Administration Backend
Command line Interface (BASH)
You need a PATH to <path-to-nora>/src/node
Call
nora
any get help
NORA - backend
usage: nora [--parameter] [value]
--project (-p) [name]
all preceding commands refer to this project
MANAGEMENT
--sql (-q) [sqlstatement] [--csv]
executes SQL statment and return result as json (or as csv if option is given)
--add (-a) [file] ...
adds list of files to project
option: --addtag tag1,tag2,... (tags the files)
--del (-d) [file] ...
deletes list files
--del_pat (-dp) [patient_id] [patients_id#studies_id] ...
deletes list of patients/studies
--out (-o) [filepattern]
computes absolute outputfilepath from filepattern (see description of filepattern below)
--pathout (-pa) [filepattern]
computes absolute outfilepath from filepattern
--select (-s) [--json (-j)] [--byfilename] [filepattern]
returns files matching filepattern, if --json is given, files are return as json filepattern
if --byfilename (together with --json) is given, files are restructered by filename
--addtag tag1,tag2,... -s [filepattern]
add tag to file
--rmtag tag1,tag2,... -s [filepattern]
removes tags fromfile
--launch (-l) [json]
launches batch from json description
--createproject (-c) [name] [module]
creates a project with [name] from [module] definition
--admin [parameter1] [parameter2] ...
calls the admin tools (see nora --admin for more help)
PROCESSING
--launch json
launches a NORA job given by json
options: --throwerror
--handle_job_result (emits DONE signal, when ready)
--launchfile jsonfile
same as --launch but json given by fileref
--launch_autoexec psid
launches the autoexecution pipeline of the project for the patient specified by psid
--import srcpath
imports dicoms located in sourcepath to given project
options: --autoexec_queue (if given autoexecuter is initiated, use DEFAULT to select default autoexecution queue given in config)
--handle_job_result (emits DONE signal, when ready)
--extrafiles_filter: if there are non-dicom files in your dicomfolder and you
want to add them to your patient folder, then, give here a comma-separated list of
accepted extensions (e.g. nii,hdr,img)
--patients_id PIZ (overwrite patients_id of imported data with PIZ )
--studies_id SID (overwrite studies_id of imported data with SID )
--pattern REGEX (use REGEX applied on srcpath of dicoms to overwrite
patients_id/studies_id, example:
--pattern "(?<studies_id>[\w\-]+)\/(?<patients_id>\w+)$"
OTHER
--exportmeta [filepattern]
exports meta data as csv. Meta content from files matching [filepattern] are exported
options: --keys a comma separated list of key-sequences, which are exported [optional]
a key sequence is given by a dot-separated list, where the first key refers to the name of
the json-file (as multiple jsons might be contained in the query). A wildcard * is possible
select multiple keys at once
examples:
nora -p XYZ --exportmeta '*' 'nodeinfo.json' // gathers also patient info
nora -p XYZ --exportmeta '*' 'META/radio*.json' --keys '*.mask.volume,*.mask.diameter'
MATLAB Interface
To setup NORA for MATLAB you change to the folder
<path-to-nora>/src/matlab
at the MATLAB prompt and start DPX_startup. This sets up all necessary paths and the database connection. To test the DB connection, make a call to DPX_Project. This should list all created projects (initially only the default project). There are a variety of management commands to manage users/project/data etc. Here a list of important ones:
- General
- DPX_startup - sets up NORA
- DPX_Project - choose a project
- DPX_getCurrentProject - get the current project information
- DPX_SQL_createUser - create a user
- DPX_SQL_createProject - create a project
- File selection
- DPX_getOutputLocation - compute the path to certain output
- DPX_selectFiles - select files based on pattern
- DPX_getFileinfo - get additional file information (no database involved)
- DPX_SQL_getFileInfo - get information from database for this file
- Processing
- DPX_demon - start the processing deamon
- DPX_debug_job - execute a debug job at the MATLAB command prompt
DPX_SQL_clearGridCmds - clear all jobs from the pipeline
The Database
There is one general database scheme containing information about users, projects, jobs, settings etc.
You can see below the table schemes.
- Projects/User management
- projects
- users
- rights - who can read which project in which role
- Batch/Jobs
- gridjobs - contains submitted and running jobs (mirror of qstat or squeue)
- Commands - contains jobs submitted from web interface, but not yet submitted to resource management system.
- Miscellaneous
- json - various types of jsons (saved batches, shares, settings, states etc.)
- notifications
- error_js
