Merge remote-tracking branch 'upstream/master' into dockerized-rstudio

Author: chreman

.docker.test.env

@@ -33,6 +33,7 @@ server/workers/tests/testutils/
 local_dev/renv/*
 local_dev/dev.env
 local_dev/paper_preview
+.docker.test.env
 
 # php files
 /server/classes/headstart/vendor

.gitignore

@@ -1,6 +1,6 @@
 # Head Start
 
-Head Start is a web-based knowledge mapping software intended to give researchers  a head start on their literature review (hence the name). It comes with a powerful backend that is is capable of automatically producing knowledge maps from a variety of data, including text, metadata and references.
+Head Start is a web-based knowledge mapping software intended to give anyone a head start on their literature search (hence the name). It comes with a scalable backend that is capable of automatically producing knowledge maps from a variety of data sources.
 
 ![Head Start](headstart.png)
 
@@ -9,7 +9,7 @@ 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`.
 
-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 command to install the Headstart dependencies:
+Make sure to have installed `node` version >= 18.20.0 and `npm` version >=10.7.0 (best way to install is with [nvm](https://github.com/nvm-sh/nvm), `nvm install 18.20.0`) and run the following command to install the Headstart dependencies:
 
     npm install
 
@@ -19,119 +19,47 @@ We use [webpack](https://webpack.github.io/) to build our client-side applicatio
 
 The browser will automatically open a new window with the example.
 
-You can run also different examples
-
-- `npm run example:pubmed` will run the PubMed example
-- `npm run example:triple` will run the GoTriple example
-- `npm run example:viper` will run the Viper example
-- `npm run example:covis` will run the CoVis example
-
-If everything has worked out, you should see the example visualization.
-
-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`
-
-Then build it with the command `npm run prod`. The build will appear in the _dist/_ folder in the root directory.
-
-You can also 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.
-
-See [client configuration](doc/README.md) for details on adapting the client.
-
- Also see visualization [options](doc/README.md#visualisation-settings).
-
-### Server
-
-See [Installing and configuring the server](doc/server_config.md) for instructions on how to install and configure the server. Also, see [HOWTO: Get the search repos example to work](doc/howto_search_repos.md).
-
-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
-    npm run dev
-
-We are using [webpack](https://webpack.github.io/) to build our client-side application. `webpack` is started in *watch mode* which means that changes to files are tracked and the created `headstart.js` is automatically updated.
-
-Now you can run a local dev server:
-
-	npm start
-
-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`).
-
-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/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/
+You can run also run the PubMed example using `npm run example:pubmed`
 
 If everything has worked out, you should see the example visualization.
 
-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`
-
-
 ## Contributors
 
-Maintainer: [Peter Kraker](https://github.com/pkraker) ([pkraker@openknowledgemaps.org](mailto:pkraker@openknowledgemaps.org))
-
-Authors: [Maxi Schramm](https://github.com/tanteuschi), [Christopher Kittel](https://github.com/chreman), [Jan Konstant](https://github.com/konstiman), [Asura Enkhbayar](https://github.com/Bubblbu), [Scott Chamberlain](https://github.com/sckott), [Rainer Bachleitner](https://github.com/rbachleitner), [Yael Stein](https://github.com/jaels), [Thomas Arrow](https://github.com/tarrow), [Mike Skaug](https://github.com/mikeskaug), [Philipp Weissensteiner](https://github.com/wpp), and the [Open Knowledge Maps team](http://openknowledgemaps.org/team)
-
-
-## Features
-
-* Interactive, web-based knowledge maps based on [D3.js](https://d3js.org), following Shneiderman's principle of "overview first, zoom and filter, then details-on-demand"
-* Synchronized list representation of documents complementing the knowledge map
-* Integrated PDF viewer and annotation tool, courtesy of [Hypothes.is](https://hypothes.is)
-* Powerful server component written in PHP and R for the creation of knowledge maps, including algorithms for clustering, ordination and labelling
-* Connectors to a number of academic search engines through [rOpenSci](https://ropensci.org), including [BASE](https://base-search.net), [PubMed](https://www.ncbi.nlm.nih.gov/pubmed), [PLOS](https://plos.org) and [DOAJ](https://doaj.org)
-* Persistence and versioning system based on SQLite
+Maintainer: [Christopher Kittel](https://github.com/chreman) ([christopher.kittel@openknowledgemaps.org](mailto:christopher.kittel@openknowledgemaps.org)), [Maxi Schramm](https://github.com/tanteuschi) ([maxi@openknowledgemaps.org](mailto:maxi@openknowledgemaps.org)), and [Peter Kraker](https://github.com/pkraker) ([pkraker@openknowledgemaps.org](mailto:pkraker@openknowledgemaps.org))
 
