Added docker-compose and updated README (#37)

* Added docker-compose and updated README

.env

@@ -1 +1,4 @@
+COMPOSE_PROJECT_NAME=sciencebeam
+IMAGE_TAG=develop
 SCIENCEBEAM_GYM_COMMIT=851eb577398d47189dff748d36a735dcc84f3adb
+GROBID_TAG=0.5.1

README.md

@@ -11,7 +11,11 @@ You might also be interested in the [ScienceBeam Gym](https://github.com/elifesc
 
 ## Status
 
-This is in a very early status and may change significantly. The Pipeline may not currently run successfully in the Cloud.
+This is in a very early status and may change significantly.
+
+## Docker
+
+Note: If you just want to use the API, you could make use of the [docker image](doc/Docker.md).
 
 ## Pre-requisites
 
@@ -114,6 +118,24 @@ python -m sciencebeam.examples.conversion_pipeline --help
 You can use the [grobid_service_pdf_to_xml.py](sciencebeam/examples/grobid_service_pdf_to_xml.py) or
 [conversion_pipeline.py](sciencebeam/examples/conversion_pipeline.py) example as a template and add your own steps.
 
+## API Server
+
+The [API](doc/API.md) server is currently available in combination with GROBID.
+
+To start the GROBID run:
+
+```bash
+docker run -p 8070:8070 lfoppiano/grobid:0.5.1
+```
+
+To start the ScienceBeam server run:
+
+```bash
+./server.sh --host=0.0.0.0 --port=8075 --grobid-url http://localhost:8070/api
+```
+
+The [ScienceBeam API](doc/API.md) will be available on port _8075_.
+
 ## Tests
 
 Unit tests are written using [pytest](https://docs.pytest.org/). Run for example `pytest` or `pytest-watch`.

doc/API.md

@@ -0,0 +1,38 @@
+# ScienceBeam API
+
+## /api/convert
+
+The currently the only API is _/api/convert_
+e.g. [http://localhost:8075/api/convert](http://localhost:8075/api/convert).
+
+It supports three modes of use.
+
+### GET
+
+A GET request will show a very simple submission form that allows the user to select a file which will be submitted to the API.
+
+### POST PDF as data
+
+The PDF can be posted as data to the API. The API will respond with the JATS XML.
+
+e.g.
+
+```bash
+curl -X POST --show-error -H "Content-Type: application/pdf" \
+  --data-binary @test.pdf \
+  http://localhost:8075/api/convert?filename=test.pdf
+```
+
+The _filename_ parameter is optional.
+
+### POST PDF as a file
+
+The PDF can also be posted as a file. The effect will be the same as posting it as data.
+
+e.g.
+
+```bash
+curl -X POST --show-error --form \
+  "file=@test.pdf;filename=test.pdf" \
+  http://localhost:8075/api/convert
+```

doc/Docker.md

@@ -0,0 +1,50 @@
+# ScienceBeam Docker Containers
+
+This section details using or building the docker images. You will need [Docker](https://www.docker.com/) and [Docker Compose](https://docs.docker.com/compose/).
+
+## Run Latest Docker Container
+
+Clone this repository and run:
+
+```bash
+docker-compose -f docker-compose.latest.yml up
+```
+
+That will start GROBID and ScienceBeam docker containers. The [ScienceBeam API](API.md) will be available on port _8075_.
+
+Alternatively run:
+
+```bash
+docker run --rm -p 8070:8070 lfoppiano/grobid:0.5.1
+```
+
+and:
+
+```bash
+docker run --rm -i -t -p 8075:8075 elifesciences/sciencebeam \
+  ./server.sh --host=0.0.0.0 --port=8075 --grobid-url http://localhost:8070/api
+```
+
+## Build and Run Docker Container with Docker Compose
+
+```bash
+docker-compose -f docker-compose.yml build
+```
+
+```bash
+docker-compose -f docker-compose.yml up
+```
+
+That will start GROBID and ScienceBeam docker containers. The [ScienceBeam API](API.md) will be available on port _8075_.
+
+## Build Docker Container Only
+
+```bash
+./build_container.sh
+```
+
+## GROBID and Crossref Consolidation
+
+GROBID is optionally using Crossref consolidation to make the results more useful for archiving.
+
+For this project, the preference is not to enable it and the _docker-compose.yml*_ files explictly use a local network to prevent that.

docker-compose.latest.yml

@@ -0,0 +1,29 @@
+version: '3'
+
+services:
+    sciencebeam:
+        image: elifesciences/sciencebeam:latest
+        command: ./server.sh \
+            --host=0.0.0.0 --port=8075 \
+            --grobid-url http://grobid:8070/api
+        ports:
+            - "8075:8075"
+        networks:
+            - default
+            - grobid
+        depends_on:
+            - grobid
+    grobid:
+        image: lfoppiano/grobid:${GROBID_TAG}
+        environment:
+            - JAVA_OPTS=-Xmx1g
+        ports:
+            - "8070:8070"
+        networks:
+            - grobid
+
+networks:
+    default:
+        internal: false
+    grobid:
+        internal: true

docker-compose.yml

@@ -0,0 +1,34 @@
+version: '3'
+
+services:
+    sciencebeam:
+        build:
+            context: .
+            dockerfile: Dockerfile
+            args:
+                sciencebeam_gym_commit: ${SCIENCEBEAM_GYM_COMMIT}
+        image: elifesciences/sciencebeam:${IMAGE_TAG}
+        command: ./server.sh \
+            --host=0.0.0.0 --port=8075 \
+            --grobid-url http://grobid:8070/api
+        ports:
+            - "8075:8075"
+        networks:
+            - default
+            - grobid
+        depends_on:
+            - grobid
+    grobid:
+        image: lfoppiano/grobid:${GROBID_TAG}
+        environment:
+            - JAVA_OPTS=-Xmx1g
+        ports:
+            - "8070:8070"
+        networks:
+            - grobid
+
+networks:
+    default:
+        internal: false
+    grobid:
+        internal: true