replace rda with gdex as needed

README.md

@@ -13,21 +13,21 @@ The package provides two categories of programs:
 |---------|-------|-------------|
 | `bashqsub` | | Submit a job as a bash batch job on a PBS node via qsub |
 | `tcshqsub` | | Submit a job as a tcsh batch job on a PBS node via qsub |
-| `rdasub` | `gdexsub` | Submit a command as a nohup background process on the local machine |
+| `gdexsub` | `rdasub` | Submit a command as a nohup background process on the local machine |
 | `pgwget` | | Download remote files by root name pattern, combining downloaded parts into a single file |
 | `gdexls` | | List local files and directories with matching metadata from the GDEX database |
-| `rdaps` | `gdexps` | Show process status for local or PBS batch processes, with filtering by PID, owner, or name |
-| `rdazip` | `gdexzip` | Compress or uncompress files using a supported format |
-| `rdaown` | `gdexown` | Change ownership of files and directories to rdadata (must be run as root) |
+| `gdexps` | `rdaps` | Show process status for local or PBS batch processes, with filtering by PID, owner, or name |
+| `gdexzip` | `rdazip` | Compress or uncompress files using a supported format |
+| `gdexown` | `rdaown` | Change ownership of files and directories to gdexdata (must be run as root) |
 | `pgrst` | | Convert .usg files to RST and push to gdex-docs-* repos on GitHub for readthedocs.io |
 
 **Run as gdexdata via setuid (requires setup below):**
 
 | Command | Alias | Connector script | Description |
 |---------|-------|-----------------|-------------|
-| `rdacp` | `gdexcp` | `setuid_rdacp` / `setuid_gdexcp` | Copy files and directories across local, remote, Object Store, or Globus endpoints |
-| `rdakill` | `gdexkill` | `setuid_rdakill` / `setuid_gdexkill` | Kill local processes and their children, or cancel PBS batch jobs |
-| `rdamod` | `gdexmod` | `setuid_rdamod` / `setuid_gdexmod` | Change permission modes for files and directories owned by rdadata |
+| `gdexcp` | `rdacp` | `setuid_gdexcp` / `setuid_rdacp` | Copy files and directories across local, remote, Object Store, or Globus endpoints |
+| `gdexkill` | `rdakill` | `setuid_gdexkill` / `setuid_rdakill` | Kill local processes and their children, or cancel PBS batch jobs |
+| `gdexmod` | `rdamod` | `setuid_gdexmod` / `setuid_rdamod` | Change permission modes for files and directories owned by gdexdata |
 
 ## Environment setup
 
@@ -86,7 +86,7 @@ pip install rda_python_miscs
 
 ## Setuid Setup
 
-The setuid programs (`rdacp`, `rdakill`, `rdamod` and their `gdex*` aliases)
+The setuid programs (`gdexcp`, `gdexkill`, `gdexmod` and their `rda*` aliases)
 execute as the common user `PGLOG['COMMONUSER']` (default `gdexdata`) via
 the `rda_python_setuid` mechanism, which is pulled in automatically as a
 dependency.  After `pip install` above, choose one of the wiring options