+Authors: [Thomas Arrow](https://github.com/tarrow), [Andrei Shket](https://github.com/andreishket), [Sergey Krutilin](https://github.com/modsen-hedgehog), [Alexandra Shubenko](https://github.com/vrednyydragon), [Jan Konstant](https://github.com/konstiman), [Asura Enkhbayar](https://github.com/Bubblbu), [Scott Chamberlain](https://github.com/sckott), [Rainer Bachleitner](https://github.com/rbachleitner), [Yael Stein](https://github.com/jaels), [Mike Skaug](https://github.com/mikeskaug), [Philipp Weissensteiner](https://github.com/wpp), and the [Open Knowledge Maps team](http://openknowledgemaps.org/team)
 
 ## Showcases
 
-* [Open Knowledge Maps](https://openknowledgemaps.org/): Creates a visualization on the fly based on a user's search in either BASE or PubMed.
-* [VIPER - The Visual Project Explorer](https://openknowledgemaps.org/viper/): Provides overviews of research projects indexed by OpenAIRE.
-* [CRIS Vis](https://ois.lbg.ac.at/en/cris-I-research-questions): Enables the exploration of crowd-sourced research questions related to mental health.
-* [Overview of Educational Technology](https://openknowledgemaps.org/educational-technology): A working prototype for the field of educational technology based on co-readership.
-* [OpenUP Dissemination Toolbox](https://www.openuphub.eu/tools): A prototype showcasing an overview of innovative dissemination case studies.
-* [Conference Navigator 3](http://halley.exp.sis.pitt.edu/cn3/visualization.php?conferenceID=131) [registration required]: An adaptation of Head Start for the conference scheduling system CN3. This version enables users to schedule papers directly from the visualization. Scheduled papers and recommended papers are highlighted.
+* [Open Knowledge Maps Search](https://openknowledgemaps.org/): Creates a visualisation on the fly based on a user's search in either BASE or PubMed.
+* [OKMaps Custom Services](https://openknowledgemaps.org/custom): Enable third parties to embed customisable search components and visualisations.
+* [VisConnect](https://openknowledgemaps.org/visconnect): Provides an interactive visual profile of a researcher’s work.
 
-## Compatibility
+## Browser compatibility
 
-The visualization has been successfully tested with Chrome, Firefox, Safari and Microsoft Edge. Unfortunately, Internet Explorer is not supported due to the fact that it is not possible to insert HTML into a foreignObject.
+The frontend has been successfully tested with Chrome, Firefox, Safari and Microsoft Edge. Unfortunately, Internet Explorer is not supported due to the fact that it is not possible to insert HTML into a foreignObject.
 
 ## Background
 
 More information can be found in the following papers:
 
+Kraker, P., Beardmore, L., Hemila, M., Johann, D., Kaczmirek, L. & Schubert, C. (2024). [Partizipative Modelle im Zusammenspiel von Bibliotheken und KI-Systemen: Drei Fallstudien zur Integration der visuellen Recherche-Plattform Open Knowledge Maps](https://www.b-i-t-online.de/heft/2024-04-fachbeitrag-kraker.pdf). B.I.T. Online,  27(4), 327-335.
+
+Kraker, P., Goyal, G., Schramm, M., Akin, J., & Kittel, C. (2021). [CoVis: A curated, collaborative & visual knowledge base for COVID-19 research](https://doi.org/10.5281/zenodo.4586079). Zenodo. doi: 10.5281/zenodo.4586079
+
 Kraker, P., Schramm, M., Kittel, C., Chamberlain, S., & Arrow, T. (2018). [VIPER: The Visual Project Explorer](https://zenodo.org/record/1248119). Zenodo. doi:10.5281/zenodo.2587129
 
 Kraker, P., Kittel, C., & Enkhbayar, A. (2016). [Open Knowledge Maps: Creating a Visual Interface to the World’s Scientific Knowledge Based on Natural Language Processing](https://doi.org/10.12685/027.7-4-2-157). 027.7 Journal for Library Culture, 4(2), 98–103. doi:10.12685/027.7-4-2-157
 
 Kraker, P., Schlögl, C. , Jack, K. & Lindstaedt, S. (2015). [Visualization of Co-Readership Patterns from an Online Reference Management System](http://arxiv.org/abs/1409.0348). Journal of Informetrics, 9(1), 169–182. doi:10.1016/j.joi.2014.12.003
 
-Kraker, P., Weißensteiner, P., & Brusilovsky, P. (2014). [Altmetrics-based Visualizations Depicting the Evolution of a Knowledge Domain](http://know-center.tugraz.at/download_extern/papers/sti_visualization_evolution_kraker_etal.pdf). In 19th International Conference on Science and Technology Indicators (pp. 330–333).
-
 Kraker, P., Körner, C., Jack, K., & Granitzer, M. (2012). [Harnessing User Library Statistics for Research Evaluation and Knowledge Domain Visualization](http://know-center.tugraz.at/download_extern/papers/user_library_statistics.pdf). Proceedings of the 21st International Conference Companion on World Wide Web (pp. 1017–1024). Lyon: ACM. doi:10.1145/2187980.2188236
 
 
 ## License
 Head Start is licensed under [MIT](LICENSE).
 
+## Funding
+<img src="https://raw.githubusercontent.com/OpenKnowledgeMaps/CoVis/master/img/EU-flag_small-270x183.png" width="60"> 
 
-## Citation
-If you use Head Start in your research, please cite it as follows:
-
-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
+This project has received funding from the European Union's Horizon 2020 and Horizon Europe research and innovation programmes, under grant agreement nos. 831644, 863420, and 101129751.

