Closed jvwong closed 1 year ago
Merging #26 (90b18d7) into main (55d1db5) will not change coverage. The diff coverage is
n/a
.
@@ Coverage Diff @@
## main #26 +/- ##
=====================================
Coverage 0.00% 0.00%
=====================================
Files 2 2
Lines 106 106
=====================================
Misses 106 106
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It looks like there's an error in the script:
2022-11-08T22:35:49.741348Z Cloning repository...
2022-11-08T22:35:53.596815Z From https://github.com/PathwayCommons/hyper-recent
2022-11-08T22:35:53.597422Z * branch e78e666665397f2d1e3b0d0b7ed17ad098c15655 -> FETCH_HEAD
2022-11-08T22:35:53.597597Z
2022-11-08T22:35:54.129442Z HEAD is now at e78e666 Merge pull request #26 from PathwayCommons/iss25_static-site
2022-11-08T22:35:54.130011Z
2022-11-08T22:35:54.27415Z
2022-11-08T22:35:54.302514Z Success: Finished cloning repository files
2022-11-08T22:35:55.129815Z Installing dependencies
2022-11-08T22:35:55.142616Z Python version set to 2.7
2022-11-08T22:35:57.013007Z Attempting node version 'v16.16.0' from .nvmrc
2022-11-08T22:35:58.509364Z Downloading and installing node v16.16.0...
2022-11-08T22:35:58.936302Z Downloading https://nodejs.org/dist/v16.16.0/node-v16.16.0-linux-x64.tar.xz...
2022-11-08T22:35:59.484539Z Computing checksum with sha256sum
2022-11-08T22:35:59.614153Z Checksums matched!
2022-11-08T22:36:03.878367Z Now using node v16.16.0 (npm v8.11.0)
2022-11-08T22:36:04.267912Z Started restoring cached build plugins
2022-11-08T22:36:04.281072Z Finished restoring cached build plugins
2022-11-08T22:36:04.767112Z Attempting ruby version 2.7.1, read from environment
2022-11-08T22:36:08.236195Z Using ruby version 2.7.1
2022-11-08T22:36:08.586182Z Using PHP version 5.6
2022-11-08T22:36:08.753857Z 5.2 is already installed.
2022-11-08T22:36:08.781Z Using Swift version 5.2
2022-11-08T22:36:08.782Z Started restoring cached node modules
2022-11-08T22:36:08.797503Z Finished restoring cached node modules
2022-11-08T22:36:09.297927Z Installing NPM modules using NPM version 8.11.0
2022-11-08T22:36:09.706224Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T22:36:09.706637Z npm WARN config location in the cache, and they are managed by
2022-11-08T22:36:09.706965Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T22:36:10.105795Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T22:36:10.106143Z npm WARN config location in the cache, and they are managed by
2022-11-08T22:36:10.106383Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T22:36:18.774088Z
2022-11-08T22:36:18.774443Z added 443 packages, and audited 444 packages in 9s
2022-11-08T22:36:18.774613Z
2022-11-08T22:36:18.774768Z 88 packages are looking for funding
2022-11-08T22:36:18.775092Z run `npm fund` for details
2022-11-08T22:36:18.778653Z
2022-11-08T22:36:18.778887Z 1 moderate severity vulnerability
2022-11-08T22:36:18.779027Z
2022-11-08T22:36:18.779153Z To address all issues, run:
2022-11-08T22:36:18.779307Z npm audit fix
2022-11-08T22:36:18.779447Z
2022-11-08T22:36:18.77956Z Run `npm audit` for details.
