{ "cells": [ { "cell_type": "code", "execution_count": 2, "id": "ac601535-9fd5-4d01-9a13-c25931848eb8", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "loadLibrary\n", "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']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, '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': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}\n", "{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n", "File C:\\Users\\studen\\temp\\labkeyInterface.zip: True\n", "loadLibrary\n", "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']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, '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': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}\n", "{'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n", "File C:\\Users\\studen\\temp\\orthancInterface.zip: True\n" ] } ], "source": [ "import sys\n", "import os\n", "import chardet\n", "import json\n", "import re\n", "import datetime\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", "nixWrapper.loadLibrary('orthancInterface')\n", "import orthancInterface\n", "import orthancDatabaseBrowser\n", "\n", "def connectDB(server):\n", " #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','{}.json'.format(server))\n", " net.init(fconfig)\n", " #this reports the certificate used\n", " try:\n", " print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n", " except KeyError:\n", " pass\n", " #This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n", " net.getCSRF()\n", " db=labkeyDatabaseBrowser.labkeyDB(net)\n", " fb=labkeyFileBrowser.labkeyFileBrowser(net)\n", " return db,fb" ] }, { "cell_type": "code", "execution_count": 27, "id": "c1d12640-8763-4bbd-9233-7fc19580db76", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "User: andrej studen CSRF: 688ac88a10e1547ace6979d9bea15d0b\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "269_19-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "269_19-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "269_19-VISIT_2_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "269_19-VISIT_2_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "4030_18-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "4030_18-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "4830_17-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "4830_17-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "5364_18-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "5364_18-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "5364_18-VISIT_2_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "5364_18-VISIT_2_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "6198_18-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "6198_18-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "7075_17-VISIT_1_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "7075_17-VISIT_1_PET_notCropped_2mmVoxel_orig.nii.gz: True\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "7075_17-VISIT_2_CT_notCropped_2mmVoxel_orig.nii.gz: True\n", "7075_17-VISIT_2_PET_notCropped_2mmVoxel_orig.nii.gz: True\n" ] } ], "source": [ "#find mismatches and create _orig backup files\n", "def getBackupFile(r,field):\n", " return re.sub('.nii.gz','_orig.nii.gz',r[field])\n", " \n", "def getBackupURL(fb,project,r,field):\n", " newName=getBackupFile(r,field)\n", " return fb.formatPathURL(project,'/'.join(['preprocessedImages',r['patientCode'],r['visitCode'],newName]))\n", "\n", "def getLocalPath(file):\n", " tempDir=os.path.join(os.path.expanduser('~'),'temp','correctVisit')\n", " if not os.path.isdir(tempDir):\n", " os.mkdir(tempDir)\n", " return os.path.join(tempDir,file)\n", " \n", "def backupFile(fb,project,r,field):\n", " oldURL=fb.formatPathURL(project,'/'.join(['preprocessedImages',r['patientCode'],r['visitCode'],r[field]]))\n", " newName=getBackupFile(r,field)\n", " #use