@@ -137,6 +144,8 @@ usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_con
   - **site**: Site ID:string
   - **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
   - **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
+  - **db_update_interval**: How often to reload the database e
+  - **operation_interval**: What is the time range in a day in which the database will be updated e.g., `{"start_time":[hours,minutes],"end_time":[hours,minutes]}`
 - **--mpps_action {create,set}**: Action to perform for MPPS either create or set
 - **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
 - **--callingAEtitle CALLINGAETITLE**: Calling AE Title for MPPS, it helps when the MWL is limited to only accept certain AE titles
@@ -152,6 +161,7 @@ As a default pylantir will try to read a JSON structured file with the following
   "db_path": "/path/to/worklist.db",
   "db_echo": "False",
   "db_update_interval": 60,
+  "operation_interval": {"start_time": [0,0],"end_time": [23,59]},
   "allowed_aet": [],
   "site": "792",
   "redcap2wl": {

{pylantir-0.0.8 → pylantir-0.1.0}/README.md

@@ -35,12 +35,19 @@ pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config
 
 ## Tests
 
-Once your modality worklist server is running you can test it running the following:
+If you want to run the tests make sure to clone the repository and run them from there.
+
+Git clone the repository:
+
+```bash
+git clone https://github.com/miltoncamacho/pylantir
+cd pylantir/tests
+```
 
 Query the worklist database to check that you have some entries using:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 Then, you can get a StudyUID from one of the entries to test the MPPS workflow. For example: 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
@@ -48,19 +55,19 @@ Then, you can get a StudyUID from one of the entries to test the MPPS workflow.
 Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
 
 ```bash
-pylantir test-mpps --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
+python test-mpps.py --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
 ```
 
 You can verify that this in fact modified your database re-running:
 
 ```bash
-pylantir query-db
+python query-db.py
 ```
 
 Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
 
 ```bash
-pylantir test-mpps --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
+python test-mpps.py --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
 ```
 
 ## Usage
@@ -90,6 +97,8 @@ usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_con
   - **site**: Site ID:string
   - **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
   - **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
+  - **db_update_interval**: How often to reload the database e
+  - **operation_interval**: What is the time range in a day in which the database will be updated e.g., `{"start_time":[hours,minutes],"end_time":[hours,minutes]}`
 - **--mpps_action {create,set}**: Action to perform for MPPS either create or set
 - **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
 - **--callingAEtitle CALLINGAETITLE**: Calling AE Title for MPPS, it helps when the MWL is limited to only accept certain AE titles
@@ -105,6 +114,7 @@ As a default pylantir will try to read a JSON structured file with the following
   "db_path": "/path/to/worklist.db",
   "db_echo": "False",
   "db_update_interval": 60,
+  "operation_interval": {"start_time": [0,0],"end_time": [23,59]},
   "allowed_aet": [],
   "site": "792",
   "redcap2wl": {

{pylantir-0.0.8 → pylantir-0.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name =  "pylantir"
-version = "0.0.8"
+version = "0.1.0"
 authors = [
     {name = "Milton Camacho", email = "miltoncamachoicc@gmail.com"},
 ]
@@ -50,7 +50,7 @@ test = [
     "flake8",
     "flake8-pyproject",
     "pre-commit==3.3.1",
-    "pylint==2.17.4",
+    "pylint==3.3.6",
     "pylint_junit",
     "pytest-cov==4.0.0",
     "pytest-mock<3.10.1",

{pylantir-0.0.8 → pylantir-0.1.0}/src/pylantir/cli/run.py

@@ -209,6 +209,9 @@ def main() -> None:
         # Extract the database update interval (default to 60 seconds if missing)
         db_update_interval = config.get("db_update_interval", 60)
 
+        # Extract the operation interval (default from 00:00 to 23:59 hours if missing)
+        operation_interval = config.get("operation_interval", {"start_time": [0,0], "end_time": [23,59]})
+
         # Extract allowed AE Titles (default to empty list if missing)
         allowed_aet = config.get("allowed_aet", [])
 
@@ -219,7 +222,6 @@ def main() -> None:
         redcap2wl = config.get("redcap2wl", {})
 
         # EXtract protocol mapping
-
         protocol = config.get("protocol", {})
 
         # Create and update the MWL database
@@ -230,6 +232,7 @@ def main() -> None:
                 protocol=protocol,
                 redcap2wl=redcap2wl,
                 interval=db_update_interval,
+                operation_interval=operation_interval,
             )
 
