Merge pull request #2 from wtsi-hgi/feature/arv-view

[arvados.git] / sdk / python / arvados / commands / put.py

diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index 4383514df5f42eb34c400a24e58d5652330cce3a..7ca6e7ca234f9b7ef2f1bc4dfc6ef84910c9c1e0 100644 (file)
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -5,6 +5,7 @@
 
 import argparse
 import arvados
+import arvados.collection
 import base64
 import datetime
 import errno
@@ -166,7 +167,9 @@ def parse_arguments(arguments):
     args = arg_parser.parse_args(arguments)
 
     if len(args.paths) == 0:
-        args.paths += ['/dev/stdin']
+        args.paths = ['-']
+
+    args.paths = map(lambda x: "-" if x == "/dev/stdin" else x, args.paths)
 
     if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
         if args.filename:
@@ -181,9 +184,9 @@ def parse_arguments(arguments):
         args.progress = True
 
     if args.paths == ['-']:
-        args.paths = ['/dev/stdin']
+        args.resume = False
         if not args.filename:
-            args.filename = '-'
+            args.filename = 'stdin'
 
     return args
 
@@ -301,12 +304,12 @@ class ArvPutCollectionWriter(arvados.ResumableCollectionWriter):
 
     def flush_data(self):
         start_buffer_len = self._data_buffer_len
-        start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE
+        start_block_count = self.bytes_written / arvados.config.KEEP_BLOCK_SIZE
         super(ArvPutCollectionWriter, self).flush_data()
         if self._data_buffer_len < start_buffer_len:  # We actually PUT data.
             self.bytes_written += (start_buffer_len - self._data_buffer_len)
             self.report_progress()
-            if (self.bytes_written / self.KEEP_BLOCK_SIZE) > start_block_count:
+            if (self.bytes_written / arvados.config.KEEP_BLOCK_SIZE) > start_block_count:
                 self.cache_state()
 
     def _record_new_input(self, input_type, source_name, dest_name):
@@ -408,10 +411,18 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
         print >>stderr, error
         sys.exit(1)
 
-    # Apply default replication, if none specified. TODO (#3410): Use
-    # default replication given by discovery document.
-    if args.replication <= 0:
-        args.replication = 2
+    # write_copies diverges from args.replication here.
+    # args.replication is how many copies we will instruct Arvados to
+    # maintain (by passing it in collections().create()) after all
+    # data is written -- and if None was given, we'll use None there.
+    # Meanwhile, write_copies is how many copies of each data block we
+    # write to Keep, which has to be a number.
+    #
+    # If we simply changed args.replication from None to a default
+    # here, we'd end up erroneously passing the default replication
+    # level (instead of None) to collections().create().
+    write_copies = (args.replication or
+                    api_client._rootDesc.get('defaultCollectionReplication', 2))
 
     if args.progress:
         reporter = progress_writer(human_progress)
@@ -437,12 +448,12 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
         writer = ArvPutCollectionWriter(
             resume_cache, reporter, bytes_expected,
             num_retries=args.retries,
-            replication=args.replication)
+            replication=write_copies)
     else:
         writer = ArvPutCollectionWriter.from_cache(
             resume_cache, reporter, bytes_expected,
             num_retries=args.retries,
-            replication=args.replication)
+            replication=write_copies)
 
     # Install our signal handler for each code in CAUGHT_SIGNALS, and save
     # the originals.
@@ -457,7 +468,16 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
     writer.report_progress()
     writer.do_queued_work()  # Do work resumed from cache.
     for path in args.paths:  # Copy file data to Keep.
-        if os.path.isdir(path):
+        if path == '-':
+            writer.start_new_stream()
+            writer.start_new_file(args.filename)
+            r = sys.stdin.read(64*1024)
+            while r:
+                # Need to bypass _queued_file check in ResumableCollectionWriter.write() to get
+                # CollectionWriter.write().
+                super(arvados.collection.ResumableCollectionWriter, writer).write(r)
+                r = sys.stdin.read(64*1024)
+        elif os.path.isdir(path):
             writer.write_directory_tree(
                 path, max_manifest_depth=args.max_manifest_depth)
         else:
@@ -471,17 +491,17 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
     if args.stream:
         output = writer.manifest_text()
         if args.normalize:
-            output = CollectionReader(output).manifest_text(normalize=True)
+            output = arvados.collection.CollectionReader(output).manifest_text(normalize=True)
     elif args.raw:
         output = ','.join(writer.data_locators())
     else:
         try:
             manifest_text = writer.manifest_text()
             if args.normalize:
-                manifest_text = CollectionReader(manifest_text).manifest_text(normalize=True)
+                manifest_text = arvados.collection.CollectionReader(manifest_text).manifest_text(normalize=True)
             replication_attr = 'replication_desired'
             if api_client._schema.schemas['Collection']['properties'].get(replication_attr, None) is None:
-                # API calls it 'redundancy' until #3410.
+                # API called it 'redundancy' before #3410.
                 replication_attr = 'redundancy'
             # Register the resulting collection in Arvados.
             collection = api_client.collections().create(