Sébastien Besson sbesson
sbesson
/ omero_update_bf.py
Last active
September 13, 2017 15:19
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| #! /usr/bin/env python | |
| # Script to update Bio-Formats server-side | |
| import urllib2 | |
| import os | |
| import shutil | |
| DONWLOADS_URL = "http://downloads.openmicroscopy.org/bio-formats" | |
| RELEASE = "5.1.4" | |
| JARS = [ |
sbesson
/ cpp_decoupling
Last active
November 9, 2015 09:52
A script to decouple the components from Bio-Formats
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| #! /bin/bash | |
| here=$(pwd) | |
| # Initial clone | |
| cd /tmp | |
| rm -rf /tmp/bioformats-cpp || echo "Already cleaned" | |
| # Clone Bio-Formats | |
| git clone https://github.com/openmicroscopy/bioformats.git bioformats-cpp |
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| c=loadOmero(hostname); | |
| s=c.createSession(user, pass); | |
| uuid = s.getAdminService().getEventContext().sessionUuid; | |
| parfor i=1:2 | |
| c2 = loadOmero(hostname); | |
| s2= c2.joinSession(uuid); | |
| s2.getAdminService().getEventContext().userName | |
| end | |
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| > Add Ant target to check existence of configuration file 9c3111a -> 4cbc8f70ab6ec24fe6ab160e3a760ddbaea71e57 | |
| > Add CLI plugin for generating Robot configuration file 1ffdf69 -> 41209db092afc6d4a148419eac931c01c92d8546 | |
| > Add new bash script to setup the Robot configuration 0dbcd80 -> de682da9b68829a748ad3e829258720c6c1603ee | |
| > Don't block 'batch annotate' panel even if canAnnotate() is F 368a9a6 -> da464b585c4dd2c78cf94921875faa59886e800d | |
| > Fix flake8 errors 6ad9333 -> accc948083f4af34590a90fe633cd8b77b0c3609 | |
| > Fix flake8 errors 729f51a -> c558f4ea67a1c0e5efe3fb90bcbf4972f78a9c90 | |
| > Fix flake8 errors 79b02ce -> 6a5d8e24f733670de80fc53c4cc60918d79dd21e | |
| > Fix heap_dump=tmp for jvmcfg f94e7f4 -> 44d7b95c99245519347a92cc1dfb65ac8da29f27 | |
| > Fix login robot test .login-logos/img |
sbesson
/ associateROIsToMovies.m
Created
November 7, 2014 09:14
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| annotations = getAnnotationTypes(); | |
| objects = getObjectTypes(); | |
| defaultownerid = session.getAdminService().getEventContext().userId; | |
| % Load existing file annotations | |
| metadataService = session.getMetadataService(); | |
| ids = toJavaList([], 'java.lang.Long'); | |
| include = toJavaList(getLCCBOmeroNamespace, 'java.lang.String'); | |
| exclude = toJavaList([], 'java.lang.String'); |
sbesson
/ stacktrace
Created
November 3, 2014 16:40
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| 2014-11-03 16:09:55,084 INFO [ ome.services.util.ServiceHandler] (rver-11233) Rslt: (ome.model.core.PlaneInfo:Id_1003590, ome.model.core.PlaneInfo:Id_1003591, ome.model.core.PlaneInfo:Id_1003592, ... 56 more) | |
| 2014-11-03 16:09:57,268 INFO [ ome.services.util.ServiceHandler] (rver-11240) Meth: interface ome.api.StatefulServiceInterface.close | |
| 2014-11-03 16:09:57,268 INFO [ ome.services.util.ServiceHandler] (rver-11240) Args: () | |
| 2014-11-03 16:09:57,296 DEBUG [ loci.formats.Memoizer] (rver-11240) loaded memo file: /mnt/sbsomero/OMERO.data/BioFormatsCache/mnt/sbsomero/OMERO.data/ManagedRepository/bharker_6/2014-09/24/17-20-53.453/.U2OS_GFP-EB3_mCherry-CenpA_MCAK-RNAi_.nd.bfmemo (583370 bytes) | |
| 2014-11-03 16:09:57,296 DEBUG [ loci.formats.Memoizer] (rver-11240) start[1415030997268] time[27] tag[loci.formats.Memoizer.loadMemo] | |
| 2014-11-03 16:09:57,296 DEBUG [ loci.formats.Memoizer] (rver-11240) start[1415030997268] time[28] tag[loci.format |
sbesson
/ artifactory_quick_test
Created
July 29, 2014 08:15
This minimal test was used while testing the artifactory priori to 5.0.3
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| brew install maven | |
| rm -rf ~/.m2 | |
| git clone https://github.com/ome/minimal-omero-client | |
| cd minimal-omero-client | |
| mvn -U -Pdev dependency:tree |
sbesson
/ format-import
Last active
August 29, 2015 14:04
A simple CLI script to import a series of format files corresponding to a ticket
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| #!/bin/bash | |
| set -e | |
| set -u | |
| FILE=$1 | |
| shift; | |
| # Define environement variables | |
| HOST=${HOST:-localhost} |
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| OMEXMLService = loci.formats.services.OMEXMLServiceImpl(); | |
| metadata = OMEXMLService.createOMEXMLMetadata(); | |
| metadata.createRoot(); | |
| metadata.setImageID('Image:0', 0); | |
| metadata.setPixelsID('Pixels:0', 0); | |
| modlo = loci.formats.CoreMetadata(); | |
| modlo.moduloT.type = loci.formats.FormatTools.LIFETIME; | |
| modlo.moduloT.unit = 'ps'; | |
| modlo.moduloT.typeDescription = 'Gated'; |
sbesson
/ CLI err usages
Last active
August 29, 2015 14:03
List all usages of self.ctx.err() across the CLI plugins
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| admin.py: self.ctx.err("No descriptor given. Using %s" SB: OK no login | |
| admin.py: self.ctx.err('Calling "stop" on remaining components') SB: OK no login | |
| admin.py: self.ctx.err("Server not running") SB: OK no login | |
| admin.py: self.ctx.err("not found") SB: OK no login | |
| admin.py: self.ctx.err("error:%s" % e) SB: OK no login | |
| admin.py: self.ctx.err(io2[1].strip()) SB: OK no login | |
| admin.py: self.ctx.err("UNKNOWN!") SB: OK no login | |
| admin.py: self.ctx.err(io2[1].strip()) SB: OK no login | |
| admin.py: self.ctx.err("Not found") SB: OK no login | |
| admin.py: self.ctx.err("Not found") SB: OK no login |