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README.md

Research Software Directory Build Status DOI

This README file has the following sections:

What is the Research Software Directory?

The Research Software Directory is a content management system that is tailored to software.

The idea is that institutes for whom research software is an important output, can run their own instance of the Research Software Directory. The system is designed to be flexible enough to allow for different data sources, database schemas, and so on. By default, the Research Software Directory is set up to collect data from GitHub, Zenodo, Zotero, as well as Medium blogs.

For each software package, a product page can be created on the Research Software Directory if the software is deemed useful to others. Here is an example of what a product page may look like:

/docs/images/20180627-webcapture-xenon.png

While the content shown on the product page can be completely customized, by default it includes a Mentions section, which can be used to characterize the context in which the software exists. The context may include links to scientific papers, but is certainly broader than that: for example, there may be links to web applications that demonstrate the use of the software, there may be links to videos on YouTube, tutorials on readthedocs.io or Jupyter notebooks, or there may be links to blog posts; really, anything that helps visitors decide if the software could be useful for them.

The Research Software Directory improves findability of software packages, partly because it provides metadata that helps search engines understand what the software is about, but more importantly because of the human centered text snippets that must be provided for each software package. After all, discovery of a software package is often not so much about finding it but knowing that you found it.

How do I enter data into an instance of the Research Software Directory?

The process is described here.

Documentation for developers

Try it out locally

Basically, the steps to get a copy of https://research-software.nl running locally (including data) are as follows:

  1. Fork this repo to your own GitHub organization or GitHub profile and clone it
  2. Configure
  3. Start the complete stack using docker-compose

For details, see below.

Make sure you have a Linux computer with docker, docker-compose, and git installed. Other operating systems might work but we develop exclusively on Linux based systems. You can find the installation instructions for each tool here:

You'll need a minimum of about 3 GB free disk space to store the images, containers and volumes that we will be making.

Optionally, add yourself to the docker group following the instructions here (our documentation assumes that you did).

Try it out, step 1/3: Fork and clone

Click the Fork button on https://github.com/research-software-directory/research-software-directory/ to fork to your own GitHub organization or GitHub profile, then:

git clone https://github.com/<your-github-organization>/research-software-directory.git

Try it out, step 2/3: Configure

The research software directory is configured using a file with environment variables called rsd-secrets.env. An example config file (rsd-secrets.env.example) is available, use it as a starting point.

cd research-software-directory
cp rsd-secrets.env.example rsd-secrets.env

The config file has some placeholder values (changeme); they must be set by editing the rsd-secrets.env file. Below are instructions on how to get the different tokens and keys.

AUTH_GITHUB_CLIENT_ID and AUTH_GITHUB_CLIENT_SECRET

These environment variables are used for authenticating a user, such that they can be granted access to the admin interface to create, read, update, and delete items in the Research Software Directory.

These are the steps to assign values:

  1. Go to https://github.com/settings/developers
  2. Click the New OAuth App button
  3. Under Application name, write something like The Research Software Directory's admin interface on localhost
  4. Under Homepage URL fill in some URL, for example, let it point to this readme on GitHub. Despite the fact that it is a required field, its value is not used as far as I can tell.
  5. Optionally add a description. This is especially useful if you have multiple OAuth apps
  6. The most important setting is the value for Authorization callback url. Set it to http://localhost/auth/get_jwt for now. We will revisit AUTH_GITHUB_CLIENT_ID and AUTH_GITHUB_CLIENT_SECRET in the section about deployment below
  7. Click Register application
  8. Assign the Client ID as value for AUTH_GITHUB_CLIENT_ID and assign the Client Secret as value for AUTH_GITHUB_CLIENT_SECRET

AUTH_GITHUB_ORGANIZATION

Data is entered into the Research Software Directory via the admin interface. Set AUTH_GITHUB_ORGANIZATION to the name of the GitHub organization whose members should be allowed access to the admin interface. Most likely, it is the name of the organization where you forked this repository to.

Note: members should make their membership of the GitHub organization public. Go to https://github.com/orgs/<your-github-organization>/people to see which users are a member of <your-github-organization>, and whether their membership is public or not.

