Merge pull request #405 from Emory-HITI/dev

Some recent contributions

modules/cold-extraction/Dockerfile

@@ -0,0 +1,22 @@
+FROM python:3.10.10-bullseye
+
+# download and add DCM4CHE
+ADD https://sourceforge.net/projects/dcm4che/files/dcm4che3/5.22.5/dcm4che-5.22.5-bin.zip/download /opt/dcm4che-5.22.5-bin.zip
+RUN set -eux; \
+# install JRE for DCM4CHE, mailutils
+    apt update && \
+    apt install -y openjdk-11-jre mailutils && \
+# extract and install DCM4CHE
+    cd /opt; \
+    unzip dcm4che-5.22.5-bin.zip && \
+    rm dcm4che-5.22.5-bin.zip; \
+# create default dicom storage directory
+    mkdir -p /opt/data/new-study
+
+COPY . /usr/src/niffler-cold-extraction
+WORKDIR /usr/src/niffler-cold-extraction
+
+# install required python packages
+RUN pip install -r requirements.txt
+
+CMD ["python", "ColdDataRetriever.py"]

modules/cold-extraction/README.md

@@ -345,3 +345,28 @@ nohup /opt/dcm4che-5.22.5/bin/movescu -c "[email protected]:104" -b "QBNIFFLE
 
 If the testing with DCM4CHE as above does not work, that is an issue likely with your PACS configuration to send DICOM data to your endpoint. Please get the above to work first in that case before attempting the execution with Niffler.
 
+## Using Docker
+
+To use as a docker container, first navigate to this directory (`modules/cold-extraction`) and build the image.
+
+```
+cd modules/cold-extraction
+docker build -t niffler/cold-extraction .
+```
+
+Then, run using the image tag used above.
+
+```
+docker run --network pacs_network --rm niffler/cold-extraction
+```
+
+Replace `pacs_network` with the docker network where the PACS is reachable.
+
+When the configuration or system JSON, as well as the CSV files change, either rebuild the image or mount as a volume before running the container.
+
+For ease, a docker compose file is also included. After configuring the volumes, networks, and everything else on the `docker-compose.yml` file, simply run:
+
+```
+docker compose up
+```
+

modules/cold-extraction/docker-compose.yml

@@ -0,0 +1,11 @@
+version: '3.1'
+services:
+  niffler-cold-extraction:
+    build: .
+    volumes:
+    - ./config.json:/usr/src/niffler-cold-extraction/config.json
+    - ./system.json:/usr/src/niffler-cold-extraction/system.json
+    - ./csv/:/usr/src/niffler-cold-extraction/csv/
+    - ./storage:/opt/data/new-study
+    networks:
+      - default

modules/cold-extraction/requirements.txt

@@ -0,0 +1,4 @@
+schedule
+pandas
+pynetdicom
+pydicom

modules/frontend/requirements.txt

@@ -1,7 +1,7 @@
 bidict==0.21.2
 click==8.0.1
 colorama==0.4.4
-Flask==2.0.1
+Flask==2.3.2
 Flask-Login==0.5.0
 Flask-SocketIO==4.3.2
 Flask-SQLAlchemy==2.5.1
@@ -21,5 +21,5 @@ pytz==2021.1
 schedule==1.1.0
 six==1.16.0
 SQLAlchemy==1.4.18
-sqlparse==0.4.2
+sqlparse==0.4.4
 Werkzeug==2.2.3

modules/meta-extraction/Dockerfile

@@ -0,0 +1,25 @@
+FROM python:3.10.10-bullseye
+
+# install JRE for DCM4CHE
+RUN set -eux; \
+    apt update && \
+    apt install -y openjdk-11-jre
+
+# install DCM4CHE
+RUN set -eux; \
+    cd /opt; \
+    curl -L https://sourceforge.net/projects/dcm4che/files/dcm4che3/5.22.5/dcm4che-5.22.5-bin.zip/download \
+         -o dcm4che-5.22.5-bin.zip; \
+    unzip dcm4che-5.22.5-bin.zip && \
+    rm dcm4che-5.22.5-bin.zip
+
+COPY . /usr/src/app
+WORKDIR /usr/src/app
+
+# install required python packages
+RUN pip install -r requirements.txt
+
+# create default dicom storage directory
+RUN mkdir /opt/niffler-dicom-root
+
+CMD ["python", "MetadataExtractor.py"]

modules/meta-extraction/docker-compose.yml

@@ -0,0 +1,11 @@
+version: '3'
+services:
+  niffler-meta-extraction:
+    build: .
+    environment:
+      MONGO_URI: user:password@mongo:27017
+  mongo:
+    image: mongo:5.0
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: user
+      MONGO_INITDB_ROOT_PASSWORD: password

modules/meta-extraction/requirements.txt

@@ -0,0 +1,5 @@
+pymongo
+pydicom
+schedule
+pandas
+requests