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PathwayCommons / hyper-recent

Hyper-recent article feed
MIT License
1 stars 0 forks source link

Updated data scripts #28

Closed jvwong closed 1 year ago

jvwong commented 1 year ago

Compatible on:

Fixed various bugs, better logging.

codecov[bot] commented 1 year ago

Codecov Report

Merging #28 (01b66b0) into main (a455c9d) will not change coverage. The diff coverage is n/a.

@@          Coverage Diff          @@
##            main     #28   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files          2       2           
  Lines        106     106           
=====================================
  Misses       106     106

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jvwong commented 1 year ago

Looks like the cloudflare build is still failing. I can't see the logs.

maxkfranz commented 1 year ago 
2022-11-09T04:36:59.410146Z Cloning repository...
2022-11-09T04:37:02.748213Z From https://github.com/PathwayCommons/hyper-recent
2022-11-09T04:37:02.748882Z  * branch            eec77062e0e222383c23898b9095641a8b09e795 -> FETCH_HEAD
2022-11-09T04:37:02.749061Z 
2022-11-09T04:37:03.293812Z HEAD is now at eec7706 Merge pull request #28 from PathwayCommons/debug-scripts
2022-11-09T04:37:03.294423Z 
2022-11-09T04:37:03.455948Z 
2022-11-09T04:37:03.486553Z Success: Finished cloning repository files
2022-11-09T04:37:04.230124Z Installing dependencies
2022-11-09T04:37:04.243359Z Python version set to 2.7
2022-11-09T04:37:06.448845Z Attempting node version 'v16.16.0' from .nvmrc
2022-11-09T04:37:07.9709Z   Downloading and installing node v16.16.0...
2022-11-09T04:37:08.430374Z Downloading https://nodejs.org/dist/v16.16.0/node-v16.16.0-linux-x64.tar.xz...
2022-11-09T04:37:09.067278Z Computing checksum with sha256sum
2022-11-09T04:37:09.20029Z  Checksums matched!
2022-11-09T04:37:13.774437Z Now using node v16.16.0 (npm v8.11.0)
2022-11-09T04:37:14.229816Z Started restoring cached build plugins
2022-11-09T04:37:14.244286Z Finished restoring cached build plugins
2022-11-09T04:37:14.813311Z Attempting ruby version 2.7.1, read from environment
2022-11-09T04:37:19.011369Z Using ruby version 2.7.1
2022-11-09T04:37:19.413052Z Using PHP version 5.6
2022-11-09T04:37:19.610049Z 5.2 is already installed.
2022-11-09T04:37:19.642012Z Using Swift version 5.2
2022-11-09T04:37:19.642641Z Started restoring cached node modules
2022-11-09T04:37:19.662112Z Finished restoring cached node modules
2022-11-09T04:37:20.2059Z   Installing NPM modules using NPM version 8.11.0
2022-11-09T04:37:20.656143Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:37:20.656616Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:37:20.656804Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:37:21.089451Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:37:21.089811Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:37:21.089983Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:37:37.142753Z 
2022-11-09T04:37:37.143165Z added 444 packages, and audited 445 packages in 16s
2022-11-09T04:37:37.143336Z 
2022-11-09T04:37:37.143485Z 89 packages are looking for funding
2022-11-09T04:37:37.143632Z   run `npm fund` for details
2022-11-09T04:37:37.147919Z 
2022-11-09T04:37:37.148524Z 1 moderate severity vulnerability
2022-11-09T04:37:37.148946Z 
2022-11-09T04:37:37.149273Z To address all issues, run:
2022-11-09T04:37:37.149641Z   npm audit fix
2022-11-09T04:37:37.149983Z 
2022-11-09T04:37:37.150178Z Run `npm audit` for details.
2022-11-09T04:37:37.165733Z NPM modules installed
2022-11-09T04:37:37.772076Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:37:37.772511Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:37:37.772755Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:37:37.793365Z Installing Hugo 0.54.0
2022-11-09T04:37:38.518183Z Hugo Static Site Generator v0.54.0-B1A82C61A/extended linux/amd64 BuildDate: 2019-02-01T10:04:38Z
2022-11-09T04:37:38.522807Z Started restoring cached go cache
2022-11-09T04:37:38.548184Z Finished restoring cached go cache
2022-11-09T04:37:38.743178Z go version go1.14.4 linux/amd64
2022-11-09T04:37:38.761535Z go version go1.14.4 linux/amd64