GITHUB_ACCESS_TOKEN

To query GitHub's API programmatically, we need an access token. Here's how you can get one:

  1. Go to https://github.com/settings/tokens
  2. Click Generate new token
  3. Under Token description, fill in something like Key to programmatically retrieve information from GitHub's API
  4. Verify that all scopes are unchecked
  5. Use token as value for GITHUB_ACCESS_TOKEN

ZOTERO_LIBRARY

When getting the references data from Zotero, this environment variable determines which library on Zotero is going to be harvested. Go to https://www.zotero.org/groups/ to see which Zotero groups you are a member of. If you click on the Group library link there, the URL will change to something like https://www.zotero.org/groups/1689348/netherlands_escience_center/items, where 1689348 is the value you need to assign to ZOTERO_LIBRARY.

ZOTERO_API_KEY

To query Zotero's API programmatically, we need an API key. Here's how you can get one:

  1. https://www.zotero.org/settings/keys
  2. Click Create new private key
  3. Type a description of the key, e.g. API key to access library X on Zotero
  4. Under Personal library, make sure only Allow library access is checked.
  5. Under Default group permissions, choose None
  6. Under Specific groups, check Per group permissions
  7. Set Read only for the group that you want to harvest your references data from; verify that any other groups are set to None
  8. Click the Save Key button at the bottom of the page.
  9. On the Key Created page, you will see a string of random character, something like bhCJSBCcjzptBvd3fvliYOoE. This is the key; assign it to ZOTERO_API_KEY

BACKUP_CMD

This environment variable is used for making a daily backup of the database with software, people, projects, etc. As it is typically only used during deployment, leave its value like it is for now; we will revisit it in the section about deployment below.

JWT_SECRET

The JWT_SECRET is simply a string of random characters. You can generate one yourself using the openssl command line tool, as follows:

openssl rand -base64 32

Assign the result to JWT_SECRET.

DOMAIN, SSL_ADMIN_EMAIL, and SSL_DOMAINS

These environment variables are not relevant when you're running your instance locally. Leave their values like they are in rsd-secrets.env.example for the time being. We will revisit them in the section about deployment below.

Try it out, step 3/3: Start the complete stack using docker-compose

# add the environment variables from rsd-secrets.env to the current terminal:
source rsd-secrets.env

# start the full stack using docker-compose:
docker-compose --project-name rsd up --build
# shorthand:
docker-compose -p rsd up --build

After the Research Software Directory instance is up and running, we want to start harvesting data from external sources such as GitHub, Zotero, Zenodo, etc. To do so, open a new terminal and run

source rsd-secrets.env
docker-compose --project-name rsd exec harvesting python app.py harvest all

You should see some feedback in the newly opened terminal.

After the harvest all task finishes, several database collections should have been updated, but we still need to use the data from those separate collections and combine them into one document that we can feed to the frontend. This is done with the resolve task, as follows:

docker-compose --project-name rsd exec harvesting python app.py resolve

By default, the resolve tasks runs every fifth minute anyway, so you could just wait for a bit, until you see some output scroll by that is generated by the rsd-harvesting container, something like:

rsd-harvesting     | 2018-07-11 10:30:02,990 cache_software [INFO] processing Xenon command line interface
rsd-harvesting     | 2018-07-11 10:30:03,013 cache_software [INFO] processing Xenon gRPC server
rsd-harvesting     | 2018-07-11 10:30:03,036 cache_software [INFO] processing xtas
rsd-harvesting     | 2018-07-11 10:30:03,059 cache_software [INFO] processing boatswain
rsd-harvesting     | 2018-07-11 10:30:03,080 cache_software [INFO] processing Research Software Directory
rsd-harvesting     | 2018-07-11 10:30:03,122 cache_software [INFO] processing cffconvert
rsd-harvesting     | 2018-07-11 10:30:03,149 cache_software [INFO] processing sv-callers

Open a web browser to verify that everything works as it should.


Customize your instance of the Research Software Directory

Let's say you followed the steps above, and have a running instance of the Research Software Directory. Now it is time to start customizing your Research Software Directory. We have prepared some FAQs for customizations that are common. For example, you can read up on the following topics:

  1. How do I change the colors?
  2. How do I change the font?
  3. How do I change the logo?
  4. How do I change when data collection scripts run?
  5. How do I empty the database?
  6. How do I make changes to the admin interface?
  7. How do I add properties to the data schema?

