Setting up GlyGen main API and frontend modules on AWS server

[rykahsay]

So far, you have successfully installed

• https://aws.data.glygen.org (data module)
• https://aws.dsapi.glygen.org/ (DSAPI or API for data module)

Next step is to set up the following modules

• https://aws.api.glygen.org/ (GlyGen main API module or API module for the main GlyGen frontend, following instructions on https://github.com/glygener/glygen-backend-api/tree/2.0)
• https://aws.glygen.org/ (GlyGen frontend module or main GlyGen frontend, following instructions on https://github.com/glygener/glygen-frontend/tree/master)

[tiwa1154]

@rykahsay I am setting up the main API. Ran into an issue in Step 3 [https://github.com/glygener/glygen-backend-api/tree/2.0#step-3-initialize-and-populate-your-mongodb-database].

I ran python3 populate_all_collections.py -s prd -v 2.0.3 -m full and received error message "Usage: populate_all_collections.py [options]

populate_all_collections.py: error: no such option: -m"

[tiwa1154]

@rykahsay For the frontend module, I followed https://github.com/glygener/glygen-frontend/blob/master/server-installation.md but the docker-glygen-frontend.service file is missing in the repo.

[tiwa1154]

@rykahsay I ran python3 populate_collections.py -s $DEP -v $VER but got error in the screenshot below:

[tiwa1154]

@rykahsay For the frontend module, which branch are we using? Master or ver_2.0?

[rykahsay]

Yes, use 2.0 branch.

For the logs, create the logs dir:

mkdir logs

[tiwa1154]

@rykahsay For the main API:

1. created the container running_glygen_api_prd but can't start the container with sudo systemctl start docker-glygen-api-prd.service. See screenshot:

For Frontend:

1. ran sudo make -f MakeFile prod and received some errors:

[tiwa1154]

Also, for the API, I ran python3 update-search-init.py -s tst, received Failed to establish a new connection, see screenshot:

[rykahsay]

We need to look into these issues on webex -- please set up a meeting on Friday after the group meeting.

[tiwa1154]

@rykahsay Sent an email invitation for Friday's meeting.

[tiwa1154]

Successfully created the frontend on the server

@rykahsay Tried to map it to a public domain of aws.glygen.org in the /etc/httpd/conf.d/awsdata.conf. However, it seems to be not connected correctly and aws.glygen.org still shows not found.

[tiwa1154]

@rykahsay For the main API implementation, also ran into issues with populating the mongodb database. See screenshot: showing FileNotFoundError

[tiwa1154]

@rykahsay

For dataset-api, had an issue with populating mongodb database: python3 load_current_release.py -s prd -v 2.0.3 -m full:

Connection refused.

[rykahsay]

For the second last comment you made, I have already gave you a solution --> scroll up and find it.

For the last comment, it is working now:

[tiwa1154]

Running the last step of API testing, ran sudo python3 run_api_test.py -m 1 -g protein -s prd, received error: Also, you mentioned modifying config.json, not sure what exactly I should modify. @rykahsay

[tiwa1154]

@rykahsay

1. I have finished setting up Main GlyGen API: aws.api.glygen.org/ and the frontend container is running on the server but seems like /aws.glygen.org/ is not created by Dacian yet.
2. I tried to reset the dataset API and APP but when I go to aws.data.glygen.org/ and aws.dsapi.glygen.org, see error in the screenshot: . I assume it's because I changed the file path in the conf file to /efc/shared instead of the original path of /data/shared/ because when I run sudo python3 create_api_container.py -s prd, some steps are shown as CACHED and making directory in the /date/shared path

[tiwa1154]

@rykahsay

1. Downloaded 2.1.1, tried to create and start docker container for the APP. Seems still not working on https://aws.data.glygen.org/. Shown as a blank page.
2. When I populated the MongoDB, using python3 load_cur rent_release.py -s {DEP} -v {VER}, encountered an error, see screenshot:

[rykahsay]

It should work now, but before you get to do that, you had to load the data. I have started the loading using the command given below.

python3 load_current_release.py  -s prd -v 2.1.1

It is loading to the last container (c_records) which takes some time.

[tiwa1154]

Thanks, @rykahsay

So I created and started the docker container for the APP but the https://aws.data.glygen.org/ is shown as a blank page. How should I troubleshoot?

[rykahsay]

I have fixed the problem --> there needs to be additional customization of the app/conf/config.json file as shown below:

[rykahsay]

[tiwa1154]

aws.glygen.org domain has been created but the certificate is invalid. Should I send an email to Dacian or @rykahsay you will handle it?

[tiwa1154]