Remove Publication Title from description in study_parser.py

[will-moore]

See ome/omero-mapr#74 (comment)

We want to simplify the Study description so that it can be parsed for searching, without duplicating the Study Title in the description.

[sbesson]

If we are looking into removing publication title from the description, a question is whether this heading should be kept at all for the relevant studies or if the value of this field should be more simply appended with 1-2 newlines

[will-moore]

by "this heading" do you mean "Study Version History"? I'm happy to remove that heading too if it's not needed?

[sbesson]

yes, I meant Study Version History but deferring to you, @khaledk2 and @francesw on what makes the most sense both in terms of UI and searchability.

[will-moore]

We want to run this on all studies...

for dir in */ ; do
  cd "$dir"
  
  # Check for a file ending with study.txt
  if [ -e *study.txt ]; then
    python /idr-utils/pyidr/study_parser.py $(find . -type f -name '*study.txt') --set
  fi
  
  cd ..
done

[sbesson]

As a one-liner I have been using the following in the past to update all descriptions/annotations of the top-level containers:

source /opt/omero/server/venv3/bin/activate
cd /uod/idr/metadata/
find . -maxdepth 2 -type f -iname *study.txt -exec python idr-utils/pyidr/study_parser.py --set {} \;

[will-moore]

Trying to pull this branch onto pilot-idr0125 for testing, but can't connect to github...

$ ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' idr0125-omeroreadwrite -L 1080:localhost:80

$ cd /uod/idr/metadata/idr-utils
$ git remote -v
origin	https://github.com/IDR/idr-utils (fetch)
origin	https://github.com/IDR/idr-utils (push)
sbesson	git://github.com/sbesson/idr-utils (fetch)
sbesson	git://github.com/sbesson/idr-utils (push)

$ sudo -Es git remote add will git://github.com/will-moore/idr-utils
$ sudo -Es git fetch will
fatal: unable to connect to github.com:
github.com[0: 140.82.121.4]: errno=Connection timed out

[sbesson]

The git:// protocol is deprecated. Do you have the same error with HTTPs?

[will-moore]

That worked, thanks!

sudo -Es git remote set-url will https://github.com/will-moore/idr-utils
sudo -Es git fetch will
 * [new branch]      study_description_no_title -> will/study_description_no_title
sudo -Es git checkout will/study_description_no_title

[will-moore]

source /opt/omero/server/venv3/bin/activate
cd /uod/idr/metadata/
omero login
find . -maxdepth 2 -type f -iname *study.txt -exec python idr-utils/pyidr/study_parser.py --set {} \;

[will-moore]

Also just ran the study_parser as above on idr-testing to update descriptions.