v0.16.1

.gitignore

@@ -9,3 +9,4 @@ npm-debug.log
 *.iml
 /download/*
 !/download/README
+.vscode

Dockerfile

@@ -31,10 +31,6 @@ RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key
 # Note: NODE_ENV is development so that dev deps are installed
 RUN NODE_ENV=development npm install
 
-# Build project
-RUN npm run clean
-RUN npm run build
-
 # Expose port
 EXPOSE 3000
 

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2020 Pathway Commons
+Copyright (c) 2020 - 2021 Pathway Commons
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the “Software”), to deal in

PRIVACY_POLICY.md

@@ -0,0 +1,56 @@
+<h2>Privacy Policy</h2>
+<p>Your privacy is important to us. It is Biofactoid&#39;s policy to respect your privacy and comply with any applicable law and regulation regarding any personal information we may collect about you, including across our website, <a href="https://biofactoid.org">https://biofactoid.org</a>, and other sites we own and operate. </p>
+<p>This policy is effective as of 25 May 2021 and was last updated on 25 May 2021. </p>
+<h3>Information We Collect</h3>
+<p>Information we collect includes both information you knowingly and actively provide us when using or participating in any of our services and promotions, and any information automatically sent by your devices in the course of accessing our products and services. </p>
+<h4>Log Data</h4>
+<p>When you visit our website, our servers may automatically log the standard data provided by your web browser. It may include your device’s Internet Protocol (IP) address, your browser type and version, the pages you visit, the time and date of your visit, the time spent on each page, other details about your visit, and technical details that occur in conjunction with any errors you may encounter. </p>
+<p>Please be aware that while this information may not be personally identifying by itself, it may be possible to combine it with other data to personally identify individual persons. </p>
+<h4>Personal Information</h4>
+<p>We may ask for personal information which may include one or more of the following: </p>
+<ul>
+   <li>Name</li>
+   <li>Email</li>
+   <li>Social media profiles</li>
+</ul>
+<h4>Legitimate Reasons for Processing Your Personal Information</h4>
+<p>We only collect and use your personal information when we have a legitimate reason for doing so. In which instance, we only collect personal information that is reasonably necessary to provide our services to you. </p>
+<h4>Collection and Use of Information</h4>
+<p>We may collect personal information from you when you do any of the following on our website: </p>
+<ul>
+   <li>Use a mobile device or web browser to access our content</li>
+   <li>Contact us via email, social media, or on any similar technologies</li>
+   <li>When you mention us on social media</li>
+</ul>
+<p>We may collect, hold, use, and disclose information for the following purposes, and personal information will not be further processed in a manner that is incompatible with these purposes: </p>
+<p>We may collect, hold, use, and disclose information for the following purposes, and personal information will not be further processed in a manner that is incompatible with these purposes: </p>
+<ul>
+   <li>to contact and communicate with you</li>
+</ul>
+<p>Please be aware that we may combine information we collect about you with general information or research data we receive from other trusted sources. </p>
+<h4>Security of Your Personal Information</h4>
+<p>When we collect and process personal information, and while we retain this information, we will protect it within commercially acceptable means to prevent loss and theft, as well as unauthorized access, disclosure, copying, use, or modification. </p>
+<p>Although we will do our best to protect the personal information you provide to us, we advise that no method of electronic transmission or storage is 100% secure, and no one can guarantee absolute data security. We will comply with laws applicable to us in respect of any data breach. </p>
+<p>You are responsible for selecting any password and its overall security strength, ensuring the security of your own information within the bounds of our services. </p>
+<h4>How Long We Keep Your Personal Information</h4>
+<p>We keep your personal information only for as long as we need to. This time period may depend on what we are using your information for, in accordance with this privacy policy. If your personal information is no longer required, we will delete it or make it anonymous by removing all details that identify you. </p>
+<p>However, if necessary, we may retain your personal information for our compliance with a legal, accounting, or reporting obligation or for archiving purposes in the public interest, scientific, or historical research purposes or statistical purposes. </p>
+<h3>Children’s Privacy</h3>
+<p>We do not aim any of our products or services directly at children under the age of 13, and we do not knowingly collect personal information about children under 13. </p>
+<h3>International Transfers of Personal Information</h3>
+<p>The personal information we collect is stored and/or processed where we or our partners, affiliates, and third-party providers maintain facilities. Please be aware that the locations to which we store, process, or transfer your personal information may not have the same data protection laws as the country in which you initially provided the information. If we transfer your personal information to third parties in other countries: (i) we will perform those transfers in accordance with the requirements of applicable law; and (ii) we will protect the transferred personal information in accordance with this privacy policy. </p>
+<h3>Your Rights and Controlling Your Personal Information</h3>
+<p>You always retain the right to withhold personal information from us, with the understanding that your experience of our website may be affected. We will not discriminate against you for exercising any of your rights over your personal information. If you do provide us with personal information you understand that we will collect, hold, use and disclose it in accordance with this privacy policy. You retain the right to request details of any personal information we hold about you. </p>
+<p>If we receive personal information about you from a third party, we will protect it as set out in this privacy policy. If you are a third party providing personal information about somebody else, you represent and warrant that you have such person’s consent to provide the personal information to us. </p>
+<p>If you have previously agreed to us using your personal information for direct marketing purposes, you may change your mind at any time. We will provide you with the ability to unsubscribe from our email-database or opt out of communications. Please be aware we may need to request specific information from you to help us confirm your identity. </p>
+<p>If you believe that any information we hold about you is inaccurate, out of date, incomplete, irrelevant, or misleading, please contact us using the details provided in this privacy policy. We will take reasonable steps to correct any information found to be inaccurate, incomplete, misleading, or out of date. </p>
+<p>If you believe that we have breached a relevant data protection law and wish to make a complaint, please contact us using the details below and provide us with full details of the alleged breach. We will promptly investigate your complaint and respond to you, in writing, setting out the outcome of our investigation and the steps we will take to deal with your complaint. You also have the right to contact a regulatory body or data protection authority in relation to your complaint. </p>
+<h3>Limits of Our Policy</h3>
+<p>Our website may link to external sites that are not operated by us. Please be aware that we have no control over the content and policies of those sites, and cannot accept responsibility or liability for their respective privacy practices. </p>
+<h3>Changes to This Policy</h3>
+<p>At our discretion, we may change our privacy policy to reflect updates to our business processes, current acceptable practices, or legislative or regulatory changes. If we decide to change this privacy policy, we will post the changes here at the same link by which you are accessing this privacy policy. </p>
+<p>If required by law, we will get your permission or give you the opportunity to opt in to or opt out of, as applicable, any new uses of your personal information. </p>
+<h3>Contact Us</h3>
+<p>For any questions or concerns regarding your privacy, you may contact us using the following details: </p>
+<p>The Biofactoid Team<br />
+info@biofactoid.org </p>