2022-11-09T04:37:38.76491Z  Installing missing commands
2022-11-09T04:37:38.765252Z Verify run directory
2022-11-09T04:37:38.765427Z Executing user command: npm run build
2022-11-09T04:37:39.290658Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:37:39.291117Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:37:39.291728Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:37:39.309757Z 
2022-11-09T04:37:39.310102Z > hyper-recent@1.0.0 build
2022-11-09T04:37:39.310253Z > run-s build:data build:css build:js
2022-11-09T04:37:39.310384Z 
2022-11-09T04:37:39.991013Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:37:39.991451Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:37:39.991623Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:37:40.007468Z 
2022-11-09T04:37:40.007833Z > hyper-recent@1.0.0 build:data
2022-11-09T04:37:40.007986Z > cd ./scripts && ./search.sh && ./recommendations.sh
2022-11-09T04:37:40.008103Z 
2022-11-09T04:37:40.738559Z START: search 
2022-11-09T04:37:40.739013Z 
2022-11-09T04:37:40.739189Z Fetching from biorxiv between 2022-10-09 and 2022-11-09
2022-11-09T04:40:25.584993Z Fetching from medrxiv between 2022-10-09 and 2022-11-09
2022-11-09T04:40:40.909409Z Combining results...
2022-11-09T04:40:41.411625Z Searching for alzheimer
2022-11-09T04:40:45.74975Z  Found 89 hits
2022-11-09T04:40:45.818317Z END: search 
2022-11-09T04:40:45.8187Z   
2022-11-09T04:40:45.828435Z START: recommendations 
2022-11-09T04:40:45.829158Z 
2022-11-09T04:40:45.830998Z Fetching from Semantic Scholar https://api.semanticscholar.org/recommendations/v1/papers/forpaper/PMID:33933186?limit=500&fields=title,year,externalIds,venue,authors,abstract
2022-11-09T04:40:45.831244Z Paper: PMID:33933186
2022-11-09T04:40:45.831401Z CATEGORY_ID: alzheimers-diagnosis
2022-11-09T04:40:47.719217Z numPapers (Total): 491
2022-11-09T04:40:47.974365Z numPapers (Filtered): 37
2022-11-09T04:40:47.991735Z numitems 37
2022-11-09T04:41:34.783308Z Fetching from Semantic Scholar https://api.semanticscholar.org/recommendations/v1/papers/forpaper/PMID:33318676?limit=500&fields=title,year,externalIds,venue,authors,abstract
2022-11-09T04:41:34.78524Z  Paper: PMID:33318676
2022-11-09T04:41:34.785491Z CATEGORY_ID: alzheimers-neuroinflammation
2022-11-09T04:41:36.099178Z numPapers (Total): 427
2022-11-09T04:41:36.250679Z numPapers (Filtered): 27
2022-11-09T04:41:36.272074Z numitems 27
2022-11-09T04:42:10.471801Z END: recommendations 
2022-11-09T04:42:10.472246Z 
2022-11-09T04:42:10.995605Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:42:10.996195Z npm WARN config location in the cache, and they are managed by
2022-11-09T04:42:10.996459Z npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:42:11.014963Z 
2022-11-09T04:42:11.015274Z > hyper-recent@1.0.0 build:css
2022-11-09T04:42:11.015456Z > esbuild --bundle src/dashboard/index.css --outfile=src/dashboard/build/bundle.css --loader:.jpg=dataurl
2022-11-09T04:42:11.01563Z  
2022-11-09T04:42:11.05538Z  
2022-11-09T04:42:11.055684Z   src/dashboard/build/bundle.css  2.9kb
2022-11-09T04:42:11.055851Z 
2022-11-09T04:42:11.05597Z  ⚡ Done in 11ms
2022-11-09T04:42:11.472627Z npm WARN config tmp This setting is no longer used.  npm stores temporary files in a special
2022-11-09T04:42:11.47313Z  npm WARN config location in the cache, and they are managed by
2022-11-09T04:42:11.47365Z  npm WARN config     [`cacache`](http://npm.im/cacache).
2022-11-09T04:42:11.490223Z 
2022-11-09T04:42:11.490537Z > hyper-recent@1.0.0 build:js
2022-11-09T04:42:11.490677Z > esbuild src/dashboard/index.js --bundle --outfile=src/dashboard/build/bundle.js
2022-11-09T04:42:11.490806Z 
2022-11-09T04:42:11.532687Z 
2022-11-09T04:42:11.533026Z   src/dashboard/build/bundle.js  125.3kb
2022-11-09T04:42:11.533175Z 
2022-11-09T04:42:11.533295Z ⚡ Done in 15ms
2022-11-09T04:42:11.563268Z Finished
2022-11-09T04:42:11.564065Z Note: No functions dir at /functions found. Skipping.
2022-11-09T04:42:11.564276Z Validating asset output directory
2022-11-09T04:42:12.931913Z Failed: an internal error occurred

It looks like the scripts are completing, but deployment is failing. Maybe the symlinks