{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "### Requirements\n", "\n", "- Installed git. More on how to use and install git can be found [here][git]. \n", "- A zip of the certificate. Particularly, you'll need the crt and key files.\n", "- A labkey access configuration file. A sample for [linux][linuxConfig] or [Windows][windowsConfig]. The file paths point to locations of extracted files from certificate zip on your disk.\n", "\n", "[git]: https://git-scm.com/\n", "[linuxConfig]: https://git0.fmf.uni-lj.si/studen/labkeyInterface/src/master/network-config-sample.json\n", "[windowsConfig]: https://git0.fmf.uni-lj.si/studen/labkeyInterface/src/master/network-config-sample.json" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json\n", "{'labkeyInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'irAEMM': {'url': 'https://git0.fmf.uni-lj.si/studen/iraemm/archive/master.zip', 'branch': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}}\n" ] } ], "source": [ "#load required libraries\n", "import sys\n", "import os\n", "import SimpleITK\n", "import numpy\n", "import matplotlib.pyplot\n", "import chardet\n", "import json\n", "\n", "#you should get nixSuite via git clone https://git0.fmf.uni-lj.si/studen/nixSuite.git\n", "#if you don't put it to $HOME/software/src/, you should update the path\n", "nixSuite=os.path.join(os.path.expanduser('~'),'software','src','nixSuite')\n", "sys.path.append(os.path.join(nixSuite,'wrapper'))\n", "import nixWrapper\n", "nixWrapper.loadLibrary('labkeyInterface')\n", "import labkeyInterface\n", "import labkeyDatabaseBrowser\n", "import labkeyFileBrowser\n", "\n" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Using: /home/studen/.labkey/astuden/astuden.crt\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n", " warnings.warn(\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "User: andrej studen CSRF: 9fb759d8ff7e7b2cf2e6b9ea13388e0c\n" ] }, { "data": { "text/plain": [ "'9fb759d8ff7e7b2cf2e6b9ea13388e0c'" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#check connectivity. This checks the configuration in $HOME/.labkey/network.json, \n", "#where paths to certificates are stored\n", "net=labkeyInterface.labkeyInterface()\n", "fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')\n", "net.init(fconfig)\n", "#this reports the certificate used\n", "print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n", "#This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n", "net.getCSRF()" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n", " warnings.warn(\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "{'ParticipantId': 'VUB_P0011', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0011', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0011//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0011', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0011//Segmentation_1.nrrd', 'CTimage': 'VUB_P0011_CT.nrrd', 'segmentation': 'VUB_P0011_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0012', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0012', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0012//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0012', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0012//Segmentation_1.nrrd', 'CTimage': 'VUB_P0012_CT.nrrd', 'segmentation': 'VUB_P0012_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0013', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0013', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0013//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0013', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0013//Segmentation_1.nrrd', 'CTimage': 'VUB_P0013_CT.nrrd', 'segmentation': 'VUB_P0013_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0014', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0014', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0014//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0014', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0014//Segmentation_1.nrrd', 'CTimage': 'VUB_P0014_CT.nrrd', 'segmentation': 'VUB_P0014_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0015', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0015', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0015//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0015', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0015//Segmentation_1.nrrd', 'CTimage': 'VUB_P0015_CT.nrrd', 'segmentation': 'VUB_P0015_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0016', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0016', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0016//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0016', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0016//Segmentation_1.nrrd', 'CTimage': 'VUB_P0016_CT.nrrd', 'segmentation': 'VUB_P0016_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0017', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0017', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0017//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0017', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0017//Segmentation_1.nrrd', 'CTimage': 'VUB_P0017_CT.nrrd', 'segmentation': 'VUB_P0017_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0018', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0018', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0018//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0018', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0018//Segmentation_1.nrrd', 'CTimage': 'VUB_P0018_CT.nrrd', 'segmentation': 'VUB_P0018_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0019', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0019', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0019//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0019', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0019//Segmentation_1.nrrd', 'CTimage': 'VUB_P0019_CT.nrrd', 'segmentation': 'VUB_P0019_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P002', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P002', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P002//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P002', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P002//Segmentation_1.nrrd', 'CTimage': 'VUB_P002_CT.nrrd', 'segmentation': 'VUB_P002_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0020', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0020', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0020//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0020', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0020//Segmentation_1.nrrd', 'CTimage': 'VUB_P0020_CT.nrrd', 'segmentation': 'VUB_P0020_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0021', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0021', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0021//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0021', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0021//Segmentation_1.nrrd', 'CTimage': 'VUB_P0021_CT.nrrd', 'segmentation': 'VUB_P0021_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0022', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0022', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0022//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0022', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0022//Segmentation_1.nrrd', 