All modules in NiDB system are run from the nidb command line program. Modules are automated by being started from cron.
nidb can be run manually to test modules and get debugging information. It can also be used when running on a cluster to insert results back into the database. Running nidb without command line parameters will display the usage.
> ./nidb
Neuroinformatics Database (NiDB)
Options:
-h, --help Displays help on commandline options.
--help-all Displays help including Qt specific options.
-v, --version Displays version information.
-d, --debug Enable debugging
-q, --quiet Dont print headers and checks
-r, --reset Reset, and then run, the specified module
-u, --submodule <submodule> For running on cluster. Sub-modules [
resultinsert, pipelinecheckin, updateanalysis,
checkcompleteanalysis ]
-a, --analysisid <analysisid> resultinsert -or- pipelinecheckin submodules
only
-s, --status <status> pipelinecheckin submodule
-m, --message <message> pipelinecheckin submodule
-c, --command <command> pipelinecheckin submodule
-t, --text <text> Insert text result (resultinsert submodule)
-n, --number <number> Insert numerical result (resultinsert
submodule)
-f, --file <filepath> Insert file result (resultinsert submodule)
-i, --image <imagepath> Insert image result (resultinsert submodule)
-e, --desc <desc> Result description (resultinsert submodule)
--unit <unit> Result unit (resultinsert submodule)
Arguments:
module Available modules: import export fileio
mriqa qc modulemanager importuploaded
upload pipeline cluster minipipeline backup
For example, to run the import module, run as the nidb user
./nidb import
This will output
-------------------------------------------------------------
----- Starting Neuroinformatics Database (NiDB) backend -----
-------------------------------------------------------------
Loading config file /nidb/nidb.cfg [Ok]
Connecting to database [Ok]
NiDB version 2023.2.942
Build date [Feb 10 2023 11:22:26]
C++ [201703]
Qt compiled [6.4.2]
Qt runtime [6.4.2]
Build system [x86_64-little_endian-lp64]
Found [0] lockfiles for module [import]
Creating lock file [/nidb/lock/import.441787] [Ok]
Creating log file [/nidb/logs/import20230428113035.log] [Ok]
Checking module into database [Ok]
.Deleting log file [/nidb/logs/import20230428113035.log] [Ok]
Module checked out of database
Deleting lock file [/nidb/lock/import.441787] [Ok]
-------------------------------------------------------------
----- Terminating (NiDB) backend ----------------------------
-------------------------------------------------------------
As with all modules, detailed log files are written to /nidb/logs and are kept for 4 days.
Running from cluster
To run nidb from the cluster, for the purpose of inserting results into the database or for checkins while running pipelines, this would be run on the cluster node itself. Access to an nidb.cfg file is necessary to run nidb somewhere other than on the main database server. A second config file /nidb/nidb-cluster.cfg can be copied to the cluster location along with the nidb executable.
pipelinecheckin
To check-in when running a pipeline, use the following
./nidb cluster -u pipelinecheckin -a <analysisid> -s <status> -m <message>
# example
./nidb cluster -u pipelinecheckin -a 12235 -s started -m "Copying data"
The analysisid is the rowid of the analysis which is bring reported on. Status can include one of the following: started, startedrerun, startedsupplement, processing, completererun, completesupplement, complete. Message can be an string, enclosed in double quotes.
updateanalysis
This option counts the byte size of the analysis directory and number of files and updates the analysis details in the main database.
./nidb cluster -u updateanalysis -a <analysisid>
checkcompleteanalysis
This option checks if the 'complete files' list exists. These files are specified as part of the pipeline definition. If the files exist, the analysis is marked as successfuly complete.
./nidb cluster -u checkcompleteanalysis -a <analysisid>
resultinsert
Text, number, and images can be inserted using this command. Examples