README.md

@@ -1,14 +1,21 @@
 # Factoid
 
+[![DOI](https://zenodo.org/badge/3910378.svg)](https://zenodo.org/badge/latestdoi/3910378)
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/PathwayCommons/factoid/blob/unstable/LICENSE)
+
 Biofactoid [(biofactoid.org)](https://biofactoid.org/), is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.
 
+Biofactoid's codebase is licensed under [MIT](LICENSE).
+
 ## Getting the data
 
 All contributed pathway data is freely available for download at https://biofactoid.org/api/document/zip which contains files for each pathway represented in:
   - JavaScript Object Notation (JSON). This is the native format for Biofactoid data and contains interaction data, metadata of the record itself, metadata of the corresponding article, and visualisation data (layout and colors as Cytoscape JSON (Franz et al. (2016) Bioinforma. Oxf. Engl., 32, 309–311.)).
   - [Biological Pathway Exchange (BioPAX)](http://www.biopax.org/) (Demir et al. (2010) Biotechnol., 28, 935–942.) for detailed semantic exchange.
   - [Systems Biology Graphical Notation Markup Language (SBGNML)](https://sbgn.github.io/), a format that supports biological process visualization (Le Novère et al. Nat. Biotechnol., 27, 735–741. (2009); van Iersel et al. (2012) Bioinforma. Oxf. Engl., 28, 2016–2021.)
 