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "rda_python_miscs"
-version = "3.0.1"
+version = "3.0.2"
 authors = [
   { name="Zaihua Ji", email="zji@ucar.edu" },
 ]
@@ -35,20 +35,20 @@ pythonpath = [
 [project.scripts]
 "bashqsub" = "rda_python_miscs.bashqsub:main"
 "tcshqsub" = "rda_python_miscs.tcshqsub:main"
-"rdasub" = "rda_python_miscs.rdasub:main"
-"gdexsub" = "rda_python_miscs.rdasub:main"
+"gdexsub" = "rda_python_miscs.gdexsub:main"
+"rdasub" = "rda_python_miscs.gdexsub:main"
 "pgwget" = "rda_python_miscs.pgwget:main"
 "gdexls" = "rda_python_miscs.gdexls:main"
-"rdaps" = "rda_python_miscs.rdaps:main"
-"gdexps" = "rda_python_miscs.rdaps:main"
-"rdazip" = "rda_python_miscs.rdazip:main"
-"gdexzip" = "rda_python_miscs.rdazip:main"
-"rdaown" = "rda_python_miscs.rdaown:main"
-"gdexown" = "rda_python_miscs.rdaown:main"
-"setuid_rdacp" = "rda_python_miscs.rdacp:main"
-"setuid_gdexcp" = "rda_python_miscs.rdacp:main"
-"setuid_rdakill" = "rda_python_miscs.rdakill:main"
-"setuid_gdexkill" = "rda_python_miscs.rdakill:main"
-"setuid_rdamod" = "rda_python_miscs.rdamod:main"
-"setuid_gdexmod" = "rda_python_miscs.rdamod:main"
+"gdexps" = "rda_python_miscs.gdexps:main"
+"rdaps" = "rda_python_miscs.gdexps:main"
+"gdexzip" = "rda_python_miscs.gdexzip:main"
+"rdazip" = "rda_python_miscs.gdexzip:main"
+"gdexown" = "rda_python_miscs.gdexown:main"
+"rdaown" = "rda_python_miscs.gdexown:main"
+"setuid_gdexcp" = "rda_python_miscs.gdexcp:main"
+"setuid_rdacp" = "rda_python_miscs.gdexcp:main"
+"setuid_gdexkill" = "rda_python_miscs.gdexkill:main"
+"setuid_rdakill" = "rda_python_miscs.gdexkill:main"
+"setuid_gdexmod" = "rda_python_miscs.gdexmod:main"
+"setuid_rdamod" = "rda_python_miscs.gdexmod:main"
 "pgrst" = "rda_python_miscs.pg_rst:main"

src/rda_python_miscs/rdacp.py → src/rda_python_miscs/gdexcp.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env python3
 ##################################################################################
-#     Title: rdacp
+#     Title: gdexcp
 #    Author: Zaihua Ji, zji@ucar.edu
 #      Date: 10/24/2020
 #            2025-03-10 transferred to package rda_python_miscs from
 #            https://github.com/NCAR/rda-utility-programs.git
-#   Purpose: copy files locally and remotely by 'rdadata'
+#   Purpose: copy files locally and remotely by 'gdexdata'
 #    Github: https://github.com/NCAR/rda-python-miscs.git
 ##################################################################################
 import re
@@ -14,16 +14,16 @@
 from os import path as op
 from rda_python_common.pg_file import PgFile
 
-class RdaCp(PgFile):
-   """Copy files and directories locally or between remote hosts via 'rdadata'.
+class GdexCp(PgFile):
+   """Copy files and directories locally or between remote hosts via 'gdexdata'.
 
    Supports local-to-local, local-to-remote, remote-to-local, and Object Store /
-   Globus transfers.  Target files are owned by 'rdadata' and created with
+   Globus transfers.  Target files are owned by 'gdexdata' and created with
    configurable permission modes.  Recursive copying is controlled by -r / -R.
    """
 
    def __init__(self):
-      """Initialize RdaCp with default copy options and runtime state."""
+      """Initialize GdexCp with default copy options and runtime state."""
       super().__init__()
       self.RDACP = {
          'fh': None,   # from host name, default to localhost
@@ -64,8 +64,8 @@ def read_parameters(self):
       argv = sys.argv[1:]
       self.set_suid(self.PGLOG['EUID'])
       self.set_help_path(__file__)
-      self.PGLOG['LOGFILE'] = "rdacp.log"   # set different log file
-      self.cmdlog("rdacp {} ({})".format(' '.join(argv), self.CINFO['curdir']))
+      self.PGLOG['LOGFILE'] = "gdexcp.log"   # set different log file
+      self.cmdlog("gdexcp {} ({})".format(' '.join(argv), self.CINFO['curdir']))
       defopt = option = 'f'
       for arg in argv:
          if re.match(r'-(h|-help)$', arg, re.I):
@@ -95,7 +95,7 @@ def read_parameters(self):
                elif option == 'fh':
                   self.CINFO['fhost'] = arg + '-'
             option = defopt
-      if dohelp or not self.RDACP['f']: self.show_usage("rdacp")
+      if dohelp or not self.RDACP['f']: self.show_usage("gdexcp")
 
