Paths and Configuration
The GUI derives most paths from DEEPPHE_ROOT. If DEEPPHE_ROOT is not set, the Java app uses the parent of the current working directory as its root.
Important Directories
| Name | Default relative to DEEPPHE_ROOT | Purpose |
|---|---|---|
| DeepPhe tools | .DeepPhe | NLP tool home. |
| Data Merge Tool | .DeepPhe/tools/dphe-pipeline | Converts NLP output and OMOP data for visualization. |
| Data API | .DeepPhe/tools/dphe-data-api | Serves the visualizer database. |
| Visualizer | .DeepPhe/tools/deepphe-visualizer-v2 | Browser UI for cohort and patient review. |
| Logs | .DeepPhe/logs | Tool and service logs. |
| Projects | .DeepPhe/resources/projects | Project list, project files, and generated CLI parameter files. |
Default Commands
| Tool | Default command |
|---|---|
| NLP Summarizer | bin/runDeepPheGUI |
| Data Merge Tool | runDbCreator |
| Data API | dphe-data-api |
| Visualizer | start-viz |
Relative commands are resolved under each tool's configured directory.
Desktop Configuration File
You can pass one configuration file to the launcher:
./runDeepPheDesktop.sh /path/to/desktop-config.txt
Configuration files use NAME=value lines. Blank lines and lines beginning with // are ignored.
DpheDir=/opt/deepphe/.DeepPhe
VizDir=/opt/deepphe/.DeepPhe/tools/deepphe-visualizer-v2
ProjectsDir=/opt/deepphe/.DeepPhe/resources/projects
StartViz=start-viz
The GUI accepts several legacy aliases for each value. For example, the visualizer directory can be configured with VizDir, VisDir, VizualizerDir, or VisualizerDir.
Project Files
Project files also use NAME=value lines, but they store the selected data paths for a run:
PROJECT_NAME=ExampleProject
PIPER_FILE=/path/to/DefaultDeepPhe.piper
CORPUS_DIR=/path/to/example_corpus
OMOP_DB=/path/to/patient_demographics.json
OUTPUT_DIR=/path/to/example_output
Project files are written when the app exits and when you switch projects.