'CTimage': 'VUB_P0022_CT.nrrd', 'segmentation': 'VUB_P0022_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0023', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0023', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0023//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0023', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0023//Segmentation_1.nrrd', 'CTimage': 'VUB_P0023_CT.nrrd', 'segmentation': 'VUB_P0023_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0024', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0024', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0024//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0024', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0024//Segmentation_1.nrrd', 'CTimage': 'VUB_P0024_CT.nrrd', 'segmentation': 'VUB_P0024_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0025', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0025', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0025//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0025', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0025//Segmentation_1.nrrd', 'CTimage': 'VUB_P0025_CT.nrrd', 'segmentation': 'VUB_P0025_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0026', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0026', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0026//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0026', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0026//Segmentation_1.nrrd', 'CTimage': 'VUB_P0026_CT.nrrd', 'segmentation': 'VUB_P0026_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0028', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0028', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0028//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0028', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0028//Segmentation_1.nrrd', 'CTimage': 'VUB_P0028_CT.nrrd', 'segmentation': 'VUB_P0028_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0029', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0029', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0029//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0029', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0029//Segmentation_1.nrrd', 'CTimage': 'VUB_P0029_CT.nrrd', 'segmentation': 'VUB_P0029_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P003', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P003', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P003//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P003', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P003//Segmentation_1.nrrd', 'CTimage': 'VUB_P003_CT.nrrd', 'segmentation': 'VUB_P003_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0030', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0030', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0030//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0030', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0030//Segmentation_1.nrrd', 'CTimage': 'VUB_P0030_CT.nrrd', 'segmentation': 'VUB_P0030_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0031', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0031', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0031//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0031', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0031//Segmentation_1.nrrd', 'CTimage': 'VUB_P0031_CT.nrrd', 'segmentation': 'VUB_P0031_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0032', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0032', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0032//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0032', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0032//Segmentation_1.nrrd', 'CTimage': 'VUB_P0032_CT.nrrd', 'segmentation': 'VUB_P0032_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0033', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0033', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0033//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0033', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0033//Segmentation_1.nrrd', 'CTimage': 'VUB_P0033_CT.nrrd', 'segmentation': 'VUB_P0033_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0034', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0034', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0034//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0034', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0034//Segmentation_1.nrrd', 'CTimage': 'VUB_P0034_CT.nrrd', 'segmentation': 'VUB_P0034_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0035', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0035', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0035//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0035', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0035//Segmentation_1.nrrd', 'CTimage': 'VUB_P0035_CT.nrrd', 'segmentation': 'VUB_P0035_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0036', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0036', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0036//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0036', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0036//Segmentation_1.nrrd', 'CTimage': 'VUB_P0036_CT.nrrd', 'segmentation': 'VUB_P0036_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0037', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0037', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0037//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0037', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0037//Segmentation_1.nrrd', 'CTimage': 'VUB_P0037_CT.nrrd', 'segmentation': 'VUB_P0037_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0038', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0038', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0038//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0038', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0038//Segmentation_1.nrrd', 'CTimage': 'VUB_P0038_CT.nrrd', 'segmentation': 'VUB_P0038_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0039', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0039', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0039//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0039', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0039//Segmentation_1.nrrd', 'CTimage': 'VUB_P0039_CT.nrrd', 'segmentation': 'VUB_P0039_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P004', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P004', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P004//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P004', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P004//Segmentation_1.nrrd', 'CTimage': 'VUB_P004_CT.nrrd', 'segmentation': 'VUB_P004_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0040', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0040', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0040//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0040', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0040//Segmentation_1.nrrd', 'CTimage': 'VUB_P0040_CT.nrrd', 