Janelia Transmogrifier - tmog

The Janelia Transmogrifier - 'tmog' - is a Java Swing application that supports the collection and validation of meta data associated with files. You can find build instructions here.

Key Features

Simple user interface for entering meta data information.
- Drop-down selection lists for enumerated values.
- Allows values entered for one file to be copied the next file with a single click.
- Supports mouse and keyboard navigation.
Configurable data field, syntax validation, and naming rules.
Validated file transfer from source to destination file systems (e.g. from local scope file system to a network mounted file system).
- Digests (default is md5) of file contents are calculated before and after transfer to ensure integrity.
Logging of renamed file information to a centralized database.
- Logged information includes:
  - full path names of the source and destination (renamed) files
  - digest of renamed file contents
  - renamed file size
- Logged information can be used for future troubleshooting or audit needs (e.g. digest can be used to determine if the file contents have changed since the move occurred).
Supports addition of external system plug-in components for validation and/or process integration.

Configuration

The application can be configured to support multiple projects with different requirements. This is designed to be a "self-serve" feature that allows researchers to make changes themselves as their environment changes.

Task Models

For each file it processes, the tool can be configured to either:

collect meta data and pass that meta data to any plug-ins for processing or
collect meta data, rename and move the file based upon that meta data, and then pass the meta data to any plug-ins for processing.

Data Fields

The specific data fields collected for each file and their validation constraints are configurable. The following data field elements can be used to collect and validate values entered by the user:

<text displayName="Promoter" pattern="[0-9A-Za-z\\-]++"/>

Inserts a user provided text value and validates against a configured Java regular expression pattern.

<number displayName="Plate" minimumValue="1" maximumValue="999"/>

Inserts a user provided integer value and validates against configured minimum and maximum values.

<decimal displayName="Interval" minimumValue="0.1" maximumValue="9.9"/>

Inserts a user provided decimal (floating point) value and validates against configured minimum and maximum values.

<validValueList displayName="Gender">
    <validValue displayName="m: Male" value="m" />
    <validValue displayName="f: Female" value="f" />
    <validValue displayName="x: Not Defined" value="x" />
</validValueList>

Inserts a user selected value from a configured list of acceptable values.

<well displayName="Well" formFactor="96"/>

Inserts a user provided well identifier and validates against a configured form factor.

The following data field elements can be used to insert derived or configured values not provided directly by the user:

<separator value="GMR-" />

Inserts a static configured text value.

<fileModificationTime datePattern="'-C'yyMMdd'-'" />

Inserts the file modification time using a configured format pattern.

<runTime datePattern="yyyyMMddHHmmssSSS" />

Inserts the rename process run time using a configured format pattern.

<pluginData displayName="imageLocationRank" format="%02d"/>

Inserts formatted text data retrieved through a configured plug-in component.

Plug-in Components

Plug-in component classes can be mapped to events in the collection process (e.g. validation, task initiation, and task completion). The components listed below have been developed to address specific lab needs. New plug-in components can be developed as new needs arise.

Session Summary File Writer
- Writes the summary message from each completed session into a file so that the information can be referenced later (e.g. for pasting into lab notebooks).
Image Data Plug-in
- Writes collected meta data into a Janelia Image database.
Image Sequence Number Plug-in
- Retrieves the next available sequence number for a configured name space from a Janelia Image database.
REST Data Plug-in
- Converts collected meta data into HTTP POST requests for a Representational State Transfer data server.

Rename Output Directory

The destination for renamed files can be explicitly configured or you can let the user manually select a destination for each session.

File List Sorting

The order in which files are sorted for each session can be configured.

Renaming the Renamer

This tool was formerly called the 'Image Renamer' because its original use was to rename microscope image files, embedding collected meta data into the new file names. As the tool's feature set expanded beyond just renaming, we decided to rename the tool itself to something less restrictive.

Don Olbris, our resident naming expert, came up with the name 'Transmogrifier' which was likely inspired by this Calvin and Hobbes cartoon sketch.

Over the years, 'Transmogrifier' got shortened to simply 'tmog' and that name has stuck.

JaneliaSciComp/tmog