9f13a83c45f20774ba2f749cc0ce25ba9c64aa73
max
  Fri Jun 27 08:20:16 2025 -0700
removing temp file after ucscDataset diffs run, because of perms problems

diff --git ucsc/datasetDiffs ucsc/datasetDiffs
index 4d1bd03..ff04dc9 100755
--- ucsc/datasetDiffs
+++ ucsc/datasetDiffs
@@ -145,49 +145,50 @@
         for dname in cb_datasets:
             cb_loc[dname] = cb_base + dname + "/dataset.json"
         threader(cb_loc, cb_djson, cb_hide)
 
         # dicts/sets to hold everything
         rr_hide = set() # holds hidden rr datasets
         rr_djson = dict() # holds contents of json files for each rr dataset
         rr_datasets = set() # holds names of all datasets on rr
         rr_paths = dict() # file paths to process via multithreading
         # Get list of dataset.json files for rr
         cmd = ['ssh', 'qateam@hgw0.soe.ucsc.edu', 'find', ct_base, '-name',\
         'dataset.json', '|', 'cut', '-f', '6-', '-d', '"/"']
         p = Popen(cmd, shell=False, stdout=PIPE, stderr=PIPE)
         cmdout, cmderr = p.communicate()
         rr_files = set(cmdout.decode().rstrip().split('\n'))
-        #with tempfile.NamedTemporaryFile(prefix='cb_', delete=False) as tmp:
-            #tmp.write(cmdout)
-        tmp = open("/data/tmp/filesForRsync.txt", "wb")
+        with tempfile.NamedTemporaryFile(prefix='cb_', delete=False) as tmp:
             tmp.write(cmdout)
-        tmp.close()
+        #tmp = open("/data/tmp/filesForRsync.txt", "wb")
+        tmp.write(cmdout)
+        tmp.flush()
 
         # Wanted to use TemporaryDirectory here but couldn't get it to work
         rr_base = '/data/tmp/cb_tmp_new'
         # Make the new directory, continue on if dir already exists
         try:
             mkdir(rr_base)
         except OSError:
             pass
         rsync_cmd = ['rsync', '--files-from=' + tmp.name, \
         'qateam@hgw0.soe.ucsc.edu:/usr/local/apache/htdocs-cells/', rr_base]
         print("running ", rsync_cmd)
         #rsync_p = Popen(rsync_cmd, shell=True, stdout=PIPE, stderr=PIPE)
         #rsync_cmdout, rsync_cmderr = p.communicate()
         subprocess.run(rsync_cmd, check=True)
+        tmp.close()
 
         #if p.returncode != 0:
             #logging.error("error when running: "+repr(" ".join(rsync_cmd)))
             #assert(False)
         # go through rr_files
         for fname in rr_files:
             # turn full path name into a simple dataset name
             fsplit = fname.strip().split('/')
             # from https://stackoverflow.com/questions/12453580/how-do-i-concatenate-items-in-a-list-to-a-single-string
             dname = '/'.join(fsplit[:-1])
             if dname != '':
                 # now turn dataset name into url
                 dpath = rr_base + '/' + dname  + '/dataset.json'
                 # add that url to a dict
                 rr_paths[dname] = dpath