    # function to start actions
    def start_actions(self):
@@ -106,7 +106,7 @@ def start_actions(self):
       when specified, then calls copy_top_list.  Logs a summary count on completion.
       """
       self.dssdb_dbname()
-      self.validate_decs_group('rdacp', self.PGLOG['CURUID'], 1)
+      self.validate_decs_group('gdexcp', self.PGLOG['CURUID'], 1)
       if not self.RDACP['R'] and self.RDACP['r']: self.RDACP['R'] = 1000
       if not self.RDACP['t']:
          self.CINFO['tpath'] = self.RDACP['t'] = "."
@@ -232,10 +232,10 @@ def copy_file(self, fromfile, isfile):
 
 # main function to execute this script
 def main():
-   """Entry point: instantiate RdaCp, parse arguments, run, and exit."""
+   """Entry point: instantiate GdexCp, parse arguments, run, and exit."""
    from rda_python_setuid.setup_guide import show_setup_guide
-   object = RdaCp()
-   show_setup_guide(object, 'rda_python_miscs', ['rdacp', 'rdakill', 'rdamod'])
+   object = GdexCp()
+   show_setup_guide(object, 'rda_python_miscs', ['gdexcp', 'gdexkill', 'gdexmod'])
    object.read_parameters()
    object.start_actions()
    object.pgexit(0)

src/rda_python_miscs/rdacp.usg → src/rda_python_miscs/gdexcp.usg

@@ -1,10 +1,10 @@
 
  Copy files and directories to a target location.  Source and target may each
  reside on the local host, a remote host, an Object Store bucket, or a Globus
- endpoint.  Target files are owned by 'rdadata' and created with configurable
+ endpoint.  Target files are owned by 'gdexdata' and created with configurable
  permission modes.
 
- Usage: rdacp [-f] FromDirectories/Files [-t ToDirectory/FileName]   \
+ Usage: gdexcp [-f] FromDirectories/Files [-t ToDirectory/FileName]   \
               [-fh FromHostName] [-th ToHostName]                     \
               [-fb FromBucket] [-tb ToBucket]                         \
               [-fp FromGlobusEndpoint] [-tp ToGlobusEndpoint]         \
@@ -14,7 +14,7 @@
           default option, so paths may be given without the -f flag.
           Shell wildcards are supported.  Use './' or '*' to copy everything
           in the current directory.  Source paths must be readable by user
-          'rdadata'; rdacp will attempt to fix the mode if they are not;
+          'gdexdata'; gdexcp will attempt to fix the mode if they are not;
 
       - Option -t, target directory or file name.  Defaults to '.' (current
           directory).  Multiple source files cannot be copied to a single
@@ -57,21 +57,21 @@
     1. Copy all files and subdirectories under the current directory to a
        remote host:
 
-          rdacp -r -f * -t /PathTo/d277006/ -th castle
+          gdexcp -r -f * -t /PathTo/d277006/ -th castle
 
     2. Copy the contents of a specific local directory to a remote location
        (trailing '/' on source omits the directory entry itself):
 
-          rdacp -r -f /PathTo/DirectoryName/ -t /PathTo/d277006/ -th castle
+          gdexcp -r -f /PathTo/DirectoryName/ -t /PathTo/d277006/ -th castle
 
        Without the trailing '/', DirectoryName itself is also copied:
 
-          rdacp -r -f /PathTo/DirectoryName -t /PathTo/d277006/ -th castle
+          gdexcp -r -f /PathTo/DirectoryName -t /PathTo/d277006/ -th castle
 
     3. Copy a single file to an Object Store bucket:
 
-          rdacp -f /PathTo/myfile.nc -tb my-bucket -t myfile.nc
+          gdexcp -f /PathTo/myfile.nc -tb my-bucket -t myfile.nc
 
     4. Copy files from a remote host to the local current directory:
 
-          rdacp -fh castle -f /PathTo/d277006/myfile.nc
+          gdexcp -fh castle -f /PathTo/d277006/myfile.nc

src/rda_python_miscs/rdakill.py → src/rda_python_miscs/gdexkill.py

@@ -1,20 +1,20 @@
 #!/usr/bin/env python3
 ##################################################################################
-#     Title: rdakill
+#     Title: gdexkill
 #    Author: Zaihua Ji, zji@ucar.edu
 #      Date: 10/24/2020
 #            2025-03-10 transferred to package rda_python_miscs from
 #            https://github.com/NCAR/rda-utility-programs.git
 #   Purpose: kill a local or batch process and its child processes for a given
-#            running process ID by 'rdadata'
+#            running process ID by 'gdexdata'
 #    Github: https://github.com/NCAR/rda-python-miscs.git
 ##################################################################################
 import re
 import sys
 import time
 from rda_python_common.pg_file import PgFile
 
-class RdaKill(PgFile):
+class GdexKill(PgFile):
    """Kill local processes or PBS batch jobs by process ID, parent PID, or status.
 
