Issues dockerizing the bert-phi-annotator

[clemEssien]

There seems to be an issue with permissions downloading the ms-bert model

docker compose up --build
[+] Running 6/6
 ⠿ nginx Pulled                                                                                      28.9s
   ⠿ 801bfaa63ef2 Pull complete                                                                       4.1s
   ⠿ b1242e25d284 Pull complete                                                                       7.0s
   ⠿ 7453d3e6b909 Pull complete                                                                       7.0s
   ⠿ 07ce7418c4f8 Pull complete                                                                       7.1s
   ⠿ e295e0624aa3 Pull complete                                                                       7.1s
[+] Building 1.7s (15/15) FINISHED                                                                         
 => [internal] load build definition from Dockerfile                                                  0.0s
 => => transferring dockerfile: 935B                                                                  0.0s
 => [internal] load .dockerignore                                                                     0.0s
 => => transferring context: 828B                                                                     0.0s
 => [internal] load metadata for docker.io/library/python:3.9.6-slim-buster                           1.6s
 => [auth] library/python:pull token for registry-1.docker.io                                         0.0s
 => [ 1/10] FROM docker.io/library/python:3.9.6-slim-buster@sha256:2c018e29a8eada75e855d78641adda978  0.0s
 => [internal] load build context                                                                     0.0s
 => => transferring context: 643.46kB                                                                 0.0s
 => CACHED [ 2/10] RUN apt-get update -qq -y     && apt-get install --no-install-recommends -qq -y    0.0s
 => CACHED [ 3/10] WORKDIR /opt/app                                                                   0.0s
 => CACHED [ 4/10] COPY openapi_server openapi_server/                                                0.0s
 => CACHED [ 5/10] COPY data data/                                                                    0.0s
 => CACHED [ 6/10] COPY requirements.txt prod-requirements.txt uwsgi.ini ./                           0.0s
 => CACHED [ 7/10] RUN pip install --no-cache-dir     -r requirements.txt -r prod-requirements.txt    0.0s
 => CACHED [ 8/10] COPY docker-entrypoint.sh .                                                        0.0s
 => CACHED [ 9/10] RUN chmod +x docker-entrypoint.sh                                                  0.0s
 => exporting to image                                                                                0.0s
 => => exporting layers                                                                               0.0s
 => => writing image sha256:c56e15657bcacca12f280d69391f0186dd00757b087e72ae0da5d677404e5341          0.0s
 => => naming to docker.synapse.org/syn22277123/phi-annotator-example:1.2.1                           0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
[+] Running 4/4
 ⠿ Network bert-phi-annotator_nlpsandbox-internal  Created                                            0.0s
 ⠿ Network bert-phi-annotator_nlpsandbox           Created                                            0.0s
 ⠿ Container phi-annotator                         Started                                            0.5s
 ⠿ Container nginx                                 Started                                            1.4s
Attaching to nginx, phi-annotator
nginx          | 10-listen-on-ipv6-by-default.sh: info: Enabled listen on IPv6 in /etc/nginx/conf.d/default.conf
nginx          | /docker-entrypoint.sh: Launching /docker-entrypoint.d/20-envsubst-on-templates.sh
nginx          | 20-envsubst-on-templates.sh: Running envsubst on /etc/nginx/templates/events.conf.template to /etc/nginx/conf.d/events.conf
nginx          | 20-envsubst-on-templates.sh: Running envsubst on /etc/nginx/templates/http.conf.template to /etc/nginx/conf.d/http.conf
nginx          | /docker-entrypoint.sh: Configuration complete; ready for start up
phi-annotator  | WSGI app 0 (mountpoint='') ready in 1 seconds on interpreter 0x557b304b1330 pid: 13 (default app)
phi-annotator  | [pid: 13|app: 0|req: 1/1] 172.18.0.3 () {54 vars in 1002 bytes} [Mon Jul 19 22:22:25 2021] GET /ui => generated 226 bytes in 1 msecs (HTTP/1.1 302) 3 headers in 121 bytes (1 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 2/2] 172.18.0.3 () {54 vars in 1016 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui => generated 260 bytes in 1 msecs (HTTP/1.1 308) 3 headers in 135 bytes (1 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 3/3] 172.18.0.3 () {54 vars in 1018 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui/ => generated 1444 bytes in 5 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 4/4] 172.18.0.3 () {52 vars in 915 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui/swagger-ui.css => generated 142839 bytes in 1 msecs via sendfile() (HTTP/1.1 200) 6 headers in 244 bytes (0 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 5/5] 172.18.0.3 () {52 vars in 913 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui/swagger-ui-bundle.js => generated 1067068 bytes in 1 msecs via sendfile() (HTTP/1.1 200) 6 headers in 265 bytes (0 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 6/6] 172.18.0.3 () {52 vars in 935 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui/swagger-ui-standalone-preset.js => generated 311248 bytes in 0 msecs via sendfile() (HTTP/1.1 200) 6 headers in 275 bytes (0 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 7/7] 172.18.0.3 () {52 vars in 904 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/openapi.json => generated 23284 bytes in 55 msecs (HTTP/1.1 200) 2 headers in 74 bytes (1 switches on core 0)
phi-annotator  | [pid: 13|app: 0|req: 8/8] 172.18.0.3 () {52 vars in 967 bytes} [Mon Jul 19 22:22:25 2021] GET /api/v1/ui/favicon-32x32.png => generated 628 bytes in 1 msecs via sendfile() (HTTP/1.1 200) 6 headers in 230 bytes (0 switches on core 0)
phi-annotator  | {'identifier': 'awesome-note',
phi-annotator  |  'patient_id': 'awesome-patient',
phi-annotator  |  'text': 'On 12/26/2025, Ms. Chloe Price met with Dr. Prescott in Seattle.',
phi-annotator  |  'type': 'loinc:LP29684-5'}
phi-annotator  | [Errno 13] Permission denied: '/var/www'
phi-annotator  | Can't load config for 'dslim/bert-base-NER'. Make sure that:
phi-annotator  | 
phi-annotator  | - 'dslim/bert-base-NER' is a correct model identifier listed on 'https://huggingface.co/models'
phi-annotator  | 
phi-annotator  | - or 'dslim/bert-base-NER' is the correct path to a directory containing a config.json file
phi-annotator  |