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Bulk annotations and streaming #5

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merged 8 commits into from
Sep 3, 2018
Merged

Bulk annotations and streaming #5

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4331cd7
Added dataset bulk annotation changes. See https://github.com/openmic…
kkoz Aug 16, 2018
957f32b
Changed parsing context to add data to tables in a streaming method r…
kkoz Aug 20, 2018
1ede450
Fixed formatting and one problem with tabletests
kkoz Aug 20, 2018
99c06e8
Updated version, removed unused import, removed info cmd line arg
kkoz Aug 21, 2018
fb9823a
Changed imports in tests to import from the package instead of the le…
kkoz Aug 22, 2018
91bc2a6
Create ParsingUtilFactory inside ParsingContext to keep constructor s…
kkoz Aug 23, 2018
6b47e3d
Fixed formatting issues after refactor
kkoz Aug 23, 2018
ef91b15
Removed explicit calls to write_to_omero in favor of writing in parse…
kkoz Aug 27, 2018
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7 changes: 7 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
CHANGES
=======

0.3.0
-----

* Added bulk annotations for Projects and Datasets
* Changed csv parsing to proceed line-by-line (streaming)


0.2.2
-----

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20 changes: 10 additions & 10 deletions src/omero_cli_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -476,20 +476,20 @@ def populate(self, args):
cfgid = cfgann.getFile().getId()
md.linkAnnotation(cfgann)

# Note some contexts only support a subset of these args
ctx = context_class(client, args.obj, file=args.file, fileid=fileid,
cfg=args.cfg, cfgid=cfgid, attach=args.attach,
options=localcfg)
ctx.parse()
loops = 0
ms = 0
if not args.dry_run:
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If I understand correctly the --dry-run argument is now largely a no-op, similarly to the -info command. Primary question is whether we might want to resurrect it at some point via some constructor option of equivalent.

wait = args.wait
if not wait:
loops = 0
ms = 0
else:
if wait:
ms = 5000
loops = int((wait * 1000) / ms) + 1
ctx.write_to_omero(batch_size=args.batch, loops=loops, ms=ms)

# Note some contexts only support a subset of these args
ctx = context_class(client, args.obj, file=args.file, fileid=fileid,
cfg=args.cfg, cfgid=cfgid, attach=args.attach,
options=localcfg, batch_size=args.batch,
loops=loops, ms=ms)
ctx.parse()

def rois(self, args):
"Manage ROIs"
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