Merge pull request #92 from CCBR/redirect_fix

redirect fix

CHANGELOG.md

@@ -1,6 +1,8 @@
 ## spacesavers2 development version
 
 - Move the report to a separate internal repository (#79, @kelly-sovacool)
+- new option `--json` for `spacesavers2_pdq`
+- `redirect` script now checks if running on BIOWULF or FRCE. If not, then checks for python version and "xxhash" library (fix #91, @kopardev)
 
 ### New features
 

bin/redirect

@@ -1,12 +1,6 @@
 #!/usr/bin/env bash
 
-# This is a wrapper for spook python script
-# It:
-# - loads the appropriate conda environment
-# - parses the variables directly to the python script
-# - deactivate enrivonment
-
-SCRIPTNAME="$0"
+SCRIPTNAME="$BASH_SOURCE"
 SCRIPTDIRNAME=$(readlink -f $(dirname "$SCRIPTNAME"))
 
 # add "bin" to PATH
@@ -16,11 +10,46 @@ fi
 
 TOOLDIR=$(dirname "$SCRIPTDIRNAME")
 TOOLNAME=$(basename "$SCRIPTNAME")
-# echo $TOOLNAME
 
-# load appropriate conda env
-. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311
+# find out if you are running on biowulf or frce
+nbiowulf=$(scontrol show config 2>/dev/null | grep -i -c biowulf)
+if [[ "$nbiowulf" > 0 ]];then ISBIOWULF=true; else ISBIOWULF=false;fi
+nfrce=$(scontrol show config 2>/dev/null | grep -i -c fsitgl)
+if [[ "$nfrce" > 0 ]];then ISFRCE=true; else ISFRCE=false;fi
+if [[ "$HOSTNAME" == "helix.nih.gov" ]];then ISBIOWULF=true; else ISBIOWULF=false;fi
 
-${TOOLDIR}/${TOOLNAME} "$@" || true
+# load conda
+run=1
+if [[ $ISBIOWULF == true ]];then
+       . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+	conda activate py311
+	run=0
+elif [[ $ISFRCE == true ]];then
+       . "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh"
+	conda activate py311
+	run=0
+else
+	echo "You are NOT running on BIOWULF or on FRCE"
+	version=$(python --version 2>/dev/null | awk '{print $NF}')
+	major=$(echo $version|awk -F"." '{print $1}')
+	minor=$(echo $version|awk -F"." '{print $2}')
+	if [[ "$major" -eq "3" ]]; then
+		if [[ "$minor" -ge "11" ]];then
+			echo "Satisfatory version of Python available: $version"
+			xxhashfound=$(python -c "import xxhash" 2> /dev/null; echo $?)
+			if [[ "$xxhashfound" -eq "0" ]];then
+				echo "xxhash python library present!"
+				run=0
+			fi
+		fi
+	fi
+	if [[ "$run" != "0" ]];then
+	echo "Please make sure that:"
+	echo "Python version >= 3.11 with xxhash library is required!"
+	fi
+fi
 
-conda deactivate 
+if [[ "$run" == "0" ]]; then
+	${TOOLDIR}/${TOOLNAME} "$@" || true
+	conda deactivate 2>/dev/null
+fi

docs/pdq.md

@@ -13,12 +13,13 @@ It is quick tool to gather datapoints to monitor filesystem usage. Typically, ca
 ### Inputs
  - `--folder`: Path to the folder to run `spacesavers2_pdq` on.
  - `--threads`: `spacesavers2_pdq` uses multiprocessing library to parallelize orchestration. This defines the number of threads to run in parallel.
- - `--outfile`: If not supplied then the optput is written to the screen.
+ - `--outfile`: If not supplied then the output is written to the screen.
+ - `--json`: Optional, if provided output is also written in JSON format.
 
