v1.5.2

Patch changes:

• Adding barcode Metadata info for NovaSeq X Plus

Add support for NovaSeq X Plus

This release adds support for detecting NovaSeq X Plus runs and specifies which completed marker file should be used for those runs.

Use custom completed marker files for different instruments

This release allows us to specify alternatives to RTAComplete.txt based on instrument type. This fixes the problem whereby a runfolder is marked complete before all of the files have been copied.

Note that completed_marker_file is being removed from the config file, since currently this value is the same in all environments.

There is also a new dev server file and updated the README to facilitate development.

Metadata section in runfolder info

Minor update:
A metadata section has been added to the info returned by the runfolders/path endpoint. The application tries to fetch "Reagent Kit Barcode" and "Library Tube Barcode" from runParameters.xml and add these values to the metadata section, if found. If the values are not found, the metadata section will be represented as an empty dictionary.

Examples
Data found:

$ curl -X GET localhost:9999/api/1.0/runfolders/path/home/runfolder | python -m json.tool
{
    "service_version": "1.4.0",
    "state": "ready",
    "host": "my_computer",
    "link": "http://localhost:9991/api/1.0/runfolders/path/home/runfolder",
    "path": "/home/runfolder
    "metadata": {
        "reagent_kit_barcode": "MS7777737-600V3"
    }
}

Data not found:

$ curl -X GET localhost:9999/api/1.0/runfolders/path/home/runfolder | python -m json.tool
{
    "service_version": "1.4.0",
    "state": "ready",
    "host": "my_computer",
    "link": "http://localhost:9991/api/1.0/runfolders/path/home/runfolder",
    "path": "/home/runfolder
    "metadata": {}
}

Metadata section in runfolder info

Merge pull request #24 from MatildaAslin/reagent_kit_barcode_in_runfo…

…lder_info

Metadata in runfolder info

Improved detection of completed runs

Improved detection of completed runs:

In order to detect when a run is completed, a list of marker files to inspect can now be specified in the config, along with a variable stating a grace time (in minutes) to wait after the creation of the marker files.

Bugfixes:
Remove misplaced import statement
Do not raise error when there is no runfolder

Bug fix: Do give 500 error message on no available runfolder

Merge pull request #22 from johandahlberg/no_error_on_next

Do not raise error when there is no runfolder

Improved detection of completed runs

In order to detect when a run is completed, a list of marker files to inspect can now be specified in the config, along with a variable stating a grace time (in minutes) to wait after the creation of the marker files.

Completion marker file configurable

This completion marker file is now configurable by the completed_marker_file in the configuration. By default is will be set to RTAComplete.txt, which is the same value that was previously used. However for use-cases where this file cannot be depended on to signal the completion of a run (or a directory transfer), this makes it possible to configure this.

Thanks to @Smeds for fixing this!

New end-point for picking up runfolders

There is now a new endpoint under /api/1.0/runfolders/pickup which will pickup a runfolder and place it in PENDING state. This is useful to make sure that the same runfolder is not presented multiple times to a client, e.g. a sensor.