old visitCode, attach orig to keep a backup copy\n", " newURL=getBackupURL(fb,project,r,field)\n", " \n", " print('{}: {}'.format(newName,fb.entryExists(newURL)))\n", " if fb.entryExists(newURL):\n", " return\n", " localName=getLocalPath(newName)\n", " #rename to orig localy\n", " if not os.path.isfile(localName):\n", " fb.readFileToFile(oldURL,localName)\n", " fb.writeFileToFile(localName,newURL)\n", "\n", "def backupMismatch():\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Imaging1'\n", " ds=db.selectRows(project,'study',query,[])\n", " filesProject='limfomiPET/Study'\n", " for r in ds['rows']:\n", " tag='VISIT_{}'.format(r['imagingVisitId'])\n", " setTag=r['visitCode']\n", " if tag==setTag:\n", " continue\n", " print(f'Old tag:{setTag} target tag:{tag}')\n", " backupFile(fb,filesProject,r,'ctResampled')\n", " backupFile(fb,filesProject,r,'petResampled')\n", " \n", "backupMismatch()" ] }, { "cell_type": "code", "execution_count": 82, "id": "e026c4ad-13b1-4fee-9cbd-1bd16675d855", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "User: andrej studen CSRF: b418be9797c17524e39f3d68c9fa101d\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "269_19-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "269_19-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: e7d0de02f99e59a6423cb17b6b5f9324\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "269_19-VISIT_3_CT_notCropped_2mmVoxel.nii.gz: True\n", "269_19-VISIT_3_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: d8d0aba348ad9bd087a3267e50ed6885\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "4030_18-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "4030_18-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: c911b98e4d09c65aa6eee5b51efc7ade\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "4830_17-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "4830_17-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: 51caee6491efbbf3c8f24d620dca87f3\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "5364_18-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "5364_18-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: f6e23f7ec94124dd175ebc918ed933d7\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "5364_18-VISIT_3_CT_notCropped_2mmVoxel.nii.gz: True\n", "5364_18-VISIT_3_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: 175f811ef1747c848d0d4224af2676bd\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "6198_18-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "6198_18-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: b4379b8d769b369a9556020512196423\n", "Old tag:VISIT_1 target tag:VISIT_2\n", "7075_17-VISIT_2_CT_notCropped_2mmVoxel.nii.gz: True\n", "7075_17-VISIT_2_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: 2f593157231501b0f75f89d611d10b7e\n", "Old tag:VISIT_2 target tag:VISIT_3\n", "7075_17-VISIT_3_CT_notCropped_2mmVoxel.nii.gz: True\n", "7075_17-VISIT_3_PET_notCropped_2mmVoxel.nii.gz: True\n", "User: andrej studen CSRF: 212b03334c3acee9377c76239d9174b4\n" ] } ], "source": [ "def getTargetFile(r,field):\n", " visitId=r['imagingVisitId']\n", " newTag=f'VISIT_{visitId}'\n", " oldTag=r['visitCode']\n", " return re.sub(oldTag,newTag,r[field])\n", "\n", "def getTargetURL(fb,project,r,field):\n", " newName=getTargetFile(r,field)\n", " visitId=r['imagingVisitId']\n", " newTag=f'VISIT_{visitId}'\n", " return fb.formatPathURL(project,'/'.join(['preprocessedImages',r['patientCode'],newTag,newName]))\n", "\n", "def updateFile(fb,project,r,field,load=True):\n", " targetURL=getTargetURL(fb,project,r,field)\n", " targetName=getTargetFile(r,field)\n", " if not load:\n", " print('{}: {}'.format(targetName,fb.entryExists(targetURL)))\n", " return targetName\n", " #print('{}: {}'.format(targetName,fb.entryExists(targetURL)))\n", " #if