Merge remote-tracking branch 'upstream/dev' into dev

Author: chreman

.gitignore

@@ -18,6 +18,7 @@ dist/
 .Rhistory
 .ipynb_checkpoints
 .Rprofile
+.Rproj*
 coverage/
 
 # local deployment files
@@ -33,4 +34,5 @@ coverage/
 /lc_browseview_cache.json
 /lc_cache.json
 /linkedcat.sqlite
-.env
+.env
+.Rproj.user

CHANGELOG.md

@@ -1,5 +1,49 @@
 # Changelog
 
+## 2022-01-31
+
+### New features
+
+- new citation button & modal generating citations (APA, MLA, Chicago, ACM) for each paper
+
+### Changes
+
+- unified appearance and functionality of copy buttons in modals
+- FontAwesome update: new icons; reduced dependency on outer page imports
+
+### Bug fixes
+
+- fixed crashing app when a pdf preview was opened during animation
+
+### Internal
+
+- removed unused local examples; added new local examples (triple, viper, covis)
+
+## 2022-01-20
+
+### New features
+
+- backend data sanitization
+- pdfs searchable by the searchbox
+
+### Changes
+
+- data preprocessing refactoring
+
+### Bug fixes
+
+- footer size on narrow screens
+
+### Internal
+
+- test database update
+
+## 2021-12-22
+
+### Changes
+
+- unified HTML & CSS of various paper tags (access tags, dataset tag, custom tags)
+
 ## 2021-12-09
 
 ### New features

README.md

@@ -9,6 +9,15 @@ Head Start is a web-based knowledge mapping software intended to give researcher
 ### Client
 To get started, clone this repository. Next, duplicate the file `config.example.js` in the root folder and rename it to `config.js`.
 
+Set the `skin` property in the config to one of the following values to use the
+particular data integration skin:
+
+- `"covis"`
+- `"triple"`
+- `"viper"`
+
+or leave it empty (`""`) for the default project website skin.
+
 Make sure to have installed `node` version >= 14.18.1 and `npm` version >=8.1.1 (best way to install is with [nvm](https://github.com/nvm-sh/nvm), `nvm install 14.18.1`) and run the following two commands to build the Headstart client:
 
     npm install
@@ -20,18 +29,24 @@ Now you can run a local dev server:
 
 	npm start
 
-To run Headstart on a different server (e.g. Apache), you need to set the publicPath in `config.js` to the URL of the `dist` directory:
-* Dev: specify the full path including protocol, e.g. `http://localhost/headstart/dist`
-* Production: specify the full path excluding protocol, e.g. `//example.org/headstart/dist`
+Note: you can also set the skin in this step as an argument to the `npm start` command (e.g. `npm start -- --env skin=triple`).
 
-Point your browser to one of the following addresses:
+The browser will automatically open a new window with the example specified by the skin.
+
+Alternatively, you can point your browser to one of the following addresses:
 
-	http://localhost:8080/local_files/
-	http://localhost:8080/local_streamgraph/
 	http://localhost:8080/project_website/base.html
 	http://localhost:8080/project_website/pubmed.html
+	http://localhost:8080/local_covis/
+	http://localhost:8080/local_triple/map.html
+	http://localhost:8080/local_triple/stream.html
+	http://localhost:8080/local_viper/
+
+If everything has worked out, you should see the example visualization.
 
-If everything has worked out, you should see the visualization shown above.
+To run Headstart on a different server (e.g. Apache), you need to set the publicPath in `config.js` to the URL of the `dist` directory:
+* Dev: specify the full path including protocol, e.g. `http://localhost/headstart/dist`
+* Production: specify the full path excluding protocol, e.g. `//example.org/headstart/dist`
 
 See [client configuration](doc/README.md) for details on adapting the client.
 