2022-11-08T22:36:18.792903Z NPM modules installed
2022-11-08T22:36:19.357352Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T22:36:19.357794Z npm WARN config location in the cache, and they are managed by
2022-11-08T22:36:19.358075Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T22:36:19.376556Z Installing Hugo 0.54.0
2022-11-08T22:36:20.101622Z Hugo Static Site Generator v0.54.0-B1A82C61A/extended linux/amd64 BuildDate: 2019-02-01T10:04:38Z
2022-11-08T22:36:20.105912Z Started restoring cached go cache
2022-11-08T22:36:20.124716Z Finished restoring cached go cache
2022-11-08T22:36:20.265424Z go version go1.14.4 linux/amd64
2022-11-08T22:36:20.280059Z go version go1.14.4 linux/amd64
2022-11-08T22:36:20.282846Z Installing missing commands
2022-11-08T22:36:20.283121Z Verify run directory
2022-11-08T22:36:20.283253Z Executing user command: npm run build
2022-11-08T22:36:20.755339Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T22:36:20.755675Z npm WARN config location in the cache, and they are managed by
2022-11-08T22:36:20.755835Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T22:36:20.772019Z
2022-11-08T22:36:20.772277Z > hyper-recent@1.0.0 build
2022-11-08T22:36:20.772432Z > run-s build:data build:css build:js
2022-11-08T22:36:20.772556Z
2022-11-08T22:36:21.377153Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T22:36:21.377517Z npm WARN config location in the cache, and they are managed by
2022-11-08T22:36:21.377673Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T22:36:21.392274Z
2022-11-08T22:36:21.392546Z > hyper-recent@1.0.0 build:data
2022-11-08T22:36:21.392685Z > cd ./scripts && ./search.sh && ./recommendations.sh
2022-11-08T22:36:21.392802Z
2022-11-08T22:36:21.424874Z date: invalid option -- 'v'
2022-11-08T22:36:21.425318Z Try 'date --help' for more information.
2022-11-08T22:36:21.43242Z Fetching from biorxiv between and 2022-11-08
2022-11-08T22:36:21.621304Z error: missing required argument 'endDate'
2022-11-08T22:36:21.643309Z numPapersRawBiorxiv:
2022-11-08T22:36:21.643641Z Fetching from medrxiv between and 2022-11-08
2022-11-08T22:36:21.818327Z error: missing required argument 'endDate'
2022-11-08T22:36:21.837753Z numPapersRawMedrxiv:
2022-11-08T22:36:21.838979Z Combining results...
2022-11-08T22:36:21.846275Z jq: error: Could not open file ../example-data/2022-11-08_*.json: No such file or directory
2022-11-08T22:36:21.855159Z jq - commandline JSON processor [version 1.5-1-a5b5cbe]
2022-11-08T22:36:21.855683Z Usage: jq [options] <jq filter> [file...]
2022-11-08T22:36:21.856898Z
2022-11-08T22:36:21.85741Z jq is a tool for processing JSON inputs, applying the
2022-11-08T22:36:21.857649Z given filter to its JSON text inputs and producing the
2022-11-08T22:36:21.857883Z filter's results as JSON on standard output.
2022-11-08T22:36:21.858124Z The simplest filter is ., which is the identity filter,
2022-11-08T22:36:21.858363Z copying jq's input to its output unmodified (except for
2022-11-08T22:36:21.858614Z formatting).
2022-11-08T22:36:21.858821Z For more advanced filters see the jq(1) manpage ("man jq")
2022-11-08T22:36:21.859017Z and/or https://stedolan.github.io/jq
2022-11-08T22:36:21.860077Z
2022-11-08T22:36:21.860427Z Some of the options include:
2022-11-08T22:36:21.860662Z -c compact instead of pretty-printed output;
2022-11-08T22:36:21.860846Z -n use `null` as the single input value;
2022-11-08T22:36:21.861005Z -e set the exit status code based on the output;
2022-11-08T22:36:21.861166Z -s read (slurp) all inputs into an array; apply filter to it;
2022-11-08T22:36:21.861285Z -r output raw strings, not JSON texts;
2022-11-08T22:36:21.861495Z -R read raw strings, not JSON texts;
2022-11-08T22:36:21.861671Z -C colorize JSON;
2022-11-08T22:36:21.86184Z -M monochrome (don't colorize JSON);
2022-11-08T22:36:21.862023Z -S sort keys of objects on output;
2022-11-08T22:36:21.862152Z --tab use tabs for indentation;
2022-11-08T22:36:21.862262Z --arg a v set variable $a to value <v>;
2022-11-08T22:36:21.86238Z --argjson a v set variable $a to JSON value <v>;
2022-11-08T22:36:21.862507Z --slurpfile a f set variable $a to an array of JSON texts read from <f>;
2022-11-08T22:36:21.862635Z See the manpage for more options.
