atarkowska

/*
 * stitching
 */
process coordinates {

  input:
  file input_dir
  val row from ch_non_clusters.mix(ch_clusters).splitCsv(header: true, sep:'\t' )

  output:

atarkowska

brew install gource
git log --pretty=format:user:%aN%n%ct --reverse --raw --encoding=UTF-8 --no-renames > bf.log
gource -s .01 -1920x1080 --auto-skip-seconds .1 --multi-sampling --stop-at-end --key --highlight-users --hide mouse,progress,filenames --file-idle-time 0 --max-files 0  --background-colour 000000  --output-ppm-stream - --output-framerate 30 bf.log --logo bf-logo.png  | avconv -y -r 30 -f image2pipe -vcodec ppm -i - -b 65536K movie-bf.mp4

atarkowska

package test;

import java.awt.BorderLayout;
import java.awt.image.BufferedImage;

/*

SEE https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/romio/src/ome/io/bioformats/BfPixelsWrapper.java#L360

 * #%L

atarkowska

OMERO_DIST='/home/omero/workspace/OMERO-server/OMERO.server'
IDR_METADATA='/tmp/idr-metadata'


# idr0008-rohn-actinome/screenA
# http://10.0.51.135/web/webclient/?show=screen-154
# delete gene annotations
$OMERO_DIST/bin/omero metadata populate --batch 10 --wait 600 --context deletemap --localcfg '{"ns":"openmicroscopy.org/mapr/gene"}' Screen:154 --report
# generate new table

atarkowska

OMERO_DIST='/home/omero/workspace/OMERO-server/OMERO.server'
IDR_METADATA='/tmp/idr-metadata'


# idr0008-rohn-actinome/screenA
# http://10.0.51.135/web/webclient/?show=screen-154
# delete gene annotations
$OMERO_DIST/bin/omero metadata populate --batch 10 --wait 600 --context deletemap --localcfg '{"ns":"openmicroscopy.org/mapr/gene"}' Screen:154 --report
# generate new table

atarkowska

(django) MacBookPro:omero.git ola$ createdb -E UTF8 -O omero test -h localhost -U postgres
(django) MacBookPro:omero.git ola$ omego db init --serverdir /Users/ola/OMERO/omero.git/dist --dbname test
2017-02-03 10:35:26,685 [omero.gatewa] ERROR No Pillow installed, line plots and split channel will fail!
2017-02-03 10:35:26,797 [    omego.db] INFO  DbAdmin: DbAdmin /Users/ola/OMERO/omero.git/dist ...
2017-02-03 10:35:26,798 [    omego.db] INFO  Failed to lookup parameter omero.db.host, using localhost
2017-02-03 10:35:26,798 [omego.extern] INFO  Executing [custom environment]: psql -d test -h localhost -U postgres -w -A -t --version
2017-02-03 10:35:26,808 [omego.extern] INFO  Completed [0.010 s]
2017-02-03 10:35:26,809 [    omego.db] INFO  psql version: psql (PostgreSQL) 9.5.3

2017-02-03 10:35:26,810 [    omego.db] INFO  Failed to lookup parameter omero.db.host, using localhost

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'

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

+ 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 ome-devel@lists.openmicroscopy.org.uk
 ---> Using cache
 ---> 4408ec196df0
Step 3 : RUN yum install -y epel-release     && yum clean all

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={}):