Added doc to run SemEHR in new NSH (SHSv2)

Author: andrewb147

doc/annotation_service_SMI.md

@@ -0,0 +1,109 @@
+# Annotation Service installation in SMI
+
+The database host is `smi-edris-db01` and the web service host is `smi-webs01`
+
+# Database
+
+The database host is configured using ansible
+https://git.ecdf.ed.ac.uk/SMI/deploy/-/blob/main/playbooks/postgres.yml
+
+The service will need a database called `semehr`.
+
+The roles (groups and logins) are specific to this host and are configured by ansible
+https://git.ecdf.ed.ac.uk/SMI/deploy/-/blob/main/inventories/nsh/host_vars/smi-edris-db01.nsh.loc/db_config.yml
+The admin role is `semehr` and the read-only role is `semehr-api` (note the dash).
+
+The rest of the database configuration is done manually, see `postgres_init_01.sh`
+
+The database is populated by editing the postgres password in `semehr_to_postgres.py`
+and running `semehr_zip_to_postgres.sh` with the zip files stored in `/mnt/beegfs/sr-nlp/annotations/complete_set_2`
+
+# Web service
+
+Create the container using the `docker/Dockerfile2`:
+```
+docker build -t howff/semehr:2 -f Dockerfile2 --build-arg GIT_DATE=$(date +%N) --progress=plain .
+```
+
+Import the container to `smi-webs01` as the `agans-smi` user:
+```
+ces-pull USER USERKEY ghcr.io/howff/semehr:2
+podman images
+```
+
+Create/edit the configuration file, containing the postgres password for the `semehr-api` user
+in this file `/localhome/agans-smi/src/smi/CogStack-SemEHR/docker/settings.json`
+
+```
+{
+  "mappings": [
+  ],
+  "mappings_dir": "./mappings_dir",
+  "transaction_dir": "./transactions",
+  "training_dir": "./training",
+  "passphrase": "^dr,rjt^",
+  "webdata_path": "/Users/honghan.wu/Documents/working/SemEHR-Working/working_dermatology",
+  "MRREL_path": "../umls/MRREL.csv",
+  "MRCONSO_path": "../umls/MRCONSO.csv",
+  "databaseBackend": "postgreSQL",
+  "postgreSQL": {
+    "host": "smi-edris-db01.nsh.loc",
+    "port": 5432,
+    "user": "semehr-api",
+    "password": "***EDIT THIS***",
+    "db": "semehr",
+    "schema": "semehr",
+    "ann_collection": "semehr_results",
+    "text_collection": "text_collection",
+  }
+}
+```
+
+Test running the service:
+
+```
+podman run --replace --rm -d --name smi-semehr \
+ -p 8485:8485 \
+ -v ~/src/smi/CogStack-SemEHR/docker/settings.json:/CogStack-SemEHR/RESTful_service/conf/settings.json \
+ ghcr.io/howff/semehr:2
+```
+
+Create the user-level systemd unit file `.config/systemd/user/container-smi-rgo.service`
+
+```
+[Unit]
+Description=SMI Researcher Generated Outputs Service
+Documentation=man:podman-generate-systemd(1)
+Wants=network-online.target
+After=network-online.target
+RequiresMountsFor=%t/containers
+
+[Service]
+Environment=PODMAN_SYSTEMD_UNIT=%n
+Restart=on-failure
+ExecStart=/usr/bin/podman run \
+    --cidfile=%t/%n.ctr-id \
+    --cgroups=no-conmon \
+    --sdnotify=conmon \
+    --pull=never \
+    --replace \
+    --rm \
+    -d \
+    -p 8485:8485 \
+    --name smi-semehr \
+    -v /localhome/agans-smi/src/smi/CogStack-SemEHR/docker/settings.json:/CogStack-SemEHR/RESTful_service/conf/settings.json \
+    ghcr.io/howff/semehr:2
+ExecStop=/usr/bin/podman stop \
+    --ignore \
+    -t 10 \
+    --cidfile=%t/%n.ctr-id
+ExecStopPost=/usr/bin/podman rm \
+    -f \
+    --ignore \
+    --cidfile=%t/%n.ctr-id
+Type=notify
+NotifyAccess=all
+
+[Install]
+WantedBy=default.target
+```