Hua work common

README.md

@@ -72,7 +72,7 @@ PgLOG.pglog("hello", PgLOG.LOGWRN)
 python -c "import rda_python_common; print(rda_python_common.__version__)"
 ```
 
-You should see the installed version (currently `2.1.10`).  If the import
+You should see the installed version (currently `2.1.11`).  If the import
 fails, double-check that the active Python environment is the one where you
 ran `pip install`.
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "rda_python_common"
-version = "2.1.10"
+version = "2.1.11"
 authors = [
   { name="Zaihua Ji", email="zji@ucar.edu" },
 ]
@@ -18,8 +18,8 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
 ]
 dependencies = [
-  "hvac",
-  "psycopg2==2.9.10",
+  "psycopg2-binary",
+  "psutil",
   "rda-python-globus",
   "unidecode",
   "hvac"

requirements.txt

@@ -1,7 +1,8 @@
 iniconfig==2.1.0
 packaging==24.2
 pluggy==1.5.0
-psycopg2==2.9.10
+psycopg2-binary==2.9.10
+psutil
 pytest==8.3.5
 rda-python-globus
 unidecode

src/rda_python_common/__init__.py

@@ -22,7 +22,7 @@
 
 from . import PgLOG, PgUtil, PgDBI, PgFile, PgLock, PgCMD, PgSIG, PgOPT, PgSplit
 
-__version__ = "2.1.10"
+__version__ = "2.1.11"
 
 __all__ = [
    "PgLOG",

src/rda_python_common/pg_file.py

@@ -19,6 +19,7 @@
 import time
 import glob
 import json
+import hashlib
 from .pg_util import PgUtil
 from .pg_sig import PgSIG
 
@@ -2874,24 +2875,32 @@ def get_md5sum(self, file, count = 0, logact = 0):
                             (with None for missing files) for multiple files, or None
                             on failure.
       """
-      cmd = 'md5sum '
       if count > 0:
          checksum = [None]*count
          for i in range(count):
             if op.isfile(file[i]):
-               chksm = self.pgsystem(cmd + file[i], logact, 20)
-               if chksm:
-                  ms = re.search(r'(\w{32})', chksm)
-                  if ms: checksum[i] = ms.group(1)
+               checksum[i] = self._file_md5(file[i], logact)
       else:
          checksum = None
          if op.isfile(file):
-            chksm = self.pgsystem(cmd + file, logact, 20)
-            if chksm:
-               ms = re.search(r'(\w{32})', chksm)
-               if ms: checksum = ms.group(1)
+            checksum = self._file_md5(file, logact)
       return checksum
 
+   def _file_md5(self, path, logact=0):
+      """Compute MD5 hex digest of *path*, reading in 1 MiB chunks.
+
+      Returns the hex digest string, or None on read error.
+      """
+      try:
+         h = hashlib.md5()
+         with open(path, 'rb') as fh:
+            for chunk in iter(lambda: fh.read(1048576), b''):
+               h.update(chunk)
+         return h.hexdigest()
+      except OSError as e:
+         self.pglog("Error md5sum {}: {}".format(path, str(e)), logact)
+         return None
+
    # Evaluate md5 checksums and compare them for two given files
    #  file1, file2: file names
    # Return: 0 if same and 1 if not

src/rda_python_common/pg_log.py

@@ -18,6 +18,7 @@
 import shlex
 import smtplib
 from email.message import EmailMessage
+import subprocess
 from subprocess import Popen, PIPE
 from os import path as op
 import time
@@ -769,7 +770,7 @@ def show_usage(self, progname, opts=None):
                      nilcnt = 0
                   if begin: sys.stdout.write(line)
       else:
-         os.system("more " + usgname)
+         subprocess.run(['more', usgname])
       self.pgexit(0)
 
    def err2std(self, line):
@@ -1600,15 +1601,12 @@ def set_specialist_home(self, specialist):
          os.environ['MAIL'] = re.sub(self.PGLOG['CURUID'], specialist, os.environ['MAIL'])   
       home = "{}/{}".format(self.PGLOG['USRHOME'], specialist)
       shell = "tcsh"
-      buf = self.pgsystem("grep ^{}: /etc/passwd".format(specialist), self.LOGWRN, 20)
-      if buf:
-         lines = buf.split('\n')
-         for line in lines:
-            ms = re.search(r':(/.+):(/.+)', line)
-            if ms:
-               home = ms.group(1)
-               shell = op.basename(ms.group(2))
-               break
+      try:
+         pwent = pwd.getpwnam(specialist)
+         home = pwent.pw_dir
+         shell = op.basename(pwent.pw_shell)
+      except KeyError:
+         pass
       if home != os.environ['HOME'] and op.exists(home):
          os.environ['HOME'] = home
       return shell