@@ -93,4 +108,4 @@ Head Start is licensed under [MIT](LICENSE).
 ## Citation
 If you use Head Start in your research, please cite it as follows:
 
-Peter Kraker, Christopher Kittel, Maxi Schramm, Rainer Bachleitner, Thomas Arrow, Scott Chamberlain, Asura Enkhbayar, Yael Stein, Philipp Weissensteiner, Mike Skaug, Katrin Leinweber & Open Knowledge Maps team and contributors. (2019, March 7). Headstart 5 (Version v5). Zenodo. http://doi.org/10.5281/zenodo.2587129
+Peter Kraker, Christopher Kittel, Maxi Schramm, Jan Konstant, Rainer Bachleitner, Thomas Arrow, Scott Chamberlain, Asura Enkhbayar, Yael Stein, Philipp Weissensteiner, Mike Skaug, Katrin Leinweber & Open Knowledge Maps team and contributors. (2019, March 7). Headstart 5 (Version v5). Zenodo. http://doi.org/10.5281/zenodo.2587129

doc/server_config.md

@@ -90,4 +90,4 @@ Duplicate config.ini in server/preprocessing/conf/ and rename it to config_local
 ## Logging configuration
 
 In the default setting, Headstart will log behavior only to the console. If you want to log to a file, please add following environment variable to your Renviron (in local mode) or Renviron.site (if called on a server). Headstart will then log events to a file on the `INFO` loglevel.
-* `HEADSTART_LOGFILE`: Path to a logfile, e.g. `/path/to/logfile.log`. Please make sure that the folder structure exists, e.g. `/path/to/`.
+* `LOGFILE`: Path to a logfile, e.g. `/path/to/logfile.log`. Please make sure that the folder structure exists, e.g. `/path/to/`.

docker-compose-dataworker.yml

@@ -0,0 +1,20 @@
+version: '3.7'
+
+services:
+
+  dataprocessing:
+    image: dataprocessing:${SERVICE_VERSION}
+    env_file:
+    - server/workers/dataprocessing/dataprocessing.env
+    environment:
+      SERVICE_VERSION: "${SERVICE_VERSION}"
+      REDIS_HOST: "${REDIS_HOST}"
+      REDIS_PORT: "${REDIS_PORT}"
+      REDIS_DB: "${REDIS_DB}"
+      REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+    restart: always
+    volumes:
+      - /opt/local/renv/cache:/renv/cache
+      - /var/log/headstart:/var/log/headstart
+    network_mode: host

docker-compose.yml

@@ -26,7 +26,7 @@ services:
       - headstart
 
   redis:
-    image: 'redis:4.0-alpine'
+    image: 'redis:6.0-alpine'
     restart: always
     hostname: "${REDIS_HOST}"
     environment:
@@ -36,6 +36,9 @@ services:
     volumes:
         - 'redis:/var/lib/redis/data'
         - ./server/workers/redis.conf:/etc/redis/redis.conf
+        - ./server/workers/certs:/etc/certs
+    ports:
+     - "127.0.0.1:${REDIS_PORT}:6379"
     restart: always
     networks: 
       - headstart
@@ -49,6 +52,11 @@ services:
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
       REDIS_DB: "${REDIS_DB}"
+      REDIS_SSL: "${REDIS_SSL}"
+      BEHIND_PROXY: "${BEHIND_PROXY}"
+      DEFAULT_DATABASE: "${DEFAULT_DATABASE}"
+      DATABASES: "${DATABASES}"
+      FLASK_ENV: "${FLASK_ENV}"
     command: ["gunicorn",  "--workers", "10", "--threads", "2", "-b", "0.0.0.0:${API_PORT}", "app:app", "--timeout", "300"]
     depends_on:
       - redis
@@ -64,6 +72,10 @@ services:
       POSTGRES_PASSWORD: "${POSTGRES_PASSWORD}"
       POSTGRES_HOST: "${POSTGRES_HOST}"
       POSTGRES_PORT: "${POSTGRES_PORT}"
+      BEHIND_PROXY: "${BEHIND_PROXY}"
+      DEFAULT_DATABASE: "${DEFAULT_DATABASE}"
+      DATABASES: "${DATABASES}"
+      FLASK_ENV: "${FLASK_ENV}"
     command: ["gunicorn",  "--workers", "10", "--threads", "2", "-b", "0.0.0.0:${API_PORT}", "app:app", "--timeout", "300"]
     networks: 
       - headstart
@@ -78,6 +90,15 @@ services:
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
+      TRIPLE_USER: "${TRIPLE_USER}"
+      TRIPLE_PASS: "${TRIPLE_PASS}"
+      TRIPLE_HOST: "${TRIPLE_HOST}"
+      TRIPLE_PORT: "${TRIPLE_PORT}"
+      TRIPLE_DOCUMENTS_INDEX: "${TRIPLE_DOCUMENTS_INDEX}"
+      TRIPLE_PROJECTS_INDEX: "${TRIPLE_PROJECTS_INDEX}"
+      TRIPLE_AUTHORS_INDEX: "${TRIPLE_AUTHORS_INDEX}"
     restart: always
     depends_on:
       - redis
@@ -94,6 +115,8 @@ services:
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
     restart: always
     depends_on:
       - redis
@@ -110,6 +133,8 @@ services:
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
     restart: always
     volumes:
       - /opt/local/renv/cache:/renv/cache
@@ -121,14 +146,21 @@ services:
 