2022-11-08T22:36:21.862754Z Searching for alzheimers-disease
2022-11-08T22:36:22.03935Z undefined:1
2022-11-08T22:36:22.039676Z
2022-11-08T22:36:22.039834Z
2022-11-08T22:36:22.039953Z SyntaxError: Unexpected end of JSON input
2022-11-08T22:36:22.040075Z at JSON.parse (<anonymous>)
2022-11-08T22:36:22.040199Z at getInput (file:///opt/buildhome/repo/src/cli.js:67:17)
2022-11-08T22:36:22.040324Z at async Command.search (file:///opt/buildhome/repo/src/cli.js:23:20)
2022-11-08T22:36:22.040478Z at async Command.parseAsync (/opt/buildhome/repo/node_modules/commander/lib/command.js:917:5)
2022-11-08T22:36:22.040598Z at async main (file:///opt/buildhome/repo/src/cli.js:103:3)
2022-11-08T22:36:22.058635Z Found hits
2022-11-08T22:36:22.080143Z jq - commandline JSON processor [version 1.5-1-a5b5cbe]
2022-11-08T22:36:22.080485Z Usage: jq [options] <jq filter> [file...]
2022-11-08T22:36:22.080641Z
2022-11-08T22:36:22.080773Z jq is a tool for processing JSON inputs, applying the
2022-11-08T22:36:22.080908Z given filter to its JSON text inputs and producing the
2022-11-08T22:36:22.08103Z filter's results as JSON on standard output.
2022-11-08T22:36:22.081139Z The simplest filter is ., which is the identity filter,
2022-11-08T22:36:22.081247Z copying jq's input to its output unmodified (except for
2022-11-08T22:36:22.08137Z formatting).
2022-11-08T22:36:22.081692Z For more advanced filters see the jq(1) manpage ("man jq")
2022-11-08T22:36:22.081834Z and/or https://stedolan.github.io/jq
2022-11-08T22:36:22.081948Z
2022-11-08T22:36:22.082055Z Some of the options include:
2022-11-08T22:36:22.082162Z -c compact instead of pretty-printed output;
2022-11-08T22:36:22.082273Z -n use `null` as the single input value;
2022-11-08T22:36:22.082404Z -e set the exit status code based on the output;
2022-11-08T22:36:22.082528Z -s read (slurp) all inputs into an array; apply filter to it;
2022-11-08T22:36:22.08264Z -r output raw strings, not JSON texts;
2022-11-08T22:36:22.082768Z -R read raw strings, not JSON texts;
2022-11-08T22:36:22.082885Z -C colorize JSON;
2022-11-08T22:36:22.082996Z -M monochrome (don't colorize JSON);
2022-11-08T22:36:22.083102Z -S sort keys of objects on output;
2022-11-08T22:36:22.083207Z --tab use tabs for indentation;
2022-11-08T22:36:22.083369Z --arg a v set variable $a to value <v>;
2022-11-08T22:36:22.083507Z --argjson a v set variable $a to JSON value <v>;
2022-11-08T22:36:22.083628Z --slurpfile a f set variable $a to an array of JSON texts read from <f>;
2022-11-08T22:36:22.083812Z See the manpage for more options.
2022-11-08T22:36:22.093703Z ERROR: "build:data" exited with 2.
2022-11-08T22:36:22.112113Z Failed: build command exited with code: 1
2022-11-08T22:36:23.061073Z Failed: an internal error occurred
The initial problem is this:
2022-11-08T22:36:21.424874Z date: invalid option -- 'v'
2022-11-08T22:36:21.425318Z Try 'date --help' for more information.
