{
"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 \"patientCode\" : \"1021_19\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1020,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1021_19-VISIT_2_adoma_731.nrrd\",\\n \"version\" : 731,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1021/19\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1021/19.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1021_19\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1021,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1021_19-VISIT_3_adoma_733.nrrd\",\\n \"version\" : 733,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 3.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1021/19.3.0000.1037\",\\n \"ParticipantId\" : \"1021/19\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_3\",\\n \"patientCode\" : \"1021_19\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1022,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_102_20-VISIT_1_adoma_720.nrrd\",\\n \"version\" : 720,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.102/20.1.0000.1037\",\\n \"ParticipantId\" : \"102/20\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"102_20\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1023,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_102_20-VISIT_2_adoma_721.nrrd\",\\n \"version\" : 721,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.102/20.2.0000.1037\",\\n \"ParticipantId\" : \"102/20\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"102_20\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1024,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_102_20-VISIT_3_adoma_724.nrrd\",\\n \"version\" : 724,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 3.0000,\\n \"ParticipantId\" : \"102/20\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.102/20.3.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_3\",\\n \"patientCode\" : \"102_20\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1025,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1035_18-VISIT_1_adoma_1035.nrrd\",\\n \"version\" : 1035,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"ParticipantId\" : \"1035/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1035/18.1.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1035_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1026,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1035_18-VISIT_2_adoma_1037.nrrd\",\\n \"version\" : 1037,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1035/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1035/18.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1035_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1027,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1035_18-VISIT_3_adoma_1038.nrrd\",\\n \"version\" : 1038,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 3.0000,\\n \"ParticipantId\" : \"1035/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1035/18.3.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_3\",\\n \"patientCode\" : \"1035_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1028,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1041_18-VISIT_1_adoma_1007.nrrd\",\\n \"version\" : 1007,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"ParticipantId\" : \"1041/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1041/18.1.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1041_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1029,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1041_18-VISIT_2_adoma_1008.nrrd\",\\n \"version\" : 1008,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1041/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1041/18.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1041_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1030,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1057_18-VISIT_1_adoma_1044.nrrd\",\\n \"version\" : 1044,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1057/18.1.0000.1037\",\\n \"ParticipantId\" : \"1057/18\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1057_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1031,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1057_18-VISIT_2_adoma_527.nrrd\",\\n \"version\" : 527,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1057/18\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1057/18.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1057_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1032,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_1_kzevnik_204.nrrd\",\\n \"version\" : 204,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.1.0000.1026\",\\n \"ParticipantId\" : \"1076/16\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1033,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_1_adoma_1045.nrrd\",\\n \"version\" : 1045,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.1.0000.1037\",\\n \"ParticipantId\" : \"1076/16\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1034,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_2_kzevnik_205.nrrd\",\\n \"version\" : 205,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1076/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.2.0000.1026\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1035,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_2_adoma_198.nrrd\",\\n \"version\" : 198,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1076/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1036,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_3_kzevnik_206.nrrd\",\\n \"version\" : 206,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 3.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.3.0000.1026\",\\n \"ParticipantId\" : \"1076/16\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_3\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1037,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1076_16-VISIT_3_adoma_199.nrrd\",\\n \"version\" : 199,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 3.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1076/16.3.0000.1037\",\\n \"ParticipantId\" : \"1076/16\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_3\",\\n \"patientCode\" : \"1076_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1038,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_13-VISIT_1_kzevnik_246.nrrd\",\\n \"version\" : 246,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/13.1.0000.1026\",\\n \"ParticipantId\" : \"1108/13\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1108_13\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1039,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_13-VISIT_1_adoma_72.nrrd\",\\n \"version\" : 72,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/13.1.0000.1037\",\\n \"ParticipantId\" : \"1108/13\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1108_13\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1040,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_13-VISIT_2_kzevnik_248.nrrd\",\\n \"version\" : 248,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/13.2.0000.1026\",\\n \"ParticipantId\" : \"1108/13\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1108_13\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1041,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_13-VISIT_2_adoma_73.nrrd\",\\n \"version\" : 73,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/13.2.0000.1037\",\\n \"ParticipantId\" : \"1108/13\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1108_13\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1042,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_18-VISIT_1_adoma_1046.nrrd\",\\n \"version\" : 1046,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/18.1.0000.1037\",\\n \"ParticipantId\" : \"1108/18\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1108_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1043,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1108_18-VISIT_2_adoma_737.nrrd\",\\n \"version\" : 737,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1108/18.2.0000.1037\",\\n \"ParticipantId\" : \"1108/18\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1108_18\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1044,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1143_16-VISIT_1_kzevnik_263.nrrd\",\\n \"version\" : 263,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"ParticipantId\" : \"1143/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1143/16.1.0000.1026\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1143_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1045,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1143_16-VISIT_1_adoma_252.nrrd\",\\n \"version\" : 252,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"ParticipantId\" : \"1143/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1143/16.1.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1143_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1046,\\n \"comments\" : null,\\n \"CreatedBy\" : 1003,\\n \"User\" : 1026,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1143_16-VISIT_2_kzevnik_265.nrrd\",\\n \"version\" : 265,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1143/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1143/16.2.0000.1026\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1143_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1047,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1143_16-VISIT_2_adoma_253.nrrd\",\\n \"version\" : 253,\\n \"SequenceNum\" : 2.0000,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"ParticipantId\" : \"1143/16\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1143/16.2.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"1143_16\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1048,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1175_20-VISIT_1_adoma_1047.nrrd\",\\n \"version\" : 1047,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"ParticipantId\" : \"1175/20\",\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1175/20.1.0000.1037\",\\n \"sourcelsid\" : null,\\n \"visitCode\" : \"VISIT_1\",\\n \"patientCode\" : \"1175_20\"\\n }, {\\n \"date\" : null,\\n \"dsrowid\" : 1049,\\n \"comments\" : null,\\n \"User\" : 1037,\\n \"CreatedBy\" : 1003,\\n \"QCState\" : null,\\n \"latestFile\" : \"Segmentation_1302_16-VISIT_1_adoma_1050.nrrd\",\\n \"version\" : 1050,\\n \"Created\" : \"2023/11/13 17:20:22\",\\n \"SequenceNum\" : 1.0000,\\n \"lsid\" : \"urn:lsid:labkey.com:Study.Data-38:5005.1302/16.1.0000.1037\",\\n \"ParticipantId\" : \"1302/16\",\\n \"sourcelsid\" : 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: null,\\n \"visitCode\" : \"VISIT_2\",\\n \"patientCode\" : \"951_19\"\\n } ],\\n \"command\" : \"insert\"\\n}'\n"
]
}
],
"source": [
"def copyImagingDataset(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='Imaging1'\n",
" #target, will be overwritten\n",
" targetProject='limfomiPET/Study'\n",
" targetQuery='Imaging1'\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",
" 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)"
]
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