atarkowska

select map.value, a.ns, count(i.id) from annotation as a 
join annotation_mapvalue as map on a.id=map.annotation_id
join imageannotationlink as ial on ial.child=a.id
join image as i on i.id=ial.parent
where
    map.name in ('Gene Symbol', 'Gene Identifier', 'Phenotype', 'siRNA Identifier', 'siRNA Pool Identifier', 'Organism')
    and a.ns like 'openmicroscopy.org/mapr/%'
group by map.value, a.ns
order by 3 DESC
limit 100

atarkowska

(omero-virtualenv)bash-4.2$ bin/omero shell
Python 2.7.5 (default, Nov 20 2015, 02:00:19) 
Type "copyright", "credits" or "license" for more information.

IPython 1.2.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

atarkowska

#!/bin/sh
# automatically configured by git-annex
FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -e '\.py$')

if [ -n "$FILES" ]; then
    if output=$(flake8 $FILES) && [ -z "$output" ]; then
        echo 'Flake8 pass. Ready to commit.'
    else
        echo 'Flake8 errors.'
        echo "$output"

atarkowska

bin/omero metadata populate --context deletemap Screen:3
bin/omero metadata populate --context deletemap Screen:102
bin/omero metadata populate --context deletemap Screen:51
bin/omero metadata populate --context deletemap Screen:202
bin/omero metadata populate --context deletemap Screen:597
bin/omero metadata populate --context deletemap Screen:751
bin/omero metadata populate --context deletemap Screen:253
bin/omero metadata populate --context deletemap Screen:201
bin/omero metadata populate --context deletemap Screen:154
bin/omero metadata populate --context deletemap Screen:206

atarkowska

(dev_tools) MacBookPro:ansible ola$ ansible-playbook -i ../../management_tools/ansible/ci/ci-test-hosts -l 10.0.51.148 -vv -u centos ci-deployment.yml 
Using /Users/ola/OMERO/SYSADMIN/infrastructure/ansible/ansible.cfg as config file

PLAYBOOK: ci-deployment.yml ****************************************************
4 plays in ci-deployment.yml

PLAY [ci-jenkins-linux] ********************************************************

TASK [setup] *******************************************************************
ok: [10.0.51.148]

atarkowska

import requests

# put here project/screen ids
containers = (101,)

list_datasets_url = "http://idr-demo.openmicroscopy.org/webclient/api/datasets/?id={container_id}&page=0"
list_images_url = "http://idr-demo.openmicroscopy.org/webclient/api/images/?id={id}&page=1"
image_link = "http://idr-demo.openmicroscopy.org/webclient/?show=image-{id}"
image_viewer_link = "http://idr-demo.openmicroscopy.org/webclient/img_detail/{id}/"
thumbnail_url = "http://idr-demo.openmicroscopy.org/webclient/render_thumbnail/size/96/{id}/"

atarkowska

import omero
from omero.rtypes import *


host = "localhost" 
port = 4064 
userpass = "ome"
user = "demo"

c = omero.client(host=host, port=port)

atarkowska

# COUNT
2016-11-03 09:53:01,116 DEBUG [                         omero_mapr.tree] (proc.00091) count_mapannotations():196 HQL QUERY: 
        select
            count(distinct mv.value) as childCount
        from ImageAnnotationLink ial
            join ial.child a
            join a.mapValue mv
            join ial.parent i
            left outer join i.wellSamples ws
            left outer join i.datasetLinks dil

atarkowska

pip install git+git://github.com/aleksandra-tarkowska/mapannotations.git.
/home/omero/OMERO.web/bin/omero config set omero.web.apps # wipe
/home/omero/OMERO.web/bin/omero config append omero.web.apps '"mapr"'
/home/omero/OMERO.web/bin/omero config set omero.web.ui.top_links '[["IDR", {"viewname": "webindex", "query_string": {"experimenter": -1}}, {"title": "Image Data Repository"}], ["Genes", {"viewname": "maprindex_gene", "query_string": {"experimenter": -1}}, {"title": "Genes browser"}], ["Phenotypes", {"viewname": "maprindex_phenotype", "query_string": {"experimenter": -1}}, {"title": "Phenotypes browser"}], ["siRNA", {"viewname": "maprindex_sirna", "query_string": {"experimenter": -1}}, {"title": "siRNA browser"}], ["Compound", {"viewname": "maprindex_compound", "query_string": {"experimenter": -1}}, {"title": "Compound browser"}], ["History", "history", {"title": "History"}], ["About", "/about/"], ["Help", "http://help.openmicroscopy.org/", {"title":"Open OMERO user guide in a new tab", "target":"new"}]]

atarkowska

(ansible) MacBookPro:DOCKER ola$ ansible-playbook  -i infrastructure/ansible/inventory/openstack.py -l ola-test-training -vv -u centos infrastructure/ansible/training-server.yml
No config file found; using defaults

PLAYBOOK: training-server.yml **************************************************
1 plays in infrastructure/ansible/training-server.yml

PLAY [localhost, all] **********************************************************

TASK [setup] *******************************************************************
ok: [b11acd75-ea3c-4459-9d75-61bb04d141a6]