    For local processes, sends SIGKILL (-9) to the matched process and all its
@@ -24,7 +24,7 @@ class RdaKill(PgFile):
    """
 
    def __init__(self):
-      """Initialize RdaKill with default kill options."""
+      """Initialize GdexKill with default kill options."""
       super().__init__()
       self.RDAKILL = {
          'a': None,    # application name
@@ -52,8 +52,8 @@ def read_parameters(self):
       self.dssdb_dbname()
       self.set_suid(self.PGLOG['EUID'])
       self.set_help_path(__file__)
-      self.PGLOG['LOGFILE'] = "rdakill.log"   # set different log file
-      self.cmdlog("rdakill {}".format(' '.join(argv)))
+      self.PGLOG['LOGFILE'] = "gdexkill.log"   # set different log file
+      self.cmdlog("gdexkill {}".format(' '.join(argv)))
       for arg in argv:
          ms = re.match(r'-([ahpPqsu])$', arg)
          if ms:
@@ -79,7 +79,7 @@ def read_parameters(self):
                optcnt += 1
             else:
                self.pglog(arg + ": pass in value without Option", self.LGEREX)
-      if not optcnt: self.show_usage("rdakill")
+      if not optcnt: self.show_usage("gdexkill")
 
    # function to start actions
    def start_actions(self):
@@ -257,10 +257,10 @@ def record_dscheck_interrupt(self, pid, host):
 
 # main function to execute this script
 def main():
-   """Entry point: instantiate RdaKill, parse arguments, run, and exit."""
+   """Entry point: instantiate GdexKill, parse arguments, run, and exit."""
    from rda_python_setuid.setup_guide import show_setup_guide
-   object = RdaKill()
-   show_setup_guide(object, 'rda_python_miscs', ['rdacp', 'rdakill', 'rdamod'])
+   object = GdexKill()
+   show_setup_guide(object, 'rda_python_miscs', ['gdexcp', 'gdexkill', 'gdexmod'])
    object.read_parameters()
    object.start_actions()
    object.pgexit(0)

src/rda_python_miscs/rdakill.usg → src/rda_python_miscs/gdexkill.usg

@@ -3,7 +3,7 @@
  other filter criteria; or cancel one or more PBS batch jobs by job ID or by
  job status.  For PBS operations the -h option must specify the PBS node name.
 
- Usage: rdakill [-h HostName] [-p ProcessID] [-P ParentProcessID]  \
+ Usage: gdexkill [-h HostName] [-p ProcessID] [-P ParentProcessID]  \
                 [-s BatchStatus] [-q BatchQueue] [-r]               \
                 [-u ProcessOwner] [-a ApplicationName]
 
@@ -36,31 +36,31 @@
           Without this option all users are included;
 
   For local processes, all child processes are also terminated recursively.
-  Usage is displayed if rdakill is run without any options or arguments.
+  Usage is displayed if gdexkill is run without any options or arguments.
 
   Examples:
 
     1. Kill a local process by PID:
 
-          rdakill -p 13199
-          rdakill 13199
+          gdexkill -p 13199
+          gdexkill 13199
 
     2. Kill a local process by PID and verify it matches a specific application:
 
-          rdakill -p 13199 -a dsrqst
+          gdexkill -p 13199 -a dsrqst
 
     3. Kill all local processes (and their children) owned by a user:
 
-          rdakill -u zji -a dsrqst
+          gdexkill -u zji -a dsrqst
 
     4. Kill a PBS batch job by job ID:
 
-          rdakill -h casper-pbs -p 334323
+          gdexkill -h casper-pbs -p 334323
 
     5. Kill all running PBS batch jobs for a user in the default queue:
 
-          rdakill -h casper-pbs -s RUN -u zji
+          gdexkill -h casper-pbs -s RUN -u zji
 
     6. Kill all pending PBS batch jobs in a specific queue:
 
-          rdakill -h casper-pbs -s PEND -q gdex
+          gdexkill -h casper-pbs -s PEND -q gdex