Onboarding for Cecilia & A’Kaia

[dondi]

@ceciliazaragoza and @akaiap can now follow the onboarding wiki page (https://github.com/dondi/GRNsight/wiki/Onboarding-Checklist) to get themselves set up w/ GRNsight. @ntran18 and @nchun2 can be consulted in case any issues come up; same with @dondi if there’s anything particularly thorny

Also review the GRNsight publications page (https://dondi.github.io/GRNsight/publications.html) starting with the 2016 PeerJ paper and reviewing some posters in order to start familiarizing yourselves with the application domain

[ceciliazaragoza]

Hi everyone, here are a few changes I think we should make to the documentation for Initial Setup.

1. GRNsight/database/README.md Pt. 1

• Install the software at this link section:
  • For MacOS users, it is recommended to install with homebrew rather than the interactive installation in order to correctly view the initdb --locale=C -E UTF-8 location-of-cluster message in the documentation.
• Start and stop the server section:
  • After installing with homebrew on MacOS, you may receive an error when you try to start the server that the server is unable to be started, and when attempting to stop the server, there terminal states there is no server running. In this case, you have to directly kill the port that the server is running on.
  • To double check that this is the issue, you can open the Activity Monitor app on your computer and search for the postgres activity. If there is one, that means the server is running, and we have to terminate the port that the server is running on.
  • First, we have to check what port the server is running on. Navigate to your homebrew installation, which is the same location-of-cluster from when the database was initialized and open that location in VSCode.
  • Search for port = in the file postgresql.conf. By default, the port should be port 5432, but keep note of this port in case it is different.
  • Refer to this Stack Overflow documentation on how to kill a server:
    • https://stackoverflow.com/questions/4075287/node-express-eaddrinuse-address-already-in-use-kill-server
  • If that doesn't work, then refer to the different methods on this link from Stack Overflow:
    • https://stackoverflow.com/questions/42416527/postgres-app-port-in-use

2. https://github.com/dondi/GRNsight/wiki/Initial-Setup#database-setup Database setup

• On MacOs if you receive the error in your terminal psql: FATAL: role "postgres" does not exist, then try this solution from Stack Overflow(https://stackoverflow.com/questions/15301826/psql-fatal-role-postgres-does-not-exist?page=2&tab=scoredesc#tab-top):
  • sudo -u postgres createuser -s postgres

[kdahlquist]

@ceciliazaragoza is finished with the initial setup. @akaiap is still in progress. She is having issues with the PPI database and plans to attend @dondi's office hours. @akaiap will also add herself to the People page and should just edit the gh-pages branch directly. They have reviewed the paper/posters/slides about GRNsight.

[dondi]

@akaiap and @dondi worked on the database loading issues and found some incompatibilities with her setup for which we did identify solutions. However, what remains to be done is to track down exactly where the incompatibility exists (e.g., is it Python version? OS version? etc.?)

Here are the links that describe the errors we encountered, along with fixes:

• urlparse issue: intermine and Python 3.10 intermine/intermine-ws-python#96 and allow to run on Python 3.10 intermine/intermine-ws-python#97
• SSL_CERTIFICATE_VERIFY_FAILED issue: https://stackoverflow.com/questions/35569042/ssl-certificate-verify-failed-with-python3 —for this solution, the fix needed to be placed in the same webservice.py file as the Interline GitHub PR above

Based on the issues and their solutions, it’s looking like Intermine may be falling behind in keeping up with the latest versions of Python. However, @akaiap will investigate this with @ceciliazaragoza and @ntran18 to pinpoint the exact software differences that reveal these incompatibilities

[dondi]

@akaiap is running into an unexpected issue where npm install doesn’t appear to be creating a node_modules folder as it should. This in turn may be leading to the command not found errors because the system can’t find the installed software

@dondi will need to investigate this further and come back with additional things to try

[dondi]

After additional investigation, @akaiap observed that the node_modules folder does appear but is subsequently deleted. This Stack Overflow question hints that iCloud Sync may be the culprit

@akaiap will try deactivating iCloud Sync once she has made a backup of her files, just in case something does wrong. Backup can be via Box if there is enough space, or also an external drive

