maayanlab/appyter-catalog

A catalog of appyter notebooks

appyter-catalog: A catalog of appyters

https://appyters.maayanlab.cloud/

This repository contains source code for the catalog and the appyters in it and is used to assemble and run them all, not to be confused with the appyter python package for actually developing appyters of your own.

Quick Links:

• Appyter Contribution Guide
• Appyter Framework Repository
• Catalog Deployment Guide

appyter-catalog's Issues

Add favicon and logo

Full READMEs should be visible on template landing pages

GTEx Tissue RNAseq Analysis: Fallopian tube has very few samples

PCA shows very few samples. Remove tissues with less than 30 samples (check first why you have too few).

Fix blue tags below the search engine bar and in appyters

These are the tags that should be listed below the search bar:
RNA-seq
scRNA-seq
Enrichr
Machine Learning
TCGA
Harmonizome
Drugmonizome
L1000
Compare Sets
microRNAs
Kinome
Aging

GTEx Tissue RNAseq Analysis: load example does not work

Permit searching by author names

GTEx Tissue RNAseq Analysis: Enrichr links with clear labels of what is compared are missing

Allow to decorate the Appyter launch pad with a representative figure

Since Appyters typically produce data visualizations, it would be nice to have a representative image with each appyter on the page that have the launch button. It is ok to specify specific dimensions.

It looks like the counts on the cards do not increment

Allow nesting in `appyters` directory for organizational purposes

Enable true data persistence

We need to add data volume mounts in the docker-compose in order to preserve data files across restarts.

Visual glitch when going from 2 cols to 3 cols with macy

How to reproduce:
Make a search that results in 2 columns and then delete the search entirely.

Thoughts:
Since it resolves after a resize, I imagine we just need to detect this and trigger the same function resize triggers.

Sort/rank appyters by runs not retrievals

Appyters are ranked by retrievals, but there are some widely used Appyters
with 0 retrieval counts that should be upgraded, perhaps rank/sort Appyters by runs

No progress bar in filefields

Remove e-mails from the appyter introduction page near author names

We do not want users contacting authors directly for help. Users should be directed to GitHub if they need help. This way we can monitor user needs and keep proper response for support.

Add the Harmonizome-ML appyter

Fix 'content-length' error when importing files from MinIO into appyters

Migrate templates properly to jupyter-template==v0.2.1

jupyter-template==v0.2.1 introduces a few breaking changes, specifically being more careful about input sanitation, .value or .safe_value should no longer be called explicitly. In the case that it is, you end up with double quotes.

Add a github action for automatically validating incoming templates

Ultra small display header/footer sizing

Probably need a min-width

Validate_merge improvements

• Execute appyter with defaults
  • Would catch things like missing requirements.txt files, obvious syntax errors, and broken examples.
• enforce versioning on PRs

GTEx Tissue RNAseq Analysis: The terms are missing from the GSEA plots

Templates should be searchable/organizable by tags/descriptions

Resize appyter logo on pages that have appyters executing

The size of the logo appears bigger on the appyter execution pages. It should be made smaller and match the size of it on the catalog landing page.

remove LINCS-BD2K DCIC logo from footer

Add release/publication date

It would be great to see the date when the appyter was published or updated.

RNAseq_Data_Metadata_Analysis: the input form should have more information about what it is and what to do.

Also the title of the form should be centered.

README image sizing should be bound much like github

Dynamic appyter-catalog appyter injection

Currently, we construct a static docker-compose with a static ui page. One convenient modification was made when we added traefik which allows us to detect new containers and mount them without needing to stop the ingest. It would be very convenient if the same could be done with the catalog -- that-is, appyters (which have their catalog metadata in a predictable place in each of the docker images) can be automatically added/removed from the catalog when the docker container gets added or removed.

Technically all we'd have to do is detect updates to the docker containers and re-construct public/appyters.json which can be done with

docker ps -q \                   # list all docker containers
  | xargs -I'{}' \               # execute for each docker container
      docker exec -it '{}' \     # run in container
        cat /app/appyter.json \  # produce appyter metadata
      2> /dev/null \             # ignore missing file in non-appyter containers
      | jq -rcs \                # collect json into a compact list
  > static/appyters.json         # update appyters.json

fetch with {cache: 'no-cache'} will still allow us to cache public/appyters.json

Drugmonizome image does not load on landing page sometimes

Process Leak and/or docker memory limits

We were basically out of memory this morning, there were several long-lived high memory usage processes running which I ended up killing because they made updating of anything impossible. We should:

• investigate whether or not processes can get orphaned (process leak)
• potentially limit individual containers from using all the systems memory

https is showing near the appyter icon on the google landing page (see screenshot)

Add option to publish appyter using our lab's CrossRef account

This needs to be done carefully...