README.md

@@ -1,13 +1,13 @@
 services:
-
   db:
-    image: 'postgres:12.2-alpine'
+    image: "postgres:12.2-alpine"
     hostname: "${POSTGRES_HOSTNAME}"
     restart: unless-stopped
     environment:
       POSTGRES_USER: "${POSTGRES_USER}"
       POSTGRES_PASSWORD: "${POSTGRES_PASSWORD}"
-    command: postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf
+    command:
+      postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf
     volumes:
       - db_data:/var/lib/postgresql/data
       - ./local_dev/pg_hba.conf:/etc/pg_hba.conf
@@ -16,18 +16,26 @@ services:
       - headstart
 
   redis:
-    image: 'redis:6.0-alpine'
+    image: "redis:6.0-alpine"
     restart: unless-stopped
     hostname: "${REDIS_HOST}"
     environment:
       REDIS_HOST: "${REDIS_HOST}"
       REDIS_PORT: "${REDIS_PORT}"
-    command: ["redis-server", "/etc/redis/redis.conf", "--bind", "${REDIS_HOST}", "--port", "${REDIS_PORT}"]
+    command:
+      [
+        "redis-server",
+        "/etc/redis/redis.conf",
+        "--bind",
+        "${REDIS_HOST}",
+        "--port",
+        "${REDIS_PORT}",
+      ]
     volumes:
-        - 'redis:/var/lib/redis/data'
-        - ./local_dev/redis.conf:/etc/redis/redis.conf
+      - "redis:/var/lib/redis/data"
+      - ./local_dev/redis.conf:/etc/redis/redis.conf
     ports:
-     - "127.0.0.1:${REDIS_PORT}:${REDIS_PORT}"
+      - "127.0.0.1:${REDIS_PORT}:${REDIS_PORT}"
     networks:
       - headstart
 
@@ -80,6 +88,7 @@ services:
       - ./server/workers/persistence/src:/api
     depends_on:
       - redis
+      - db
     networks:
       - headstart
 
@@ -236,6 +245,8 @@ services:
       LANG: "en_US.UTF-8"
       RENV_PATHS_CACHE: /renv/cache
       PYTHONIOENCODING: "utf-8"
+      R_ALTMETRIC_APIKEY: "${R_ALTMETRIC_APIKEY}"
+      R_CROSSREF_APIMAIL: "${R_CROSSREF_APIMAIL}"
     restart: unless-stopped
     volumes:
       - ./local_dev/renv/cache:/renv/cache
@@ -262,7 +273,6 @@ services:
     networks:
       - headstart
 
-
 volumes:
   redis:
   db_data:

docker-compose.yml

@@ -7,11 +7,11 @@ RUN a2enmod rewrite
 RUN apt-get update && apt-get install -y \
     curl libsqlite3-dev libonig-dev libxml2-dev \
     libasound2 libatk1.0-0 libatk-bridge2.0-0 libc6 libcairo2 libcups2 \
-    libdbus-1-3 libexpat1 libfontconfig1 libgcc-s1 libgdk-pixbuf-2.0-0 \
+    libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgdk-pixbuf-2.0-0 \
     libglib2.0-0 libgtk-3-0 libnspr4 libpango-1.0-0 libpangocairo-1.0-0 libstdc++6 \
     libx11-6 libx11-xcb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxext6 \
     libxfixes3 libxi6 libxrandr2 libxrender1 libxss1 libxtst6 ca-certificates \
-    fonts-liberation libappindicator3-1 libnss3 lsb-release xdg-utils wget
+    fonts-liberation libnss3 lsb-release xdg-utils wget
 
 RUN docker-php-ext-install pdo pdo_sqlite mbstring xml fileinfo
 

headstart.png

@@ -0,0 +1 @@
+{"author":null,"documents":"[]"}

local_dev/dev.env

@@ -0,0 +1,15 @@
+{
+  "endpoint": "http://127.0.0.1:8081/dev/persistence/createVisualization/dev",
+  "visualizations": [
+    {
+      "vis_id": "81abae6d3af6e47761e2a761a47c2c11",
+      "vis_title": "base",
+      "vis_clean_query": "digital education",
+      "vis_query": "digital education",
+      "vis_params": "{\"from\":\"1665-01-01\",\"to\":\"2025-12-03\",\"document_types\":[\"121\"],\"sorting\":\"most-relevant\",\"min_descsize\":\"300\",\"lang_id\":[\"all-lang\"]}",
+      "data_file": "81abae6d3af6e47761e2a761a47c2c11.json"
+    }
+  ]
+}
+
+