fb.entryExists(targetURL):\n", " # return\n", " backupFile=getBackupFile(r,field)\n", " localPath=getLocalPath(backupFile)\n", " print(f'{backupFile}->{targetName}')\n", " if not os.path.isfile(localPath):\n", " backupURL=getBackupURL(fb,project,r,field)\n", " if not fb.entryExists(backupURL):\n", " print('Troubles loading {}'.format(backupFile))\n", " return\n", " fb.readFileToFile(backupURL,localPath)\n", " fb.writeFileToFile(localPath,targetURL)\n", " return targetName\n", "\n", "def updateFiles(uploadFiles=True):\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Imaging1'\n", " ds=db.selectRows(project,'study',query,[])\n", " filesProject='limfomiPET/Study'\n", " for r in ds['rows']:\n", " tag='VISIT_{}'.format(r['imagingVisitId'])\n", " setTag=r['visitCode']\n", " if tag==setTag:\n", " continue\n", " print(f'Old tag:{setTag} target tag:{tag}')\n", " r['ctResampled']=updateFile(fb,filesProject,r,'ctResampled',uploadFiles)\n", " r['petResampled']=updateFile(fb,filesProject,r,'petResampled',uploadFiles)\n", " #to separate loading of files and updating of visitCode\n", " #once visitCode is set, there is no way to find those that need updating\n", " if uploadFiles:\n", " continue\n", " r['visitCode']=tag\n", " r['SequenceNum']=r['imagingVisitId']+0.1\n", " db.modifyRows('update',project,'study',query,[r])\n", " \n", "#run with True first to upload files, for checking, uploadFiles can be set to false\n", "#it will still report whether expected files are available\n", "updateFiles(uploadFiles=False)" ] }, { "cell_type": "code", "execution_count": 81, "id": "106a8d34-4a79-411a-9c0f-7f2c03f536ea", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "User: andrej studen CSRF: 3af4741467fbfa9e1920f6f94b0c6b64\n", "User: andrej studen CSRF: 192b731fada4836e8692055f7c838d4f\n", "User: andrej studen CSRF: 692190100a43954dabf64c995b3d230a\n", "User: andrej studen CSRF: 03f50115622cc8d00d7019a2ac5e9e00\n", "User: andrej studen CSRF: 367d258a4c514100e1e97ca9264b7e5b\n", "User: andrej studen CSRF: 43e022d6410efb4d39c576adf5043e44\n", "User: andrej studen CSRF: 525a2b87e9518a64af154d41e0f32d6a\n", "User: andrej studen CSRF: 902e9b92bac560e47360781cf8da3569\n", "User: andrej studen CSRF: cf79754661e8f7fe01ca999d62bc550f\n" ] } ], "source": [ "def copySegmentation():\n", " #copy via list archive, this just compares\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='segmentationList'\n", " ds=db.selectRows(project,'lists',query,[])\n", " rows=ds['rows']\n", " keys=set([r['Key'] for r in rows])\n", " \n", " project='limfomiPET/Study'\n", " ds=db.selectRows(project,'lists',query,[])\n", " rows=ds['rows']\n", " keys1=set([r['Key'] for r in rows])\n", " print('Study-Study2023: {}'.format(keys1-keys))\n", " print('Study2023-Study: {}'.format(keys-keys1))\n", "\n", "def getBackup(file):\n", " return re.sub('.nrrd','_orig.nrrd',file)\n", " \n", "def updateTag(segFile,oldRow,newRow):\n", " oldTag=oldRow['visitCode']\n", " newTag=newRow['visitCode']\n", " return re.sub(oldTag,newTag,segFile)\n", "\n", "def getSegFileURL(fb,project,r,file):\n", " return fb.formatPathURL(project,'/'.join(['preprocessedImages',r['patientCode'],r['visitCode'],'Segmentations',file]))\n", "\n", "def backupSegmentation(fb,project,r):\n", " segFile=r['segmentation']\n", " segURL=getSegFileURL(fb,project,r,segFile)\n", " segFileBackup=getBackup(segFile)\n", " segBackupURL=getSegFileURL(fb,project,r,segFileBackup)\n", " print('{}: {}'.format(segFileBackup,fb.entryExists(segBackupURL)))\n", " if fb.entryExists(segBackupURL):\n", " return\n", " localFile=getLocalPath(segFileBackup)\n", " if not os.path.isfile(localFile):\n", " fb.readFileToFile(segURL,localFile)\n", " fb.writeFileToFile(localFile,segBackupURL)\n", " \n", "\n", "def backupSegmentations():\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Imaging1'\n", " ds=db.selectRows(project,'study',query,[])\n", " rows=ds['rows']\n", " projectFiles='limfomiPET/Study'\n", " for