 > NOTE: `spacesavers2_pdq` reports errors (eg. cannot read file) to STDERR
 
 ```bash
-usage: spacesavers2_pdq [-h] -f FOLDER [-p THREADS] [-o OUTFILE] [-v]
+usage: spacesavers2_pdq [-h] -f FOLDER [-p THREADS] [-o OUTFILE] [-j JSON] [-v]
 
 spacesavers2_pdq: get quick per user info (number of files and bytes).
 
@@ -29,11 +30,12 @@ options:
   -p THREADS, --threads THREADS
                         number of threads to be used (default 4)
   -o OUTFILE, --outfile OUTFILE
-                        outfile ... catalog file .. by default output is printed to screen
+                        outfile ... by default output is printed to screen
+  -j JSON, --json JSON  outfile file in JSON format.
   -v, --version         show program's version number and exit
 
 Version:
-    v0.11.5
+    v0.11.6
 Example:
     > spacesavers2_pdq -f /path/to/folder -p 4 -o /path/to/output_file
 ```
@@ -58,3 +60,24 @@ The 3 items in the line are as follows:
 | 1      | username                 | "user1" |
 | 2      | total no. of files owned     | 1386138                                                                                          |
 | 3      | total no. of bytes occupied      | 6089531321856                                                                                        |
+
+## JSON output 
+
+Here is an example output:
+
+```
+{
+ "/data/CCBR_Pipeliner/Tools/spacesavers2": {
+  "37513": {
+   "username": "kopardevn",
+   "nfiles": 1267,
+   "nbytes": 96084992
+  },
+  "60731": {
+   "username": "sovacoolkl",
+   "nfiles": 895,
+   "nbytes": 89249280
+  }
+ }
+}
+```

spacesavers2_pdq

@@ -15,6 +15,7 @@ from src.pdq import pdq
 from multiprocessing import Pool
 import argparse
 from pathlib import Path
+import json
 
 
 def task(f):
@@ -62,15 +63,23 @@ def main():
         dest="outfile",
         required=False,
         type=str,
-        help="outfile ... catalog file .. by default output is printed to screen",
+        help="outfile ...  by default output is printed to screen",
+    )
+    parser.add_argument(
+        "-j",
+        "--json",
+        dest="json",
+        required=False,
+        type=str,
+        help="outfile file in JSON format.",
     )
     parser.add_argument("-v", "--version", action="version", version=__version__)
 
     global args
     args = parser.parse_args()
 
     folder = args.folder
-    p = Path(folder)
+    p = Path(folder).absolute()
     files = [p]
     files2 = p.glob("**/*")
     files.extend(files2)
@@ -80,6 +89,9 @@ def main():
     else:
         outfh = sys.stdout
 
+    if args.json:
+        outjson = open(args.json, 'w')
+
     bigdict=dict()
 
     with Pool(processes=args.threads) as pool:
@@ -89,15 +101,26 @@ def main():
             if not uid in bigdict: bigdict[uid]=dict()
             inode = fd.get_inode()
             if not inode in bigdict[uid]: bigdict[uid][inode]=fd.get_size()
-
+
+    outdict=dict()
+    outdict[str(p)]=dict()
+
     for uid in bigdict.keys():
         username = get_username_groupname(uid)
+        outdict[str(p)][str(uid)]=dict()
         nfiles = len(bigdict[uid])
         nbytes = 0
         for inode in bigdict[uid].keys():
             nbytes += bigdict[uid][inode]
+        outdict[str(p)][str(uid)]['username']=username
+        outdict[str(p)][str(uid)]['nfiles']=nfiles
+        outdict[str(p)][str(uid)]['nbytes']=nbytes
         outfh.write(f"{username}\t{nfiles}\t{nbytes}\n")
 
+    if args.json:
+        json.dump(outdict,outjson,indent=1)
+        outjson.close()
+
     if args.outfile:
         outfh.close()
 

src/VERSION

@@ -1 +1 @@
-0.11.5
+0.11.6