✨ mrrc_dbupdate + 02_update_db.py: cron ready updates

.gitignore

@@ -17,3 +17,4 @@ templates.tsv
 .test.*
 *.sw[op]
 creds/
+log/

02_update_db.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+cd "$(dirname "$0")"
+mkdir -p log
+! test -r ./db.sqlite && echo "no DB file '$_'!" && exit 1
+. .venv/bin/activate
+./mrrc_dbupdate.py  >> log/update-db.log 2>&1 

mrrc_dbupdate.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python3
+"""
+Find MRRC organized study acquisitions directories newer than what's in the DB
+and update them.
+"""
+import logging
+import os
+import re
+import subprocess
+from datetime import timedelta
+from glob import glob
+
+import acq2sqlite
+import dcmmeta2tsv
+
+
+def is_project(pdir: str) -> bool:
+    """
+    Is input a MR project dir?
+    should have subfolder like ``2024.06.27-09.19.11/``
+
+    :param pdir: directory to test
+    :return: True if is a project directory
+
+    #>>> is_project('/disk/mace2/scan_data/WPC-8620/')
+    #True
+    #>>> is_project('/disk/mace2/scan_data/7T/')
+    #False
+    """
+    if not os.path.isdir(pdir):
+        return False
+    for sesdir in os.listdir(pdir):
+        if re.search("^2[0-9.-]{18}$", sesdir):
+            return True
+    return False
+
+
+PathLike = str
+
+
+def find_first_dicoms(session_root: PathLike) -> list[PathLike]:
+    """
+    Find a representative dicom for each acquisition in ``session_root``.
+
+    :param session_root: path to session root directory. likely like ``.../ProjectName/yyyy.mm.dd-hh.mm.ss``
+    :return: list of first dicoms like ``sessroot/subjid/acquisitonname/MR*``
+    """
+    first_dicoms = []
+    if not os.path.isdir(session_root):
+        raise Exception(f"{session_root} is not a directory!")
+    for seqdir in glob(os.path.join(session_root, "*/*/")):
+        if not os.path.isdir(seqdir) or re.search("PhysioLog|PhoenixZIPReport", seqdir):
+            continue
+        findcmd = f"find '{seqdir}' -maxdepth 1 -type f \( -iname '*.dcm' -or -iname 'MR.*' -or -iname '*.IMA' \) -print -quit"
+        dcm = subprocess.check_output(findcmd, shell=True).decode("utf-8").strip()
+        if dcm:
+            logging.debug("found first dcm '%s'", dcm)
+            first_dicoms.append(dcm)
+        else:
+            logging.warning("no dicoms found in %s", seqdir)
+    return first_dicoms
+
+
+def update_mrrc_db(project_dir_list: list[PathLike] = None):
+    """
+    Use DB dates to find projects with new sessions. Add acquisitions.
+    Dicoms in structure like ``Project/yyyy.mm.dd-*/SessionId/AcqustionName-FOV.num/MR*``
+
+    :param project_dir_list: list of project dirs. Default is ``glob("/disk/mace2/scan_data/*")``.
+    """
+    if not project_dir_list:
+        project_dir_list = glob("/disk/mace2/scan_data/*")
+
+    db = acq2sqlite.DBQuery()
+    dtr = dcmmeta2tsv.DicomTagReader()
+    VERYRECENT = db.most_recent()
+    for pdir in project_dir_list:
+        if not is_project(pdir):
+            next
+        project = os.path.basename(pdir)
+        recent = db.most_recent("%" + project)
+
+        #: if no data from any other pass, use the most recent DB pass as time to check
+        #: this will be a problem if this script isn't used to update and a existing folder is updated in between runs
+        if not recent or recent == "None":
+            recent = VERYRECENT
+
+        #: sequence time is older than folder copy to gyrus time
+        #: reset time to midnight and go one day ahead
+        nextday = recent.date() + timedelta(days=1)
+        newer = f"-newermt '{nextday}'"
+
+        # use external find command to list all the directories newer than our cutoff
+        cmd = f"find '{pdir}' -maxdepth 1 -mindepth 1 {newer} -type d -print0"
+        res = subprocess.check_output(cmd, shell=True)
+        newsessions = res.decode("utf-8").split("\0")[0:-1]
+        logging.info(
+            f"project:'{project}'; res='{recent}'; search for {newer}: {len(newsessions)}"
+        )
+
+        for ses in newsessions:
+            acq_dicoms = find_first_dicoms(ses)
+            logging.info("ses '%s' has %d dicoms found", ses, len(acq_dicoms))
+            for acq in acq_dicoms:
+                logging.debug("processing first dcm from newer acq '%s'", acq)
+                if not acq or not os.path.isfile(acq):
+                    logging.warning("%s bad acq file '%s'", ses, acq)
+                    continue
+                all_tags = dtr.read_dicom_tags(acq)
+                if os.environ.get("DRYRUN"):
+                    logging.info(all_tags)
+                else:
+                    db.dict_to_db_row(all_tags)
+
+        db.sql.commit()
+
+
+if __name__ == "__main__":
+    update_mrrc_db()

sphinx/index.rst

@@ -24,6 +24,7 @@ Code
    change_header
    template_checker
    compliance_check_html
+   mrrc_dbupdate
 
 
 Overview