2022-11-08T22:36:21.43242Z Fetching from biorxiv between and 2022-11-08
2022-11-08T22:36:21.621304Z error: missing required argument 'endDate'
date
is different on Mac than it is on Linux, so either a more general command/options should be used or we could just hardcode the dates for now.
The date is OK (now), but the data processing is failing:
2022-11-08T23:10:55.652744Z Cloning repository...
2022-11-08T23:10:58.764597Z From https://github.com/PathwayCommons/hyper-recent
2022-11-08T23:10:58.765089Z * branch a455c9d6997caf9afb9447eb75327b0768bb026b -> FETCH_HEAD
2022-11-08T23:10:58.765224Z
2022-11-08T23:10:59.223999Z HEAD is now at a455c9d OS-agnostic dates #26
2022-11-08T23:10:59.224421Z
2022-11-08T23:10:59.340196Z
2022-11-08T23:10:59.364775Z Success: Finished cloning repository files
2022-11-08T23:11:00.130095Z Installing dependencies
2022-11-08T23:11:00.139041Z Python version set to 2.7
2022-11-08T23:11:01.659244Z Attempting node version 'v16.16.0' from .nvmrc
2022-11-08T23:11:02.844653Z Downloading and installing node v16.16.0...
2022-11-08T23:11:03.20416Z Downloading https://nodejs.org/dist/v16.16.0/node-v16.16.0-linux-x64.tar.xz...
2022-11-08T23:11:03.619321Z Computing checksum with sha256sum
2022-11-08T23:11:03.738395Z Checksums matched!
2022-11-08T23:11:07.391256Z Now using node v16.16.0 (npm v8.11.0)
2022-11-08T23:11:07.730741Z Started restoring cached build plugins
2022-11-08T23:11:07.741565Z Finished restoring cached build plugins
2022-11-08T23:11:08.149397Z Attempting ruby version 2.7.1, read from environment
2022-11-08T23:11:11.01931Z Using ruby version 2.7.1
2022-11-08T23:11:11.318024Z Using PHP version 5.6
2022-11-08T23:11:11.446839Z 5.2 is already installed.
2022-11-08T23:11:11.472923Z Using Swift version 5.2
2022-11-08T23:11:11.474051Z Started restoring cached node modules
2022-11-08T23:11:11.487159Z Finished restoring cached node modules
2022-11-08T23:11:11.892673Z Installing NPM modules using NPM version 8.11.0
2022-11-08T23:11:12.220589Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T23:11:12.220905Z npm WARN config location in the cache, and they are managed by
2022-11-08T23:11:12.221072Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T23:11:12.546342Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T23:11:12.546614Z npm WARN config location in the cache, and they are managed by
2022-11-08T23:11:12.546733Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T23:11:23.98791Z
2022-11-08T23:11:23.988205Z added 444 packages, and audited 445 packages in 11s
2022-11-08T23:11:23.988326Z
2022-11-08T23:11:23.988419Z 89 packages are looking for funding
2022-11-08T23:11:23.98851Z run `npm fund` for details
2022-11-08T23:11:23.991936Z
2022-11-08T23:11:23.992168Z 1 moderate severity vulnerability
2022-11-08T23:11:23.992303Z
2022-11-08T23:11:23.992474Z To address all issues, run:
2022-11-08T23:11:23.992628Z npm audit fix
2022-11-08T23:11:23.992738Z
2022-11-08T23:11:23.992862Z Run `npm audit` for details.