                 # sync_redcap_to_db(

{pylantir-0.0.8 → pylantir-0.1.0}/src/pylantir/config/mwl_config.json

@@ -3,6 +3,16 @@
     "db_echo": "0",
     "db_update_interval": 60,
     "allowed_aet": [],
+    "operation_interval": {
+        "start_time": [
+            0,
+            0
+        ],
+        "end_time": [
+            23,
+            59
+        ]
+    },
     "mri_visit_session_mapping": {
         "t1_arm_1": "1",
         "t2_arm_1": "2",
@@ -10,7 +20,7 @@
     },
     "site": "792",
     "redcap2wl": {
-        "study_id" : "study_id",
+        "study_id": "study_id",
         "family_id": "family_id",
         "youth_dob_y": "youth_dob_y",
         "t1_date": "t1_date",
@@ -22,7 +32,7 @@
         "performing_physician": "performing_physician",
         "station_name": "station_name",
         "status": "performed_procedure_step_status"
-        },
+    },
     "protocol": {
         "792": "BRAIN_MRI_3T"
     }

{pylantir-0.0.8 → pylantir-0.1.0}/src/pylantir/models.py

@@ -37,7 +37,10 @@ class WorklistItem(Base):
     procedure_description = Column(String(200))
     protocol_name = Column(String(100))
     station_name = Column(String(100))
-    hisris_coding_designator = Column(String(100))
+    try:
+        hisris_coding_designator = Column(String(100))
+    except:
+        lgr.warning("Could not get hisris_coding_designator check models.py ")
     performed_procedure_step_status = Column(String, default="SCHEDULED")
 
 

{pylantir-0.0.8 → pylantir-0.1.0}/src/pylantir/redcap_to_db.py

@@ -8,6 +8,7 @@ from .db_setup import engine
 from .models import WorklistItem
 import time
 import threading
+from datetime import datetime, time, date, timedelta
 
 lgr = logging.getLogger(__name__)
 
@@ -22,7 +23,7 @@ Session = sessionmaker(bind=engine)
 
 
 
-def fetch_redcap_entries(redcap_fields: list) -> list:
+def fetch_redcap_entries(redcap_fields: list, interval: float) -> list:
     """Fetch REDCap entries using PyCap and return a list of filtered dicts."""
     project = Project(REDCAP_API_URL, REDCAP_API_TOKEN)
 
@@ -41,7 +42,9 @@ def fetch_redcap_entries(redcap_fields: list) -> list:
     lgr.info(f"Fetching REDCap data for fields: {redcap_fields}")
 
     # Export data
-    records = project.export_records(fields=redcap_fields, format_type="df")
+    datetime_now = datetime.now()
+    datetime_interval = datetime_now - timedelta(seconds=interval)
+    records = project.export_records(fields=redcap_fields, date_begin=datetime_interval, date_end=datetime_now, format_type="df")
 
     if records.empty:
         lgr.warning("No records retrieved from REDCap.")
@@ -102,11 +105,13 @@ def sync_redcap_to_db(
     site_id: str,
     protocol: dict,
     redcap2wl: dict,
+    interval: float = 60.0,
 ) -> None:
     """Sync REDCap patient data with the worklist database."""
 
     if not redcap2wl:
         lgr.error("No field mapping (redcap2wl) provided for syncing.")
+        return
 
     session = Session()
 
@@ -120,7 +125,7 @@ def sync_redcap_to_db(
         if i not in redcap_fields:
             redcap_fields.append(i)
 
-    redcap_entries = fetch_redcap_entries(redcap_fields)
+    redcap_entries = fetch_redcap_entries(redcap_fields, interval)
 
     for record in redcap_entries:
         study_id = record.get("study_id")
@@ -133,7 +138,8 @@ def sync_redcap_to_db(
         ses_id = record.get("mri_instance")
 
         PatientName = f"cpip-id-{study_id}^fa-{family_id}"
-        PatientID = f"sub-{study_id}_ses-{ses_id}_fam-{family_id}_site-{site_id}"
+        PatientID = f"sub_{study_id}_ses_{ses_id}_fam_{family_id}_site_{site_id}"
+        PatientID_ = f"sub-{study_id}_ses-{ses_id}_fam-{family_id}_site-{site_id}"
 
         if not PatientID:
             lgr.warning("Skipping record due to missing Study ID.")
@@ -149,8 +155,18 @@ def sync_redcap_to_db(
             .first()
         )
 
