breck7 / cancerdb Goto Github PK

Interesting project, it took me a while to understand what this is attempting to be.

I also noted that this uses JTree notation, which wasn't obvious at first, and could use better docs: https://github.com/breck7/jtree
Scroll gave more insight: https://github.com/breck7/scroll

For example, how specifically is grammar supported here? I would personally think more in graph terms, node, edge, relation, etc.

I have my own personal knowledge notes for cancer, and I have been thinking about a markdown-as-graph-db tool as well (Aspen/Obsidian).

The goal is noble, but without a license many will be hesitant to clone, and share.

STR:

• go to https://cancerdb.com/
• search anything
• returns error

According to https://www.iccp-portal.org/cancer-registries

"Worldwide, there are more than 700 cancer registries."

We currently only have 1: https://cancerdb.com/search.html?q=select+type%0D%0Awhere+type+includes+tumorRegistry

@breck7 Hi, good work! most of the site tabs are now good. Only experiencing it for the /pages/about.html

Reference Issue
#20

https://cancerdb.com/search.html?q=notMissing+uscsMortalityRate%0D%0Aselect+uscsMortalityRate+uscsDeathsPerYear%0D%0AsortBy+uscsMortalityRate%0D%0Areverse%0D%0Atitle+Highest+mortality+rates%0D%0Adescription+Annual+cancer+deaths+divided+by+annual+new+cases.+Not+a+perfect+measure+but+gives+a+rough+estimate+of+deadliness+of+cancer+types.+Data+is+from+the+2019+United+States+Cancer+Statistics+dataset+from+the+CDC.

Sometimes when I start the site the above query works. Sometimes it doesn't. For some reason uscsMortalityRate does not get set in this line extendedTqlGrammar.getNode("columnNameCell").set("enum", folder.colNamesForCsv.join(" "))

I tried a few dumb things to debug but couldn't figure it out. Smells like a race condition, but even that I'm not sure about.

I guess it happens both on Mac and Linux.

PLDB obviously works but CANCERDB does not. cancerDB doesn't feel right—should we just go all lowercase?

I'm voting all lowercase, unless anyone else has other opinions.

Do we need to hardcode the height and width into the HTML tag in the YouTube embeds?

https://cancerdb.com/posts/index.html

Not all cancer registries have websites, especially ones outside the west.

To cover the entire planet, will cancer DB allow key "reference" instead of website ?

There seems to be no documented way to clean files that were created by cdb that were added by mistake but were successfully compiled into the deployment directory.

Deploying from a directory already containing a previous successfully compiled checkout could lead to confusion.

Hi Breck (@breck7),

A recent run has the following error:

2022-09-12T19:06:36.2695175Z 📜📜📜 WELCOME TO SCROLL (v31.6.0) 📜📜📜
2022-09-12T19:06:36.2700903Z 
2022-09-12T19:06:36.2701649Z 👷 building folder '/home/runner/work/CancerDB/CancerDB/site'
2022-09-12T19:06:36.2702598Z 
2022-09-12T19:06:36.2765595Z node:fs:594
2022-09-12T19:06:36.2769164Z   handleErrorFromBinding(ctx);
2022-09-12T19:06:36.2770382Z   ^
2022-09-12T19:06:36.2770912Z 
2022-09-12T19:06:36.2771860Z Error: ENOENT: no such file or directory, open '/home/runner/work/CancerDB/pldb/site/scrollExtensions.scroll'
2022-09-12T19:06:36.2772652Z     at Object.openSync (node:fs:594:3)
2022-09-12T19:06:36.2773411Z     at Object.readFileSync (node:fs:462:35)
2022-09-12T19:06:36.2774273Z     at Function.Disk.read (/usr/local/lib/node_modules/scroll-cli/node_modules/jtree/products/Disk.node.js:11:24)
2022-09-12T19:06:36.2804021Z     at readFileWithCache (/usr/local/lib/node_modules/scroll-cli/scroll.js:60:55)
2022-09-12T19:06:36.2805395Z     at getFullyExpandedFile (/usr/local/lib/node_modules/scroll-cli/scroll.js:69:15)
2022-09-12T19:06:36.2811601Z     at /usr/local/lib/node_modules/scroll-cli/scroll.js:84:25
2022-09-12T19:06:36.2812355Z     at Array.forEach (<anonymous>)
2022-09-12T19:06:36.2813075Z     at getFullyExpandedFile (/usr/local/lib/node_modules/scroll-cli/scroll.js:80:8)
2022-09-12T19:06:36.2813583Z     at /usr/local/lib/node_modules/scroll-cli/scroll.js:84:25
2022-09-12T19:06:36.2813889Z     at Array.forEach (<anonymous>) {
2022-09-12T19:06:36.2814173Z   errno: -2,
2022-09-12T19:06:36.2814412Z   syscall: 'open',
2022-09-12T19:06:36.2814794Z   code: 'ENOENT',
2022-09-12T19:06:36.2815218Z   path: '/home/runner/work/CancerDB/pldb/site/scrollExtensions.scroll'
2022-09-12T19:06:36.2815619Z }
2022-09-12T19:06:36.2834778Z ##[error]Process completed with exit code 1.
2022-09-12T19:06:36.2904274Z Post job cleanup.

The problem is with open '/home/runner/work/CancerDB/pldb/site/scrollExtensions.scroll' Is the folder or the scroll missing?

Kind Regards,
Liam

the value of key reference seems to have an issue interpreting its values.

The value for key reference value containing URL https://extranet.who.int/ncdccs/Data/ALB_B5_NCCP%20Albania%20English.pdf is interpreted on the cancer DB web portal as https://extranet.who.int/ncdccs/Data/ALB%3C/em%3EB5_NCCP%20Albania%20English.pdf

The value for key reference containing URL https://www.iccp-portal.org/system/files/plans/ALB_2020.pdf is interpreted on the cancer DB portal as https://www.iccp-portal.org/system/files/plans/ALB%3Cem%3E2020.pdf

The issue seems to be interpretation of underscore in the value, if it is part of some sub-string of the reference keys value for some reason.

A website with pictures of mitosis. Who wants to lead?

@breck

The lack of tests in cancerDB seems to make contribution to CancerDB difficult.

Are there plans to include tests, are contributions welcome ?

The latest version of Scroll seems to have broken character encoding:

What are some options to fix this

Not all trailing spaces in cancerdb seems to be caught.

It seems to be reported only for certain types of nodes.

Add https://cancerdb.com/lists/commonCancerTypes.html