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

(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

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

#!/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

(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

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

import requests

COOKIE_NAME = "sessionid_demo3c"
HOST = "http://idr-clone.openmicroscopy.org"
INDEX_PAGE = "{host}/webclient".format(**{'host': HOST})
THUMBNAIL_URL = "{host}/webgateway/render_thumbnail/{image_id}/"
MAP_IMAGE_URL = "{host}/webclient/api/annotations/?type=map&image={image_id}"


def prepare_url(url, params={}):

atarkowska

+ docker-compose -f test/docker-compose.yml up --build --abort-on-container-exit
WARNING: The SKIP_UPGRADE_CHECK variable is not set. Defaulting to a blank string.
WARNING: The OMEROBUILD variable is not set. Defaulting to a blank string.
Building omeroserver
Step 1 : FROM openmicroscopy/omero-ssh-daemon-c7:0.1.1
 ---> 02e6d0e5628d
Step 2 : MAINTAINER [email protected]
 ---> Using cache
 ---> 4408ec196df0
Step 3 : RUN yum install -y epel-release     && yum clean all

atarkowska

SELECT                                                                               
    count (distinct mv.value), mv.name, (substring(mv.value from '(https?://([^/]*){1})')) as url
FROM
    annotation_mapvalue as mv
WHERE 
    (substring(mv.value from '(https?://([^/]*){1})')) is not null
GROUP BY mv.name, url
ORDER BY 2;

atarkowska

select el.*, ev.* from eventlog  as el
inner join event as ev on (el.event=ev.id)
inner join wellannotationlink as wal on (wal.id = el.entityid)
inner join well as w on (wal.parent=w.id)
inner join plate as p on (w.plate=p.id)
inner join screenplatelink as spl on (spl.child=p.id)
where ev."time" > '2017-01-31 16:00:00.000'
and spl.parent = 1203
and el.action != 'REINDEX'
and el.entitytype = 'ome.model.annotations.WellAnnotationLink'