#!/usr/bin/env python
+#
+# decompress-all.py
+#
+# Decompress all compressed files in the collection using the "dtrx" tool and
+# produce a new collection with the contents. Uncompressed files
+# are passed through.
+#
+# input:
+# A collection at script_parameters["input"]
+#
+# output:
+# A manifest of the uncompressed contents of the input collection.
+
import arvados
import re
import subprocess
+import os
+import sys
+import crunchutil.robust_put as robust_put
arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True,
input_as_path=True)
input_file = task['parameters']['input']
-result = re.match(r"(^[a-f0-9]{32}\+\d+)(\+\S+)*(/.*)(/.*)?$", input_file)
+infile_parts = re.match(r"(^[a-f0-9]{32}\+\d+)(\+\S+)*(/.*)?(/[^/]+)$", input_file)
outdir = os.path.join(task.tmpdir, "output")
-os.mkdirs(outdir)
+os.makedirs(outdir)
os.chdir(outdir)
-if result != None:
- cr = arvados.CollectionReader(re.group(1))
- streamname = '.'
- if re.group(3) != None:
- streamname += re.group(2)
- filename = re.group(3)[1:]
- else:
- filename = re.group(2)[1:]
+if infile_parts is None:
+ print >>sys.stderr, "Failed to parse input filename '%s' as a Keep file\n" % input_file
+ sys.exit(1)
+
+cr = arvados.CollectionReader(infile_parts.group(1))
+streamname = infile_parts.group(3)[1:]
+filename = infile_parts.group(4)[1:]
- os.mkdirs(streamname)
+if streamname is not None:
+ subprocess.call(["mkdir", "-p", streamname])
os.chdir(streamname)
- streamreader = filter(lambda s: s.name() == streamname, cr.all_streams())[0]
- filereader = stream.files()[filename]
- rc = subprocess.call("dtrx", "-r", "-n", arvados.get_task_param_mount('input'))
+else:
+ streamname = '.'
+
+m = re.match(r'.*\.(gz|Z|bz2|tgz|tbz|zip|rar|7z|cab|deb|rpm|cpio|gem)$', arvados.get_task_param_mount('input'), re.IGNORECASE)
+
+if m is not None:
+ rc = subprocess.call(["dtrx", "-r", "-n", "-q", arvados.get_task_param_mount('input')])
if rc == 0:
- out.write_directory_tree(outdir, max_manifest_depth=0)
- arvados.task_set_output(out.finish())
+ task.set_output(robust_put.upload(outdir))
else:
- arvados.task_set_output(streamname + filereader.as_manifest()[1:])
+ sys.exit(rc)
else:
- sys.exit(1)
+ streamreader = filter(lambda s: s.name() == streamname, cr.all_streams())[0]
+ filereader = streamreader.files()[filename]
+ task.set_output(streamname + filereader.as_manifest()[1:])