r in rows:\n", " targetTag='VISIT_{}'.format(r['imagingVisitId'])\n", " setTag=r['visitCode']\n", " if targetTag==setTag:\n", " continue\n", " qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in ['patientCode','visitCode']]\n", " ds=db.selectRows(project,'lists','segmentationList',qFilter)\n", " for r1 in ds['rows']:\n", " oldTag=r1['visitCode']\n", " print(f'{oldTag}->{targetTag}')\n", " backupSegmentation(fb,projectFiles,r1)\n", "\n", "def uploadSegmentation(fb,project,oldRow,newRow):\n", " targetFile=updateTag(oldRow['segmentation'],oldRow,newRow)\n", " targetURL=getSegFileURL(fb,project,newRow,targetFile)\n", " print('{}: {}'.format(targetFile,fb.entryExists(targetURL)))\n", " if fb.entryExists(targetURL):\n", " return targetFile\n", " backupFile=getBackup(oldRow['segmentation'])\n", " print(f'{backupFile}->{targetFile}')\n", " localFile=getLocalPath(backupFile)\n", " if not os.path.isfile(localFile):\n", " backupURL=getSegFileURL(fb,project,oldRow,backupFile)\n", " if not fb.entryExists(backupURL):\n", " print(f'Failed to load {backupFile}')\n", " return targetFile\n", " fb.readFileToFile(backupURL,localFile)\n", " fb.writeFileToFile(localFile,targetURL)\n", " return targetFile\n", " \n", " \n", "def updateSegmentations():\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Imaging1'\n", " ds=db.selectRows(project,'study',query,[])\n", " rows=ds['rows']\n", " projectFiles='limfomiPET/Study'\n", " managedRows=[]\n", " for r in rows:\n", " targetTag='VISIT_{}'.format(r['imagingVisitId'])\n", " setTag=r['visitCode']\n", " if targetTag==setTag:\n", " continue\n", " code=r['patientCode']\n", " #print(f'{code} {setTag}->{targetTag}')\n", " qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in ['patientCode','visitCode']]\n", " ds=db.selectRows(project,'lists','segmentationList',qFilter)\n", " for r1 in ds['rows']:\n", " r1['targetTag']=targetTag\n", " managedRows.append(r1)\n", " \n", " for r in managedRows:\n", " oldRow={x:r[x] for x in r}\n", " newRow={x:r[x] for x in r}\n", " newRow['visitCode']=r['targetTag']\n", " oldTag=oldRow['visitCode']\n", " targetTag=r['targetTag']\n", " code=r['patientCode']\n", " print(f'{code} {oldTag}->{targetTag}')\n", " #newRow['segmentation']=uploadSegmentation(fb,projectFiles,oldRow,newRow)\n", " #print(newRow['segmentation'])\n", " #db.modifyRows('update',project,'lists','segmentationList',[newRow])\n", "\n", "\n", " \n", "#updateSegmentations()\n", "#dataset\n", "def copySegmentationDataset():\n", " #copy via list archive, this just compares\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Segmentations'\n", " ds=db.selectRows(project,'study',query,[])\n", " rows=ds['rows']\n", " db.modifyRows('delete',project,'study',query,rows)\n", " #copy from Study\n", " project='limfomiPET/Study'\n", " ds=db.selectRows(project,'study',query,[])\n", " rows=ds['rows']\n", " #insert to Study2023\n", " project='limfomiPET/Study2023'\n", " db.modifyRows('insert',project,'study',query,rows)\n", " \n", "\n", "def updateSegmentationDataset():\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Imaging1'\n", " ds=db.selectRows(project,'study',query,[])\n", " rows=ds['rows']\n", " projectFiles='limfomiPET/Study'\n", " managedRows=[]\n", " for r in rows:\n", " targetTag='VISIT_{}'.format(r['imagingVisitId'])\n", " setTag=r['visitCode']\n", " if targetTag==setTag:\n", " continue\n", " qFilter=[{'variable':x,'value':'{}'.format(r[x]),'oper':'eq'} for x in ['patientCode','SequenceNum']]\n", " ds=db.selectRows(project,'study','Segmentations',qFilter)\n", " n=len(ds['rows'])\n", " if n!