Add footer with affiliations, contact, license and links to GitHub and documentation

GTEx Tissue RNAseq Analysis: Create bold title for the tissue that was selected

Rename to appyters catalog

RNAseq_Data_Metadata_Analysis: why only some terms have a GSEA plot? What is the criteria?

GTEx Tissue RNAseq Analysis: form order should be changed

The tissue selection should be at the top of the form.
The form should have more details about what it is.
Title should be RNA-seq not RNAseq.

Enrichr_Consensus_Terms: Add sleep() for enrichment

Ideally, addList and enrich (cell [10]) should contain sleep() for a few seconds (identical to this), as enrichment for long lists and retrieving results for big libraries take long time and it instantaneous results retrieval will fail.

RNAseq_Data_Metadata_Analysis: load example bars look like "in progress"

It is expected that the load green bars will turn solid green after the loading is complete

Starting the catalog throws an error

Attempting to start the catalog throws the following error:

charlesdai@Charle-PC:~/Projects/appyter-catalog$ make start
( make pull || make build ) && docker-compose up -d
make[1]: Entering directory '/home/charlesdai/Projects/appyter-catalog'
docker-compose pull
make[1]: docker-compose: Command not found
Makefile:42: recipe for target 'pull' failed
make[1]: *** [pull] Error 127
make[1]: Leaving directory '/home/charlesdai/Projects/appyter-catalog'
make[1]: Entering directory '/home/charlesdai/Projects/appyter-catalog'
cd app && npm i && npm run build && cd .. && docker-compose build app && touch app/.build
npm WARN [email protected] requires a peer of [email protected] - 3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of popper.js@^1.16.0 but none is installed. You must install peer dependencies yourself.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: [email protected] (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

audited 828 packages in 4.252s

25 packages are looking for funding
  run `npm fund` for details

found 0 vulnerabilities


> [email protected] build /home/charlesdai/Projects/appyter-catalog/app
> parcel build --no-cache public/index.html

🚨  /home/charlesdai/Projects/appyter-catalog/app/public/appyters.json: Unexpected token: punc (;)
    at Z.get (/home/charlesdai/Projects/appyter-catalog/app/node_modules/terser/dist/bundle.min.js:1:525)
    at Object.errorToJson (/home/charlesdai/Projects/appyter-catalog/app/node_modules/@parcel/utils/src/errorUtils.js:9:20)
    at Pipeline.process (/home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/Pipeline.js:29:26)
    at async Object.run (/home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/worker.js:15:12)
    at async Bundler.loadAsset (/home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/Bundler.js:577:19)
    at async /home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/Bundler.js:610:13
    at async Promise.all (index 12)
    at async Bundler.loadAsset (/home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/Bundler.js:599:21)
    at async /home/charlesdai/Projects/appyter-catalog/app/node_modules/parcel-bundler/src/Bundler.js:610:13
    at async Promise.all (index 3)
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] build: `parcel build --no-cache public/index.html`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] build script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/charlesdai/.npm/_logs/2020-06-24T20_37_35_688Z-debug.log
Makefile:20: recipe for target 'app/.build' failed
make[1]: *** [app/.build] Error 1
make[1]: Leaving directory '/home/charlesdai/Projects/appyter-catalog'
Makefile:46: recipe for target 'start' failed
make: *** [start] Error 2

Enforce cleared jupyter notebooks without embedded output

Improve resiliency with execution service

Currently, many of our notebooks use tons of RAM. As it is, our server has 15G of ram and multiple notebooks running at once can easily consume all resources. To improve the resiliency of this system, we'll likely need to trigger containers as jobs and let an orchestration system like kubernetes (perhaps even locally) execute them when there are resources available / kill jobs if they use too much memory.

The simplest way to start making this a reality is to setup an execution service where we send jobs to be executed. It is up to the execution service how exactly / when it gets dispatched.

Support local ubuntu .deb packages in deps/*.deb

Add counters to each appyter

Add counter for card clicks
Add counter for times the appyter was executed
Add counter for the number of downloads
Add a likes button and a counter for number of likes (that one is a maybe)

As we accumulate more and more appyters, it would be great to help user to decide which ones they should use...

and Julie Karama -> Julie Karam

Fix this text in the About page

Short name on Google shortcuts shows https instead of Appyters

RNAseq_Data_Metadata_Analysis: name of appyter needs to be changed

The appyter that Nicole developed is TCGA specific, so it needs to have TCGA in appyter name.
The appyter that was developed by Sherry is more general for analysis of any patient cohort, so the name can be similar to the name of Nicole's appyter.

github action to trigger AWS deployment update (`make update`)

Thumbnail image aspect ratios not being preserved