   base:
     image: base:${SERVICE_VERSION}
-    env_file:
-      - server/workers/base/base.env
     environment:
       SERVICE_VERSION: "${SERVICE_VERSION}"
       REDIS_HOST: "${REDIS_HOST}"
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
+      LOGFILE: "/var/log/headstart/headstart.log"
+      RENV_VERSION: 0.14.0-5
+      CRAN_REPOS: https://cran.wu.ac.at
+      LC_ALL: "en_US.UTF-8"
+      LANG: "en_US.UTF-8"
+      RENV_PATHS_CACHE: /renv/cache
+      PYTHONIOENCODING: "utf-8"
     restart: always
     volumes:
       - /opt/local/renv/cache:/renv/cache
@@ -140,14 +172,21 @@ services:
 
   pubmed:
     image: pubmed:${SERVICE_VERSION}
-    env_file:
-      - server/workers/pubmed/pubmed.env
     environment:
       SERVICE_VERSION: "${SERVICE_VERSION}"
       REDIS_HOST: "${REDIS_HOST}"
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
+      LOGFILE: "/var/log/headstart/headstart.log"
+      RENV_VERSION: 0.14.0-5
+      CRAN_REPOS: https://cran.wu.ac.at
+      LC_ALL: "en_US.UTF-8"
+      LANG: "en_US.UTF-8"
+      RENV_PATHS_CACHE: /renv/cache
+      PYTHONIOENCODING: "utf-8"
     restart: always
     volumes:
       - /opt/local/renv/cache:/renv/cache
@@ -159,14 +198,21 @@ services:
 
   openaire:
     image: openaire:${SERVICE_VERSION}
-    env_file:
-      - server/workers/openaire/openaire.env
     environment:
       SERVICE_VERSION: "${SERVICE_VERSION}"
       REDIS_HOST: "${REDIS_HOST}"
       REDIS_PORT: "${REDIS_PORT}"
       REDIS_DB: "${REDIS_DB}"
       REDIS_PASSWORD: "${REDIS_PASSWORD}"
+      REDIS_SSL: "${REDIS_SSL}"
+      LOGLEVEL: "${LOGLEVEL}"
+      LOGFILE: "/var/log/headstart/headstart.log"
+      RENV_VERSION: 0.14.0-5
+      CRAN_REPOS: https://cran.wu.ac.at
+      LC_ALL: "en_US.UTF-8"
+      LANG: "en_US.UTF-8"
+      RENV_PATHS_CACHE: /renv/cache
+      PYTHONIOENCODING: "utf-8"
     restart: always
     volumes:
       - /opt/local/renv/cache:/renv/cache