Administration Backend

 

 

 

Command line Interface (BASH)

 

You need a PATH to <path-to-nora>/src/node

Call nora

And some more intro to project jsons …..

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

--del (-d) [file] ...           

      deletes list files

--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)] [filepattern]   

           returns files matching filepattern, if --json is given, files are return as json filepattern  

--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  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