2022-11-08T23:11:24.007821Z NPM modules installed
2022-11-08T23:11:24.449177Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T23:11:24.449436Z npm WARN config location in the cache, and they are managed by
2022-11-08T23:11:24.449555Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T23:11:24.465438Z Installing Hugo 0.54.0
2022-11-08T23:11:25.105439Z Hugo Static Site Generator v0.54.0-B1A82C61A/extended linux/amd64 BuildDate: 2019-02-01T10:04:38Z
2022-11-08T23:11:25.108959Z Started restoring cached go cache
2022-11-08T23:11:25.124036Z Finished restoring cached go cache
2022-11-08T23:11:25.236643Z go version go1.14.4 linux/amd64
2022-11-08T23:11:25.248289Z go version go1.14.4 linux/amd64
2022-11-08T23:11:25.250692Z Installing missing commands
2022-11-08T23:11:25.250895Z Verify run directory
2022-11-08T23:11:25.25101Z Executing user command: npm run build
2022-11-08T23:11:25.630393Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T23:11:25.630752Z npm WARN config location in the cache, and they are managed by
2022-11-08T23:11:25.630873Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T23:11:25.644604Z
2022-11-08T23:11:25.644819Z > hyper-recent@1.0.0 build
2022-11-08T23:11:25.644922Z > run-s build:data build:css build:js
2022-11-08T23:11:25.645013Z
2022-11-08T23:11:26.142219Z npm WARN config tmp This setting is no longer used. npm stores temporary files in a special
2022-11-08T23:11:26.142505Z npm WARN config location in the cache, and they are managed by
2022-11-08T23:11:26.14263Z npm WARN config [`cacache`](http://npm.im/cacache).
2022-11-08T23:11:26.154628Z
2022-11-08T23:11:26.154988Z > hyper-recent@1.0.0 build:data
2022-11-08T23:11:26.155123Z > cd ./scripts && ./search.sh && ./recommendations.sh
2022-11-08T23:11:26.15525Z
2022-11-08T23:11:26.667362Z Fetching from biorxiv between 2022-10-08 and 2022-11-08
2022-11-08T23:14:13.102351Z numPapersRawBiorxiv:
2022-11-08T23:14:13.103282Z Fetching from medrxiv between 2022-10-08 and 2022-11-08
2022-11-08T23:14:28.356771Z numPapersRawMedrxiv:
2022-11-08T23:14:28.357284Z Combining results...
2022-11-08T23:14:29.028963Z jq - commandline JSON processor [version 1.5-1-a5b5cbe]
2022-11-08T23:14:29.029259Z Usage: jq [options] <jq filter> [file...]
2022-11-08T23:14:29.02938Z
2022-11-08T23:14:29.029476Z jq is a tool for processing JSON inputs, applying the
2022-11-08T23:14:29.029575Z given filter to its JSON text inputs and producing the
2022-11-08T23:14:29.029702Z filter's results as JSON on standard output.
2022-11-08T23:14:29.029962Z The simplest filter is ., which is the identity filter,
2022-11-08T23:14:29.030109Z copying jq's input to its output unmodified (except for
2022-11-08T23:14:29.030202Z formatting).
2022-11-08T23:14:29.030299Z For more advanced filters see the jq(1) manpage ("man jq")
2022-11-08T23:14:29.030394Z and/or https://stedolan.github.io/jq
2022-11-08T23:14:29.030489Z
2022-11-08T23:14:29.030579Z Some of the options include:
2022-11-08T23:14:29.030672Z -c compact instead of pretty-printed output;
2022-11-08T23:14:29.030761Z -n use `null` as the single input value;
2022-11-08T23:14:29.030892Z -e set the exit status code based on the output;
2022-11-08T23:14:29.030995Z -s read (slurp) all inputs into an array; apply filter to it;
2022-11-08T23:14:29.031107Z -r output raw strings, not JSON texts;
2022-11-08T23:14:29.031203Z -R read raw strings, not JSON texts;
2022-11-08T23:14:29.031302Z -C colorize JSON;
2022-11-08T23:14:29.031392Z -M monochrome (don't colorize JSON);
2022-11-08T23:14:29.031483Z -S sort keys of objects on output;
2022-11-08T23:14:29.031573Z --tab use tabs for indentation;
2022-11-08T23:14:29.031665Z --arg a v set variable $a to value <v>;
2022-11-08T23:14:29.031757Z --argjson a v set variable $a to JSON value <v>;
2022-11-08T23:14:29.031858Z --slurpfile a f set variable $a to an array of JSON texts read from <f>;
2022-11-08T23:14:29.03195Z See the manpage for more options.