'segmentation': 'VUB_P0040_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0041', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0041', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0041//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0041', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0041//Segmentation_1.nrrd', 'CTimage': 'VUB_P0041_CT.nrrd', 'segmentation': 'VUB_P0041_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0042', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0042', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0042//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0042', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0042//Segmentation_1.nrrd', 'CTimage': 'VUB_P0042_CT.nrrd', 'segmentation': 'VUB_P0042_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0043', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0043', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0043//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0043', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0043//Segmentation_1.nrrd', 'CTimage': 'VUB_P0043_CT.nrrd', 'segmentation': 'VUB_P0043_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0044', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0044', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0044//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0044', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0044//Segmentation_1.nrrd', 'CTimage': 'VUB_P0044_CT.nrrd', 'segmentation': 'VUB_P0044_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0045', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0045', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0045//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0045', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0045//Segmentation_1.nrrd', 'CTimage': 'VUB_P0045_CT.nrrd', 'segmentation': 'VUB_P0045_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0046', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0046', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0046//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0046', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0046//Segmentation_1.nrrd', 'CTimage': 'VUB_P0046_CT.nrrd', 'segmentation': 'VUB_P0046_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0047', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0047', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0047//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0047', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0047//Segmentation_1.nrrd', 'CTimage': 'VUB_P0047_CT.nrrd', 'segmentation': 'VUB_P0047_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0048', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0048', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0048//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0048', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0048//Segmentation_1.nrrd', 'CTimage': 'VUB_P0048_CT.nrrd', 'segmentation': 'VUB_P0048_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0049', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0049', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0049//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0049', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0049//Segmentation_1.nrrd', 'CTimage': 'VUB_P0049_CT.nrrd', 'segmentation': 'VUB_P0049_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P0050', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P0050', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0050//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P0050', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P0050//Segmentation_1.nrrd', 'CTimage': 'VUB_P0050_CT.nrrd', 'segmentation': 'VUB_P0050_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P006', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P006', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P006//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P006', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P006//Segmentation_1.nrrd', 'CTimage': 'VUB_P006_CT.nrrd', 'segmentation': 'VUB_P006_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P007', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P007', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P007//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P007', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P007//Segmentation_1.nrrd', 'CTimage': 'VUB_P007_CT.nrrd', 'segmentation': 'VUB_P007_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P008', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P008', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P008//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P008', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P008//Segmentation_1.nrrd', 'CTimage': 'VUB_P008_CT.nrrd', 'segmentation': 'VUB_P008_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_P009', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_P009', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P009//CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_P009', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_P009//Segmentation_1.nrrd', 'CTimage': 'VUB_P009_CT.nrrd', 'segmentation': 'VUB_P009_Aorta.nrrd', 'visitCode': None, 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_PA1', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_PA1', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_PA1/Visit_0/CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_PA1', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_PA1/Visit_0/Segmentation_1.nrrd', 'CTimage': 'VUB_P001_CT.nrrd', 'segmentation': 'VUB_P001_Aorta.nrrd', 'visitCode': 'Visit_0', 'SequenceNum': -1.0}\n", "{'ParticipantId': 'VUB_PA10', 'lsid': 'urn:lsid:ijs.si:Study.Data-151:5001.VUB_PA10', '_labkeyurl_CTimage': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_PA10/Visit_0/CTimage.nrrd', '_labkeyurl_ParticipantId': '/labkey/EUtopia/Study/study-participant.view?participantId=VUB_PA10', '_labkeyurl_segmentation': 'https://merlin.fmf.uni-lj.si/labkey/_webdav/EUtopia/Study/%40files/images/VUB_PA10/Visit_0/Segmentation_1.nrrd', 'CTimage': 'VUB_P0010_CT.nrrd', 'segmentation': 'VUB_P0010_Aorta.nrrd', 'visitCode': 'Visit_0', 'SequenceNum': -1.0}\n" ] } ], "source": [ "db=labkeyDatabaseBrowser.labkeyDB(net)\n", "fb=labkeyFileBrowser.labkeyFileBrowser(net)\n", "#select a project\n", "project='EUtopia/Study'\n", "dataset='Imaging'\n", "idFilter={'variable':'ParticipantId','value':'VUB_PA1','oper':'eq'}\n", "#empty filter\n", "qFilter=[]\n", "#qFilter can be a list of filters used in conjugation (logical AND)\n", "#qFilter=[idFilter]\n", "ds=db.selectRows(project,'study',dataset,qFilter)\n", "rows=ds['rows']\n", "for row in rows:\n", " #row as a dictionary\n", " print(row)\n", " #update row\n", " #depending on field type adjust newValue\n", " row['field']='newValue'\n", " #print the new row\n", " print(row)\n", " #change the value of the field in database \n", " #if field is not in database, it will NOT be added and no changes will occur\n", " #db.modifyRows('update',project,'study',dataset,[row]) \n", " " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.10" } }, "nbformat": 4, "nbformat_minor": 4 }