It is suggested that you first do one or more of:

  1. How do I change the colors?
  2. How do I change the font?
  3. How do I change the logo?

Then, learn how to add properties to the schema:

  1. How do I add properties to the data schema?

Finally, learn how to empty the database, such that you can replace the sample data with your own:

  1. How do I empty the database?

General workflow when making changes

After making your changes, here's how you get to see them:

  1. Go to the terminal where you started docker-compose

  2. Use Ctrl+C to stop the running instance of Research Software Directory

  3. Check which docker containers you have with:

    docker-compose --project-name rsd ps
    # shorthand:
    docker-compose -p rsd ps
    

    For example, mine says:

    docker-compose -p rsd ps
           Name                     Command                State     Ports 
    ----------------------------------------------------------------------
    rsd-admin            sh -c rm -rf /build/* && c ...   Exit 0           
    rsd-authentication   /bin/sh -c gunicorn --prel ...   Exit 0           
    rsd-backend          /bin/sh -c gunicorn --prel ...   Exit 0           
    rsd-database         /mongo.sh --bind_ip 0.0.0.0      Exit 137         
    rsd-frontend         /bin/sh -c sh -c "mkdir -p ...   Exit 0           
    rsd-nginx-ssl        /bin/sh -c /start.sh             Exit 137         
    rsd-reverse-proxy    /bin/sh -c nginx -g 'daemo ...   Exit 137         
    rsd-harvesting       /bin/sh -c crond -d7 -f          Exit 137  
    

    Use docker-compose rm to delete container by their service name, e.g. the rsd-frontend container:

    docker-compose --project-name rsd rm frontend
    # shorthand: 
    docker-compose -p rsd rm frontend
    

    List all docker images on your system:

    docker images
    

    Note that image names consist of whatever you entered as --project-name, followed by _, followed by the service name. Remove as follows:

    docker rmi rsd_frontend
    
  4. Make changes to the source code of the service whose container and image you just removed

  5. Rebuild containers as necessary, using:

    docker-compose --project-name rsd build frontend
    docker-compose --project-name rsd up frontend
    

Make your instance available to others by hosting it online (deployment)

Amazon Web Services (AWS) is a online service provider that offers all kinds of services relating to compute, storage, and hosting. The Netherlands eScience Center uses AWS to run their instance of the Research Software Directory. This section describes how to deploy your own customized instance of the Research Software Directory to AWS.

Go to https://aws.amazon.com/console/. Once there, you'll see something like:

AWS Management Console login

Create a free account if you don't already have one, and subsequently click Sign In to the Console.

Once in the console, you'll be presented with an overview of all the services that Amazon Web Services has to offer:

AWS Management Console Services Overview

It's easy to get lost in this plethora of services, but for running an instance of the Research Software Directory, you'll only need 3 of them:

  1. EC2: this is where we will run your customized instance of the Research Software Directory and host it online; jump to the EC2 section
  2. IAM: we use this to create a user with limited privileges, so we don't have to use root credentials when we don't have to; jump to the IAM section
  3. S3: this is where we will store our daily backups; jump to the S3 section

Configuring EC2

In the All Services overview, click EC2 or use this link https://console.aws.amazon.com/ec2.

  1. Click the blue Launch instance button

  2. Scroll down to where it says Ubuntu Server 18.04 LTS, click Select

  3. Choose instance type t2.small

  4. Proceed in the wizard by clicking Next until you get to Configure Security Group. It should already have one rule listed. However, its security settings should be a bit more secure, because currently it allows SSH connections from any IP. Click the Source dropdown button, select My IP.

  5. Now click the blue Review and Launch button in the lower right corner

  6. In the Review screen, click the blue Launch button in the lower right corner to bring the instance up

  7. In the Keypair popup, select Create a new key pair, try to give it a meaningful name, e.g. rsd-instance-on-aws or something

  8. Click Download Key Pair, save the *.pem file in ~/.ssh on your local machine, then click Launch Instances (it takes a moment to initialize).

  9. On your local machine, open a terminal and go to ~/.ssh. Change the permissions of the key file to octal 400 (readable only by user):

    chmod 400 <the keyfile>
    
  10. Verify that the .ssh directory itself has octal permission 700 (readable, writable, and executable by user only).

  11. Go back to Amazon, click View instances

  12. Make a note of your instance's public IPv4, e.g. 3.92.182.176

  13. On your own machine use a terminal to log in to your instance

  14. ssh -i path-to-the-keyfile ubuntu@<your-instance-public-ip>

  15. Once logged in to the remote machine, install docker and docker-compose, then add user ubuntu to the group docker, same as before (see section Documentation for developers above).

