| #!/usr/bin/env python | |
| from argparse import ( | |
| ArgumentParser, | |
| FileType, | |
| ) | |
| from collections import ( | |
| defaultdict, | |
| ) | |
| from datetime import ( |
| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| import omero.scripts as scripts | |
| client = scripts.client( | |
| 'Register_in_iRODS.py', | |
| scripts.Long("Image_ID", optional=False), | |
| scripts.String("Logical_Path", optional=False), |
| from pyshacl import validate | |
| from rdflib import Graph | |
| import pytest | |
| import json | |
| def assert_graph(shacl, graph, valid=True): | |
| s = Graph().parse(data=shacl, format="turtle") | |
| d = Graph().parse(data=graph, format="json-ld") |
| #!/usr/bin/env python | |
| """ | |
| <Image ID="Image:0" Name="image_0000247585 (R0)"> | |
| <AcquisitionDate>2020-01-15T06:29:11.537</AcquisitionDate> | |
| <Description>Collection ImageCollection__0000042467</Description> | |
| <InstrumentRef ID="Instrument:0"/> | |
| <ObjectiveSettings ID="Objective:0:0"/> | |
| <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="16.438446163366336" PhysicalSizeXUnit="µm" PhysicalSizeY="16.438446015424162" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="3" SizeT="1" SizeX="1616" SizeY="4668" SizeZ="1" Type="uint8"> | |
| <Channel ID="Channel:0:0" IlluminationType="Transmitted" SamplesPerPixel="3"> |
| docker run -ti --rm --entrypoint=python -v $PWD:/dropbox openmicroscopy/omero-server /dropbox/test.py |
| FROM ubuntu:16.04 | |
| RUN apt-get update && apt-get install -y locales && rm -rf /var/lib/apt/lists/* \ | |
| && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 | |
| ENV LANG en_US.utf8 | |
| env OMERO_OPT_DIR=/opt/omero | |
| RUN apt-get update |
| $ NEW_UUID=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1) | |
| $ echo $NEW_UUID | |
| rGS3QV3NpsCjT1Jei643raLebi3Io2S7 | |
| $ bin/omero -q obj new Dataset name=$NEW_UUID | |
| Dataset:1 | |
| $ bin/omero search Dataset $NEW_UUID | |
| Using session for root@localhost:4064. Idle timeout: 10 min. Current group: system | |
| # | Class | Id | name | details |
| from fileinput import input | |
| import requests | |
| # cat image ids to this script to loop over annotations | |
| # e.g.: cut -f2 image_ids.tsv | python get_idr_annotations.py | |
| def connect(): | |
| import omero | |
| from omero.gateway import BlitzGateway | |
| from omero.sys import ParametersI |
| import omero | |
| compounds = unwrap(q.projection(("select distinct mv1.value, mv2.value from Image i " | |
| "join i.annotationLinks l1 join l1.child as a1 join a1.mapValue as mv1 " | |
| "join i.annotationLinks l2 join l2.child as a2 join a2.mapValue as mv2 " | |
| "join i.wellSamples ws join ws.well w join w.plate p " | |
| "where p.id = 4403 and mv1.name = 'Product Use Annotation' and mv2.name = 'Compound Name'"), None)) |