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Installed layout

After a successful install there are two top-level locations: the program (inside the install directory) and the user's data (in the home directory).

Program: <install dir>/.DeepPhe/​

install4j lays these mount points out under the chosen install directory:

.DeepPhe/
├── conf/                       # launcher.conf lives here
├── logs/
│   ├── deepphe/
│   ├── viz/
│   └── launcher/
├── bin/                        # runDeepPhe*.sh / .bat (from DeepPhe-NLP.zip, patched)
├── lib/                        # DeepPhe / cTAKES jars, ontology db jar
├── resources/
│   ├── pipeline/               # piper files (installer overlay applied here)
│   ├── hsqldb/ · neo4j/        # embedded dictionary + ontology graph
│   └── projects/               # ProjectList.txt, ExampleProject.txt
├── piperfiles/                 # staged installer piper overrides
└── tools/
    ├── dphe-pipeline/          # DeepPheVizDbCreator + runDpheVizDbCreator.sh/.bat
    ├── dphe-data-api/          # dphe-data-api-<platform>
    └── deepphe-visualizer-v2/  # deepphe-visualizer-v2-<platform>

.DeepPhe is the launcher's working directory. Only the binaries for the current platform are downloaded, so (for example) a Mac install contains just the -macos-* tool binaries.

The Java 26 configure step deletes the incompatible log4j-1.2-api-* bridge jar from this directory after extracting the NLP zip.

Why the leading dot?

Naming the program folder .DeepPhe keeps it out of the way in file browsers and signals that it is managed by the installer, not something the user edits by hand.

Data: ~/DeepPheDocs/​

This is the install4j root ${installer:sys.userHome}/DeepPheDocs, deliberately separate from the program so it survives reinstalls:

~/DeepPheDocs/
├── input/                       # reports you want to process
├── output/                      # pipeline results
├── example_corpus/              # from DeepPhe-examples.zip
├── example_omop/
│   └── patient_demographics.json  # normalized to { "patients": … }
├── example_output/
└── visualizer_database/
    ├── deepphe.sqlite3          # built by the DB creator
    ├── omop.sqlite3
    ├── extraction/data/
    └── legacy_pipeline_output/  # migrated from older installs, if any

The example project (ExampleProject.txt) wires these together:

PROJECT_NAME=ExampleProject
CONFIG_FILE=<install>/.DeepPhe/resources/projects/ExampleProject.txt
PIPER_FILE=<install>/.DeepPhe/resources/pipeline/DefaultDeepPhe.piper
CORPUS_DIR=~/DeepPheDocs/example_corpus
OMOP_DB=~/DeepPheDocs/example_omop/patient_demographics.json
OUTPUT_DIR=~/DeepPheDocs/example_output

What the uninstaller removes​

The uninstaller removes .DeepPhe and the launcher. It offers an optional checkbox to also delete ~/DeepPheDocs, with a warning that doing so removes all input and output files. Leaving it unchecked preserves the user's data.