  16. Make a new directory and change into it:

    cd ~
    mkdir rsd
    cd rsd
    
  17. The machine should have git installed, use it to git clone your customized Research Software Directory instance into the current directory as follows:

    git clone https://github.com/<your-github-organization>/research-software-directory.git .
    

    (Note the dot at the end)

  18. Open a new terminal and secure-copy your local rsd-secrets.env file to the Amazon machine as follows:

    cd <where rsd-secrets.env is>
    scp -i path-to-the-keyfile ./rsd-secrets.env \
    ubuntu@<your-instance-public-ip>:/home/ubuntu/rsd/rsd-secrets.env
  19. Follow the instructions above to make a second key pair AUTH_GITHUB_CLIENT_ID and AUTH_GITHUB_CLIENT_SECRET. However, let this one's Authorization callback url be https:// plus your instance's IPv4 plus /auth/get_jwt. Update the Amazon copy of rsd-secrets.env according to the new client ID and secret.

  20. Start the Research Software Directory instance with:

    cd ~/rsd
    source rsd-secrets.env
    docker-compose --project-name rsd up --build &
  21. On your local machine, open a new terminal. Connect to the Amazon instance, run the harvesters, and resolve the foreign keys:

    ssh -i path-to-the-keyfile ubuntu@<your-instance-public-ip>
    
    cd ~/rsd
    
    source rsd-secrets.env
    
    docker-compose --project-name rsd exec harvesting \
    python app.py harvest all
    
    docker-compose --project-name rsd exec harvesting \
    python app.py resolve

At this point we should have a world-reachable, custom instance of the Research Software Directory running at https://<your-instance-public-ip>/. However, if we go there using a browser like Firefox or Google Chrome, we get a warning that the connection is not secure.

To fix this, we need to configure the security credentials, but this in turn requires us to claim a domain and configure a DNS record. There are free services available that you can use for this, e.g. https://noip.com. Here's how:

  1. Go to https://noip.com, sign up and log in.

  2. Under My services, find DNS Records

  3. Click the Add a hostname button

  4. Choose your free (sub)domain name, e.g. I chose myrsd.ddns.net

  5. Fill in the IP address of your Amazon machine. In my case, https://myrsd.ddns.net will serve as an alias for https://3.92.182.176

  6. Once you have the (sub)domain name, update DOMAIN and SSL_DOMAINS in the file rsd-secrets.env on your Amazon instance (leave out the https:// part, as well as anything after the .com, .nl, .org or whatever you may have).

  7. Fill in your e-mail for SSL_ADMIN_EMAIL.

  8. Finally, revisit your OAuth app here https://github.com/settings/developers, replace the Amazon IP address in the Authorization callback url with your freshly minted domain name.

  9. Now, stop the Research Software Directory if it is still running with Ctrl-c or docker-compose -p rsd stop.

  10. Update the environment variables by sourceing your secrets again:

    cd ~/rsd
    source rsd-secrets.env
    
  11. Start the Research Software Directory back up

    cd ~/rsd
    docker-compose -p rsd up
    
  12. Pointing your browser to your (sub)domain name should now show your instance of the Research Software Directory (although be aware that sometimes it takes a while before the domain name resolves to the IP address.

Configuring IAM

  1. In the All Services overview, click IAM or use this link https://console.aws.amazon.com/iam.
  2. In the menu on the left, click Groups.
  3. Click the Create New Group button.
  4. Name the group s3-users.
  5. When asked to attach a (security) policy, use the search bar to find AmazonS3FullAccess and check its checkbox.
  6. Click the Next step button in the lower right corner.
  7. Review your group, go back if need be. When you're ready, click the Create Group button in the lower right corner.
  8. Now you should be presented with a group, but the group is still empty; there are no users.
  9. In the menu on the left, click Users.
  10. Click the Add user button in the top left corner.
  11. Choose your user name. I chose to call mine rsd-backup-maker. For this user, check the checkbox labeled Programmatic access. This user won't need AWS Management Console access, so leave that box unchecked.
  12. In the lower right corner, click the Next: Permissions button.
  13. Select Add user to group, and make user rsd-backup-maker a member of group s3-users.
  14. In the lower right corner, click the Next: Tags button. We don't need to assign any tags, so proceed to the next page by clicking Next: Review. Go back if you need to, but if everything looks OK, click Create User. You will be presented with the new user's credentials. Download the CSV file now; we'll use the Access key ID and the Secret access key later to set up the backup mechanism.