[akaiap]

I moved the files from iCloud Sync-- to the machine. After running npm update, install and run start dev. A new error was given. `> parallelshell --wait "nodemon web-client/app.js" "nodemon server/app.js" "webpack --watch --mode=development"

sh: parallelshell: command not found
npm ERR! code ELIFECYCLE
npm ERR! syscall spawn
npm ERR! file sh
npm ERR! errno ENOENT
npm ERR! grnsight@6.0.7 start-dev: parallelshell --wait "nodemon web-client/app.js" "nodemon server/app.js" "webpack --watch --mode=development"
npm ERR! spawn ENOENT
npm ERR!
npm ERR! Failed at the grnsight@6.0.7 start-dev script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above`. Will work with @dondi to fix this error.

[dondi]

“Command not found” still implies to me that the software isn’t fully installed, and hints that the observed deletion might still be taking place. The comment says that the files were moved, but didn’t say that iCloud Sync was actually turned off. @akaiap is iCloud Sync fully deactivated? (again with the reminder to make sure you have a reliable backup of your files before you do this)

[akaiap]

After fully deactivating the iCloud Sync and creating a backup for the files, I reinstalled npm, and ran the command npm run start-dev. The node modules did not appear, so I ran other files that use npm and I got the same result. sh: parallelshell: command not found npm ERR! code ELIFECYCLE npm ERR! syscall spawn npm ERR! file sh npm ERR! errno ENOENT npm ERR! grnsight@6.0.7 start-dev: parallelshell --wait "nodemon web-client/app.js" "nodemon server/app.js" "webpack --watch --mode=development"npm ERR! spawn ENOENT npm ERR! After getting this error-- I did the steps as done earlier. (Deleted NodeModules, and package-lock.json, the ndid npm install. The install could not finish and I received this after 10 minutes of waiting for it to install npm WARN deprecated urix@0.1.0: Please see https://github.com/lydell/urix#deprecated ⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMetadata: sill resolveWithNewModule ctype@0.5.3 chec⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMetadata: sill resolveWithNewModule ctype@0.5.3 chec⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMetadata: sill resol⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMeta⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMetadata: sill resolveWithNewModule ctype@0.5.3 chec⸨ ░░░░░░░░░░░░░░░⸩ ⠏ fetchMetadata: sill resolveWithNewModule ctype@0.5.3 chec⸨ ░░░░░░⸩ ⠸ extract:rxjs: sill extract rxjs@^5.5.2 extracted to /Use Recloned the repo and received (new)this error `npm WARN tar ENOENT: no such file or directory, open '/Users/aphelps/GRNsight2/GRNsight/node_modules/.staging/rxjs-3bcfbfee/LICENSE.txt'
npm WARN tar ENOENT: no such file or directory, open '/Users/aphelps/GRNsight2/GRNsight/node_modules/.staging/rxjs-3bcfbfee/src/LICENSE.txt'
npm WARN notsup Unsupported engine for commander@12.0.0: wanted: {"node":">=18"} (current: {"node":"14.21.3","npm":"6.14.18"})
npm WARN notsup Not compatible with your version of node/npm: commander@12.0.0
npm WARN notsup Unsupported engine for commander@12.0.0: wanted: {"node":">=18"} (current: {"node":"14.21.3","npm":"6.14.18"})
npm WARN notsup Not compatible with your version of node/npm: commander@12.0.0
...npm ERR! Error while executing:
npm ERR! /usr/bin/git ls-remote -h -t ssh://git@github.com/eligrey/FileSaver.js.git
npm ERR!
npm ERR! git@github.com: Permission denied (publickey).
npm ERR! fatal: Could not read from remote repository.
npm ERR!
npm ERR! Please make sure you have the correct access rights
npm ERR! and the repository exists.
npm ERR!
npm ERR! exited with error code: 128

npm ERR! A complete log of this run can be found in:
npm ERR! /Users/aphelps/.npm/_logs/2024-02-20T09_27_59_731Z-debug.log
aphelps@MacBook-Air-3 GRNsight %
`