=1:\n", " print('{}/{} Got {} rows'.format(r['patientCode'],setTag,n))\n", " continue\n", " qr=ds['rows'][0]\n", " lf=qr['latestFile']\n", " qr['latestFile']=re.sub(setTag,targetTag,lf)\n", " qr['visitCode']=targetTag\n", " qr['SequenceNum']=r['imagingVisitId']+0.1\n", " db.modifyRows('update',project,'study','Segmentations',[qr])\n", " print('seq {} code {} file {}'.format(qr['SequenceNum'],qr['visitCode'],qr['latestFile']))\n", "\n", "def resetSeqNum():\n", " db,fb=connectDB('onko-nix')\n", " project='limfomiPET/Study2023'\n", " query='Segmentations'\n", " ds=db.selectRows(project,'study',query,[])\n", " for r in ds['rows']:\n", " qi=int(re.sub('VISIT_','',r['visitCode']))\n", " sn=r['SequenceNum']\n", " if sn-qi==0:\n", " continue\n", " r['SequenceNum']=qi\n", " db.modifyRows('update',project,'study',query,[r])\n", "\n", "resetSeqNum()\n", "#copySegmentationDataset()\n", "#updateSegmentationDataset() \n", " " ] }, { "cell_type": "code", "execution_count": 22, "id": "e4c38ad6-e2fc-40b7-8550-ca1f6159adf8", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "User: andrej studen CSRF: c2bb4caaf782b55c8a7d7e7df615be42\n", "Deleting 462 rows\n", "User: andrej studen CSRF: dc188211786072440bac29b4a4d16f66\n", "Inserting 462 rows\n", "User: andrej studen CSRF: 5a1694a6e4a525d788240ad2d3df2985\n", "b'{\\n \"rowsAffected\" : 462,\\n \"queryName\" : \"Segmentations\",\\n \"schemaName\" : \"study\",\\n \"containerPath\" : \"/limfomiPET/Study\",\\n \"rows\" : [ {\\n \"date\" : null,\\n \"dsrowid\" : 1019,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1021_19-VISIT_1_adoma_730.nrrd\",\\n \"version\" : 730,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1021/19.1.0000.1037\",\\n \"ParticipantId\" : \"1021/19\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n 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db.modifyRows('delete',targetProject,'study',targetQuery,rows)\n", " #copy from Study\n", " ds=db.selectRows(sourceProject,'study',sourceQuery,[])\n", " rows=ds['rows']\n", " print('Inserting {} rows'.format(len(rows)))\n", " if modify:\n", " db.modifyRows('insert',targetProject,'study',targetQuery,rows)\n", " \n", " \n", "def copySegmentationDataset(modify=False):\n", " #copy via list archive, this just compares\n", " db,fb=connectDB('onko-nix')\n", " #source, readonly\n", " sourceProject='limfomiPET/Study2023'\n", " sourceQuery='Segmentations'\n", " #target, will be overwritten\n", " targetProject='limfomiPET/Study'\n", " targetQuery='Segmentations' \n", " ds=db.selectRows(targetProject,'study',targetQuery,[])\n", " rows=ds['rows']\n", " print('Deleting {} rows'.format(len(rows)))\n", " if modify:\n", " db.modifyRows('delete',targetProject,'study',targetQuery,rows)\n", " #copy from Study\n", " ds=db.selectRows(sourceProject,'study',sourceQuery,[])\n", " rows=ds['rows']\n", " print('Inserting {} rows'.format(len(rows)))\n", " if modify:\n", " print(db.modifyRows('insert',targetProject,'study',targetQuery,rows))\n", " \n", "def copySegmentationList(modify=False):\n", " #copy via list archive, this just compares\n", " db,fb=connectDB('onko-nix')\n", " #source, readonly\n", " sourceProject='limfomiPET/Study2023'\n", " sourceQuery='segmentationList'\n", " #target, will be overwritten\n", " targetProject='limfomiPET/Study'\n", " targetQuery='segmentationList' \n", " ds=db.selectRows(targetProject,'lists',targetQuery,[])\n", " rows=ds['rows']\n", " print('Deleting {} rows'.format(len(rows)))\n", " if modify:\n", " db.modifyRows('delete',targetProject,'lists',targetQuery,rows)\n", " #copy from Study\n", " ds=db.selectRows(sourceProject,'lists',sourceQuery,[])\n", " rows=ds['rows']\n", " print('Inserting {} rows'.format(len(rows)))\n", " if modify:\n", " print(db.modifyRows('insert',targetProject,'lists',targetQuery,rows))\n", "\n", "#copyImagingDataset()\n", "copySegmentationDataset(modify=True)\n", "#copySegmentationList(modify=True)" ] }, { "cell_type": "code", "execution_count": null, "id": "d6ae9fbf-4d17-4eed-8206-b2927693116c", "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": "3.9.0" } }, "nbformat": 4, "nbformat_minor": 5 }