+Our data is licensed under [CC0](https://creativecommons.org/publicdomain/zero/1.0/legalcode).
+
 ## Required software
 
 - [Node.js](https://nodejs.org/en/) >=10
@@ -32,6 +39,7 @@ CRON:
 - `DOCUMENT_CRON_UPDATE_PERIOD_DAYS` : The minimum time between successive Document cron update calls
 - `DOCUMENT_CRON_CREATED_AGE_DAYS` : Only Documents created fewer than this many days will be selecte for update. When undefined (default), ignores filtering on creation date.
 - `DOCUMENT_CRON_REFRESH_ENABLED` : Flag to enable existing Document metadata to be refreshed (e.g. PubMed UID) (default true).
+- `DOCUMENT_CRON_UNEDITED_DAYS` : Number of days since Documemt was last edited; criteria for trashing
 
 Database:
 
@@ -149,80 +157,7 @@ The following environment variables should always be set in production instances
 
 ## Running via Docker
 
-### Requirements
-
-Dockerized system has been successfully deployed on:
-  - Ubuntu 16.04.5 LTS (GNU/Linux 4.4.0-145-generic x86_64)
-    - Docker version 19.03.12
-    - docker-compose version 1.26.2
-  - OSX 10.15.1 (Catalina)
-    - Docker version 19.03.12
-    - docker-compose version 1.26.2
-
-### Docker Compose
-
-In the directory containing the `docker-compose.yml` file, execute:
-
-```sh
-docker-compose up -d
-```
-
-Monitor stdout of the system:
-
-```sh
-docker-compose logs -ft
-```
-
-Stop and remove services:
-```sh
-docker-compose down
-```
-
-#### Notes
-
-- Environment variables:
-  - Docker Compose will draw environment variables from the shell or from an `.env` file in the same directory. Please see private [remote](https://github.com/BaderLab/sysadmin/blob/master/websites/factoid.md) for production-level file settings.
-
-- Database service:
-  - Do not restart a stopped container. Rather, remove and run anew.
-
-- OS specifics:
-  - For Ubuntu 16.04.5 LTS to [play nice with elasticsearch](https://github.com/docker-library/elasticsearch/issues/111#issuecomment-268511769) needed to set `sudo sysctl -w vm.max_map_count=262144`.
-
-### Dump and restore Rethinkdb data
-
-NB: RethinkDB [dump and restore](https://rethinkdb.com/docs/backup/) command-line utility depends on the [Python driver](https://rethinkdb.com/docs/install-drivers/python/). The `docker/Dockerfile-rethinkdb` file documents these requirements.
-
-#### Dump
-
-To create an archive of data in RethinkDB, use the supplied bash script `/docker/dump_rethinkdb.sh`.
-
-- The script accepts four arguments:
-  - `-c` (required) The container name
-  - `-e` (optional) Limit the dump to the given database and/or table; Use dot notation e.g. 'test.authors'
-  - `-n` (optional) The dump archive name; `.tar.gz` will be appended
-  - `-d` (optional) Output to the specified directory on the host; defaults to `pwd`
-
-Example: To dump a running container `db_container` with database named `factoid` to an archive named `factoid_dump_latest` in a directory on the host named `/backups`:
-
-```sh
-./dump_rethinkdb.sh -c db_container -e factoid -n factoid_dump_latest -d /backups
-```
-
-#### Restore
-
-To populate RethinkDB from an archive, use the supplied bash script `/docker/restore_rethinkdb.sh`.
-
-- The script accepts three arguments:
-  - `-c` (required) The container name
-  - `-f` (required) Archive file path on host
-  - `-i` (optional) Limit the restore to the given database and/or table; Use dot notation e.g. 'test.authors'. By default, the script will overwrite any existing database/table data.
-
-Example: To restore a running container `db_container` with database named `factoid` from an archive named `/backups/factoid_dump_latest.tar.gz`:
-
-```sh
-./restore_rethinkdb.sh -c db_container -f /backups/factoid_dump_latest.tar.gz -i factoid
-```
+Images are maintained at [dockerhub](https://hub.docker.com/repository/docker/pathwaycommons/factoid). Also see [factoid-docker-config](https://github.com/PathwayCommons/factoid-docker-config).
 
 ## Testing
 
@@ -247,6 +182,7 @@ Notes:
   1. For a breaking API change, run `npm version major.`
   1. For a specific version number (e.g. 1.2.3), run `npm version 1.2.3`.
 1. Push the release: `git push origin --tags`
+1. [Publish a GitHub release](https://github.com/PathwayCommons/factoid/releases/new) so that Zenodo creates a DOI for this version.
 
 ## Related software