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Hi Simon,<br>
<br>
Thanks for the quick response.<br>
<br>
<div class="moz-cite-prefix">On 8/15/2016 2:31 AM, Simon Li wrote:<br>
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Just a few questions and possibly there are some
suggestions for improvement hidden in there:<br>
1) when I upload a .csv file with "bin/omero metadata
populate --file filename.csv --context csv
Screen:<screen_id>"<br>
the resulting Table is called "bulk_annotations". Is
there a way to upload with a different name?<br>
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<div>Not at the moment, though it should be possible to
change the name since OMERO.web uses the file-annotation's
namespace. You can change it manually if you want:<br>
<br>
omero obj update OriginalFile:123
Name=experimental-data.h5<br>
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Ah yes, good thought. I'll try to do that.<br>
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<div bgcolor="#FFFFFF" text="#000000">2) one reason I ask
is that I would like to upload 2 different annotations
to a Screen: #1 is the experimental metadata that
describes the experiment and #2 is a feature
measurements file after analysis which is likely to be
done at a later time, thus the desire to separate that
from the experimental metadata. Currently both attached
Tables care named bulk_annotations.<br>
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<div>That sounds similar to something we're doing at the
moment in the IDR, though we're not displaying the feature
values at the moment. One thing we're considering is
having a separate namespace for the bulk-annotations and
the feature analysis.<br>
<br>
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<div>Do you have some ideas for how this should be
presented, or is the current tabular display OK for you?<br>
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For now, the tabular display is fine since our current feature
tables are per-image summary statistics, not per-cell feature
measurement data. Once one wants to store per-cell features as a
table per image (and we will want to do so in the near future) the
simple tabular display will no longer suffice since it will be at
least a multi-column table. In order to display anything like, you
probably will need a separate window/table, maybe similar to:
<a class="moz-txt-link-freetext" href="http://www.openmicroscopy.org/site/support/omero5.2/developers/analysis.html#third-party-analysis-and-omero-tables">http://www.openmicroscopy.org/site/support/omero5.2/developers/analysis.html#third-party-analysis-and-omero-tables</a><br>
But that's probably something for a serious design review and I
presume will rely on all the new ROI work going on, right?<br>
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<div bgcolor="#FFFFFF" text="#000000">3) so while it is
possible to upload 2 different annotation files and both
show up as Attachments to the Screen object (with the
same "bulk_annotations" name), when I look at the Image
objects within that Screen, they only show in the Tables
tab the contents from the most recently uploaded
annotation file.<br>
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<div>That was a workaround we implemented a few years ago<br>
<a moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/pull/512#issuecomment-11372968"
target="_blank">https://github.com/<wbr>openmicroscopy/openmicroscopy/<wbr>pull/512#issuecomment-11372968</a><br>
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<div>Now that the metadata work is seeing more use it's
something we should improve.<br>
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Ah, I see. For now there are a few work-arounds that I can use: 1)
merge all my annotation files into one and upload that (and redo
that when the due to a new analysis algorithm there are different
measured features), and 2) (and this is what I am currently doing)
upload the static experimental metadata, create the key-value pairs
using the metadata populate functionality for everything I want
people to see, then upload the feature annotation file and that then
shows up in the Tables tab. A little clunky but workable.<br>
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<div bgcolor="#FFFFFF" text="#000000">4) the metadata
annotation works great for "normal" plates that have
numbered columns and "lettered" rows. However, when one
has lettered columns and numbered rows, everything gets
jumbled and when there are more than 26 rows the routine
throws an exception (see my earlier message). I worked
around this issue (mostly with Will Moore's help, see:
<a moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/pull/4743"
target="_blank">
https://github.com/openmicrosc<wbr>opy/openmicroscopy/pull/4743</a>)
but it would be great if that issue was really fixed
before releasing the metadata functionality into the
wild.<br>
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<div>Again this is something that's only come to light as
more people use it, I've added it to our bug-list.<br>
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Thanks. That is actually a bug I'd love to see disappear.<br>
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<div>Thanks for your feedback!<br>
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And thank you guys for building all this functionality I need.<br>
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One more question: in my current workflow I do not create a column
in my experimental metadata annotation file called "Image Name",
mostly because I wouldn't know what for to use that, and thus the
populator generates lots of messages:
"INFO:omero.util.populate_metadata:Missing image name column,
skipping."<br>
Not a big problem but annoying. Since it appears to be just an INFO
message, is there a way to make it appear only once? Or am I missing
something and I really should have a Image Name column?<br>
<br>
Cheers,<br>
- Damir<br>
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<div>Simon<br>
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<div bgcolor="#FFFFFF" text="#000000">Thanks,<br>
- Damir<br>
<br>
<div>On 6/27/2016 2:03 PM, Eleanor Williams wrote:<br>
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<p>Hi Damir</p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">To
convert the omero tables to key-value pairs
annotations we are again using the CLI metadata
populate script along with a yaml-format
configuration file to specify which columns we
want to take from the omero tables and put into
Key-Value Annotations.
<br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"><br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">This
component of the metadata functionality is still
in the development stage and so to use it you need
to:</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"><br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">1.
use the latest version of omero (5.2.4) and</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">2.
then run as</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">OMERO_DEV_PLUGINS=1
bin/omero metadata populate --context bulkmap
--cfg bulkmap-config.yml Screen:n</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">where
n is the screen number in omero.</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"><br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">An
example config file for one of our screens is here</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a
moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml"
style="text-decoration:none" target="_blank"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline"></span></a><a
moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml"
target="_blank">https://github.com/IDR/idr-met<wbr>adata/blob/master/idr0002-heri<wbr>che-condensation/screenA/idr00<wbr>02-screenA-bulkmap-config.yml</a></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"><br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">You
can see I have just picked out some of the columns
from the</span><a moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-annotation.csv"
style="text-decoration:none" target="_blank"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><span
style="font-size:14.6667px;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline">annotation.csv</span></a><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">
file, in this case ones that I thought IDR users
might use as search terms, and I have specified
URLs for some. You can also change the 'display
name' of the column using the ' clientname' tag
and create URLs using the 'clientvalue' tag. </span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"><br>
</span></p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span
style="font-size:14.6667px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Let
us know if you have any problems running this, or
suggestions for improvement.</span></p>
Best regards<br>
Eleanor<br>
<br>
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<pre class="moz-signature" cols="72">--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
<a class="moz-txt-link-freetext" href="http://biosciences.lbl.gov/profiles/damir-sudar-2/">http://biosciences.lbl.gov/profiles/damir-sudar-2/</a>
Visiting Scientist, Oregon Health & Science University</pre>
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