+        existing_entry_ = (
+            session.query(WorklistItem)
+            .filter_by(patient_id=PatientID_)
+            .first()
+        )
         if existing_entry:
             logging.debug(f"Updating existing worklist entry for PatientID {PatientID}")
+        elif existing_entry_:
+            logging.debug(f"Updating existing worklist entry for PatientID {PatientID_}")
+            existing_entry = existing_entry_
+
+        if existing_entry:
             existing_entry.patient_name = PatientName
             existing_entry.patient_id = PatientID
             existing_entry.patient_birth_date = record.get("youth_dob_y", "19000101")
@@ -205,38 +221,102 @@ def sync_redcap_to_db_repeatedly(
     site_id=None,
     protocol=None,
     redcap2wl=None,
-    interval=60
+    interval=60,
+    operation_interval={"start_time": [00,00], "end_time": [23,59]},
 ):
     """
-    Keep syncing with REDCap in a loop every `interval` seconds.
+    Keep syncing with REDCap in a loop every `interval` seconds,
+    but only between operation_interval[start_time] and operation_interval[end_time].
     Exit cleanly when STOP_EVENT is set.
     """
+    if operation_interval is None:
+        operation_interval = {"start_time": [0, 0], "end_time": [23, 59]}
+
+    start_h, start_m = operation_interval.get("start_time", [0, 0])
+    end_h, end_m = operation_interval.get("end_time", [23, 59])
+    start_time = time(start_h, start_m)
+    end_time = time(end_h, end_m)
+
+    # last_sync_date = datetime.now().date()
+    last_sync_date = datetime.now().date() - timedelta(days=1)
+    interval_sync = interval + 600 # add 10 minutes to the interval to overlap with the previous sync and avoid missing data
+
     while not STOP_EVENT.is_set():
-        try:
-            sync_redcap_to_db(
-                site_id=site_id,
-                protocol=protocol,
-                redcap2wl=redcap2wl,
+        # === 1) BASELINE: set defaults for flags and wait-time each iteration ===
+        is_first_run = False
+        extended_interval = interval
+
+        # === 2) FIGURE OUT "NOW" in hours/minutes (zero out seconds) ===
+        now_dt = datetime.now().replace(second=0, microsecond=0)
+        now_time = now_dt.time()
+        today_date = now_dt.date()
+
+        # === 3) ONLY SYNC IF WE'RE WITHIN [start_time, end_time] ===
+        if start_time <= now_time <= end_time:
+            # Check if we haven't synced today yet
+            is_first_run = (last_sync_date != today_date)
+
+            # If it really *is* the first sync of this new day (and it's not the very first run ever)
+            if is_first_run and (last_sync_date is not None):
+                logging.info(f"First sync of the day for site {site_id} at {now_time}.")
+                # Calculate how many seconds from "end_time of yesterday" until "start_time of today"
+                yesterday = last_sync_date
+                dt_end_yesterday = datetime.combine(yesterday, end_time)
+                dt_start_today = datetime.combine(today_date, start_time)
+                delta = dt_start_today - dt_end_yesterday
+                # guaranteed to be positive if yesterday < today
+                extended_interval = delta.total_seconds()
+                logging.info(f"Using extended interval: {extended_interval}, {interval} seconds until next sync.")
+            else:
+                # Either not first run, or last_sync_date is None (this is first-ever run)
+                logging.info("Using default interval {interval} seconds.")
+
+            # --- CALL THE SYNC FUNCTION INSIDE A TRY/EXCEPT ---
+            logging.debug(f"Syncing REDCap to DB for site {site_id} at {now_time}.")
+            logging.debug(f"First run {is_first_run}")
+            try:
+                logging.debug(f"last_sync_date was: {last_sync_date}")
+                if is_first_run and (last_sync_date is not None):
+                    sync_redcap_to_db(
+                        site_id=site_id,
+                        protocol=protocol,
+                        redcap2wl=redcap2wl,
+                        interval=extended_interval,
+                    )
+                else:
+                    sync_redcap_to_db(
+                        site_id=site_id,
+                        protocol=protocol,
+                        redcap2wl=redcap2wl,
+                        interval=interval_sync,
+                    )
+                last_sync_date = today_date
+                logging.debug(f"REDCap sync completed at {now_time}. Next sync atempt in {interval} seconds.")
+            except Exception as exc:
+                logging.error(f"Error in REDCap sync: {exc}")
+        else:
+            # We're outside of operation hours. Just log once and sleep a bit.
+            logging.debug(
+                f"Current time {now_time} is outside operation window "
+                f"({start_time}–{end_time}). Sleeping for {interval} seconds."
             )
-        except Exception as exc:
-            logging.error(f"Error in REDCap sync: {exc}")
 
-        # Wait up to `interval` seconds, or break early if STOP_EVENT is set
+        # === 4) WAIT before the next iteration. We already set extended_interval above. ===
+        logging.debug(f"Sleeping for {interval} seconds before next check...")
         STOP_EVENT.wait(interval)
 
     logging.info("Exiting sync_redcap_to_db_repeatedly because STOP_EVENT was set.")
 
 
 if __name__ == "__main__":
-    # This block is just a demo usage. In practice, you might set STOP_EVENT
-    # from a signal handler or from another part of your code.
     try:
         sync_redcap_to_db_repeatedly(
             site_id=None,
             protocol=None,
             redcap2wl=None,
-            interval=60
+            interval=60,
+            operation_interval={"start_time": [0, 0], "end_time": [23, 59]},
         )
     except KeyboardInterrupt:
         logging.info("KeyboardInterrupt received. Stopping background sync...")
-        STOP_EVENT.set()
+        STOP_EVENT.set()

pylantir-0.0.8/src/pylantir/.env

@@ -1,2 +0,0 @@
-DB_ECHO='0'
-DB_PATH='/Users/milton/Desktop/worklist.db'