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Ola Tarkowska atarkowska

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@atarkowska
atarkowska / jquery.html
Created July 4, 2016 08:54
CORS
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>load demo</title>
<style>
body {
font-size: 12px;
font-family: Arial;
}
@atarkowska
atarkowska / test_missing_maps.py
Created July 4, 2016 13:19
missing maps
import omero, os, traceback
import omero.gateway
import time, datetime
from omero.rtypes import *
from omero.rtypes import unwrap
host = "localhost"
port = 4064
@atarkowska
atarkowska / bf.log
Last active July 17, 2016 22:22
BF maven docker build
using:
FROM maven:3.3.3-jdk-8
WORKDIR /usr/src/app/bf.git
ONBUILD RUN mvn install -DskipTests
CMD ["mvn", "install", "-DskipTests"]
maven_1 | [INFO] Scanning for projects...
maven_1 | Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-webdav-jackrabbit/1.0/wagon-webdav-jackrabbit-1.0.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-webdav-jackrabbit/1.0/wagon-webdav-jackrabbit-1.0.pom (4 KB at 17.6 KB/sec)
@atarkowska
atarkowska / compose2
Last active September 21, 2016 13:33
verbose of docker-compose v2
FILE: docker-compose2.yml
version: '2'
services:
test:
image: openmicroscopy/omero-ssh-daemon-c7:0.1.1
ports:
- "2222:22"
test2:
@atarkowska
atarkowska / compose
Last active September 21, 2016 13:33
verbose of docker-compose
FILE:docker-compose.yml
test:
image: openmicroscopy/omero-ssh-daemon-c7:0.1.1
ports:
- "2222:22"
test2:
image: openmicroscopy/omero-ssh-daemon-c7:0.1.1
ports:
- "2223:22"
@atarkowska
atarkowska / gist:71ebc9a9b53ed6ca8edf09827f4786b6
Last active August 4, 2016 14:13
meeting
http://users.openmicroscopy.org.uk/~atarkowska/viewer.html
idr-demo.openmicroscopy.org/webgateway/render_thumbnail/122770/96/
http://idr-demo.openmicroscopy.org/webclient/?show=image-122770
@atarkowska
atarkowska / gist:11dd9cc0d8ec7b70f289fe33f7460f21
Created August 17, 2016 15:29
install trainin server
(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]
@atarkowska
atarkowska / mapr_setup
Last active August 19, 2016 11:02
mapr installation
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
atarkowska / mapr_hql_queries
Last active November 9, 2016 14:58
mapr hql queries
# 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
atarkowska / test.py
Last active August 23, 2016 15:28
mapr hql script
import omero
from omero.rtypes import *
host = "localhost"
port = 4064
userpass = "ome"
user = "demo"
c = omero.client(host=host, port=port)