2022-11-08T23:14:30.792735Z Searching for alzheimers-disease
2022-11-08T23:14:30.952441Z undefined:1
2022-11-08T23:14:30.95274Z
2022-11-08T23:14:30.952882Z
2022-11-08T23:14:30.953031Z SyntaxError: Unexpected end of JSON input
2022-11-08T23:14:30.95316Z at JSON.parse (<anonymous>)
2022-11-08T23:14:30.953291Z at getInput (file:///opt/buildhome/repo/src/cli.js:67:17)
2022-11-08T23:14:30.953396Z at async Command.search (file:///opt/buildhome/repo/src/cli.js:23:20)
2022-11-08T23:14:30.953501Z at async Command.parseAsync (/opt/buildhome/repo/node_modules/commander/lib/command.js:917:5)
2022-11-08T23:14:30.953605Z at async main (file:///opt/buildhome/repo/src/cli.js:103:3)
2022-11-08T23:14:30.970202Z Found hits
2022-11-08T23:14:30.989054Z jq - commandline JSON processor [version 1.5-1-a5b5cbe]
2022-11-08T23:14:30.98945Z Usage: jq [options] <jq filter> [file...]
2022-11-08T23:14:30.989592Z
2022-11-08T23:14:30.98969Z jq is a tool for processing JSON inputs, applying the
2022-11-08T23:14:30.989787Z given filter to its JSON text inputs and producing the
2022-11-08T23:14:30.989877Z filter's results as JSON on standard output.
2022-11-08T23:14:30.989978Z The simplest filter is ., which is the identity filter,
2022-11-08T23:14:30.990143Z copying jq's input to its output unmodified (except for
2022-11-08T23:14:30.990239Z formatting).
2022-11-08T23:14:30.99033Z For more advanced filters see the jq(1) manpage ("man jq")
2022-11-08T23:14:30.990423Z and/or https://stedolan.github.io/jq
2022-11-08T23:14:30.990513Z
2022-11-08T23:14:30.990617Z Some of the options include:
2022-11-08T23:14:30.990732Z -c compact instead of pretty-printed output;
2022-11-08T23:14:30.990827Z -n use `null` as the single input value;
2022-11-08T23:14:30.990921Z -e set the exit status code based on the output;
2022-11-08T23:14:30.991046Z -s read (slurp) all inputs into an array; apply filter to it;
2022-11-08T23:14:30.991146Z -r output raw strings, not JSON texts;
2022-11-08T23:14:30.991236Z -R read raw strings, not JSON texts;
2022-11-08T23:14:30.991325Z -C colorize JSON;
2022-11-08T23:14:30.991419Z -M monochrome (don't colorize JSON);
2022-11-08T23:14:30.99151Z -S sort keys of objects on output;
2022-11-08T23:14:30.991601Z --tab use tabs for indentation;
2022-11-08T23:14:30.991692Z --arg a v set variable $a to value <v>;
2022-11-08T23:14:30.991794Z --argjson a v set variable $a to JSON value <v>;
2022-11-08T23:14:30.99189Z --slurpfile a f set variable $a to an array of JSON texts read from <f>;
2022-11-08T23:14:30.991983Z See the manpage for more options.
2022-11-08T23:14:30.998576Z ERROR: "build:data" exited with 2.
2022-11-08T23:14:31.013194Z Failed: build command exited with code: 1
2022-11-08T23:14:31.961925Z Failed: an internal error occurred
Maybe I need to make sure this works on linux.
Can reproduce error on Ubuntu 16.04.7 LTS, node 16.16, jq-1.5-1-a5b5cbe ...
A)
build
script now triggersbuild:data
which fetches article data B) Symlink from./dist
to./src/dashboard
etc - not sure if this is what you were looking for?Refs #25