Configuring S3

In the All Services overview, click S3 or use this link https://console.aws.amazon.com/s3.

  1. create a bucket with a random name (bucket names must be globally unique; websites like https://www.random.org/strings/ are useful to get a random string)

  2. in that bucket, make a directory, e.g. rsd-backups

  3. The backup service contains a program (xenon-cli) that can copy to a range of storage providers. You can use it to make daily backups of the MongoDB database, and store the backups on Amazon's S3. For this, configure the environmental variable BACKUP_CMD as follows (naturally, you'll need to use a different location, username, and password; see explanation below):

    BACKUP_CMD='xenon filesystem s3 \
    --location http://s3-us-west-2.amazonaws.com/nyor-yiwy-fepm-dind/ \
    --username AKIAJ52LWSUUKATRQZ2A \
    --password xQ3ezZLKN7XcxIwRko2xkKhV9gdJ5etA4OyLbXN/ \
    upload rsd-backup.tar.gz /rsd-backups/rsd-backup-$BACKUP_DATE.tar.gz'
    
    • The bucket name is nyor-yiwy-fepm-dind. It is physically located in zone us-west-2.
    • We access the bucket as a limited-privileges IAM user, for whom we created an access key (it has been deactivated since). The Access key ID is AKIAJ52LWSUUKATRQZ2A, and its corresponding Secret access key is xQ3ezZLKN7XcxIwRko2xkKhV9gdJ5etA4OyLbXN/.
    • The variable BACKUP_DATE is set by the backup script (see /backup/backup.sh); no need to change this for your application.
    • rsd-backup.tar.gz is the name of the backup archive as it is called inside the container; no need to change this for your application.
    • /rsd-backups/rsd-backup-$BACKUP_DATE.tar.gz is the path inside the bucket. It includes the date to avoid overwriting previously existing archives; no need to change this for your application.
  4. Test the setup by stopping the Research Software Directory on Amazon, by

    #ssh into the remote machine
    cd rsd
    docker-compose -p rsd stop
    # update BACKUP_CMD by editing the rsd-secrets.env file
    source rsd-secrets.env
    docker-compose -p rsd up
    

    Wait until the Research Software Directory is up and running again, then open a second terminal and

    #ssh into the remote machine
    cd rsd
    docker-compose -p rsd exec backup /bin/sh
    /app # /bin/sh backup.sh
    

Documentation for maintainers

Visualizing docker-compose.yml

It is sometimes helpful to visualize the structure in the docker-compose.yml file. Use https://github.com/pmsipilot/docker-compose-viz to generate a png image.

docker run --rm -it --name dcv -v $(pwd):/input pmsipilot/docker-compose-viz render -m image --output-file=docs/images/docker-compose.png docker-compose.yml

For example,

/docs/images/docker-compose.png

Making a release

  1. Write the release notes

  2. Update CITATION.cff

  3. Generate the metadata file for Zenodo using cffconvert.

    pip install --user cffconvert
    cffconvert --outputformat zenodo --ignore-suspect-keys --outfile .zenodo.json
    # git add, commit, and push everything
  4. Make sure that everything is pushed

    cd $(mktemp -d)
    git clone https://github.com/research-software-directory/research-software-directory.git
    cd research-software-directory
  5. Follow the notes from the 'For developers' section above, and verify that it all works as it should.

  6. Use GitHub's Draft a new release button here to make a release.

Pulling in changes from upstream using a three-way merge

Set UPSTREAM and DOWNSTREAM to the different sources you want to three-way merge between, e.g.

UPSTREAM=https://github.com/research-software-directory/research-software-directory.git
DOWNSTREAM=https://github.com/process-project/research-software-directory.git

Then:

cd $(mktemp -d)
mkdir left middle right
cd left && git clone $UPSTREAM . && cd -
cd middle && git clone $DOWNSTREAM . && git branch develop && git checkout develop && cd -
cd right && git clone $DOWNSTREAM . && cd -
meld left middle right &

You should only make changes to the middle one. When you're done making your changes,

git add <the files>
git commit
git push origin develop
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