Prod

2026-01-06

Updated Ebola virus sequencing data (dataset, downloads, experiments)
Updated Lassa virus sequencing data (dataset, downloads, experiments)
Reloaded all dataset objects (accidental delete)
Sync'd public <-> private

2021-12-15

Upgraded to Angular 12.2.14 via local --> dev --> package.json update, wipe of node_modules and npm install. Ran npm audit fix
Updated npm to 8.3.0: sudo npm install -g npm@latest
Upgraded node to higher version (14.15.4; latest had dependency issues.): sudo n 14.15.4
npm cache verify to clean the cache.
Upgraded to Angular 13.1.1 via local --> package.json update, wipe of node_modules and npm install. Also ran npm audit fix to clear security audits. Final specs for local, dev, prod:

Angular CLI: 13.1.1
Node: 14.15.4
Package Manager: npm 6.14.10
OS: linux x64

Angular: 13.1.0
... animations, cdk, common, compiler, compiler-cli, core, forms
... language-service, material, platform-browser
... platform-browser-dynamic, platform-server, router

Package                         Version
---------------------------------------------------------
@angular-devkit/architect       0.1301.1
@angular-devkit/build-angular   13.1.1
@angular-devkit/core            13.1.1
@angular-devkit/schematics      13.1.1
@angular/cli                    13.1.1
@angular/flex-layout            8.0.0-beta.27
@nguniversal/builders           13.0.1
@nguniversal/common             13.0.1
@nguniversal/express-engine     13.0.1
@schematics/angular             8.3.29
rxjs                            6.5.5
typescript                      4.5.4

2021-12-14

Upgraded to Angular 11.2.15 via local --> dev --> package.json update, wipe of node_modules and npm install

2021-11-24

Pulled dev branch
sudo n 12.22.7 --> update Node to node-v12.22.7
npx @angular/cli@10 update @angular/material@10 --force --> upgrade to Angular Material 10
npx @angular/cli@10 update @angular/core@10 @angular/cli@10 --> upgrade to Angular 10.2.3
ng update
That update sequence accidentally --> Angular Core 11 being installed.
npm uninstall @angular/cli
npm uninstall @angular/core
rm -r node_modules
npm install
npx @angular/cli@10 update @angular/core@10 @angular/cli@10

2021-11-23 v0.2.4

Wiped and reloaded ebola-virus-seq
- 1 dataset
- 2,309 experiments
- 2,310 data downloads

2020-11-24

Updated Lassa-virus-seq data (dataset, downloads, experiments, patients)
Rebuilt schema (minor changes to Symptoms)

2020-11-19

Rebuilt schema (minor changes to DataCatalog)

2020-11-17 / 2020-11-18

Deleted /patient index and recreated, without infectionDate as a DateRange
- KGH acute patients
- KGH survivor patients (excluding those w/ a G-id)
- SARS-CoV-2 sequencing patients
- EBOV sequencing patients (non-KGH)
- LASV sequencing patients (non-KGH)
New datasets
- removed and updated ebola-virus-seq
- systems-serology-32783920 (SARS-CoV-2 serology)
- rtcpr-32783920
- blood-counts-vhf
- blood-chemistry-vhf
- rtpcr-vhf
- rapid-diagnostics-vhf
- vitals-vhf
New datadownloads
- removed and updated ebola-virus-seq
- systems-serology-32783920 (SARS-CoV-2 serology)
- rtcpr-32783920
- blood-counts-vhf
- blood-chemistry-vhf
- rtpcr-vhf
- rapid-diagnostics-vhf
- vitals-vhf
New experiments
- removed and updated ebola-virus-seq
- systems-serology-32783920 (SARS-CoV-2 serology)
- rtcpr-32783920
- blood-counts-vhf
- blood-chemistry-vhf
- rtpcr-vhf
- rapid-diagnostics-vhf
- vitals-vhf
updated data catalog
rebuilt schema
sync'd public/private indices

2020-11-03

Wiped and updated SARS-CoV-2 experiments to include "data" field
Updated datacatalog
public/private sync

2020-09-15

Wiped, reinstalled and npm update fix'd node_modules.

2020-08-28

Wiped and readded SARS-CoV-2 experiment data, now totals 1195 again.
pub/priv sync

2020-08-27

Wiped and readded SARS-CoV-2 experiment data adding sourceCitation
Wiped and readded SARS-CoV-2 patient information removing duplicate entries
SARS-CoV-2 totals now 1134 experiments and 1195 patients
Reran public / private sync

2020-08-27 v0.2.3

Re-ran schema generation to add Ghana
Wiped and reloaded ebola-virus-seq
- 1 dataset
- 2,309 experiments
- 2,310 data downloads
Wiped, re-ran, and reloaded lassa-virus-seq
- 1 dataset
- 1,318 experiments
- 1,807 data downloads
Updated datacatalog

Not updated but logging:

HLA
- 1 dataset
- 370 experiments
- 371 data downloads
Serology (Ebola/Lassa)
- 1 dataset
- 2,554 experiments
- 1 data download
SARS-CoV-2 Virus Seq
- 1 dataset
- 1,195 experiments
- 1,195 patients

2020-08-25

Updated schema (prod and dev): added Country options for Jordan and Mexico.
Added in SARS-CoV2 sequencing data.
synchronized public + private

2020-06-23

Updated schema (prod and dev): removed requiredness of country
updated Ebola virus sequence data
- removed Ebola virus dataset, data downloads, experiment
- uploaded new Ebola virus dataset, data downloads, experiment
updated Ebola virus sequence new patient data
- Added non-KGH patients; replaced previous entries for the existing IDs
sync'd public/private

2020-06-22

Updated schema (prod and dev), based on the addition of exposureLocation

2020-06-19

updated Ebola virus sequence data
- removed Ebola virus dataset, data downloads, experiment
- uploaded new Ebola virus dataset, data downloads, experiment
rebuilt schema
updated Ebola virus sequence new patient data
- Added non-KGH patients; replaced previous entries for the existing IDs
updated release notes on data catalog
- removed data catalog
- added new data catalog
synchronized public/private data
updated upload scripts to look for existing IDs, so data can be replaced if it already exists.

2020-05-20

synchronized public/private data

2020-02-20: Angular 9 install

Pulled dev changes

sudo npm install -g npm@latest: update latest version of node from 6.4.1 to 6.13.7
sudo npm install n -g: install n to update node
sudo n stable: update node from 10.12 to 12.16.0
ng update @angular/core@8 @angular/cli@8 --create-commits : make sure v. 8 at latest
ng update @angular/cli @angular/core --create-commits: install v. 9
ng update @angular/material --force // already up to date
ng update @nguniversal/express-engine
ng update --> ng update rxjs
npm uninstall webpack-cli
npm install
npm audit fix

rm -rf node_modules npm install



### v 0.3: 2020-02-12
1. Pulled all changes from [dev](https://github.com/cvisb/cvisb_data/pull/39).
2. ran `npm install` to update packages (and install FortAwesome Module)
3. schema rebuilt
4. Sync'd public/private ES indices

### v 0.2: 2019-11-15
- temp fix: in Biothings package, modify POST arguments to .pop `version` from query_kwargs in `ne ~/cvisb/pyenv/lib/python3.5/site-packages/biothings/web/api/es/query.py`
1. Pulled all changes from [dev](https://github.com/cvisb/cvisb_data/pull/17).
2.  updated all packages; migrated to Angular 8:

ng update --all --force ng update // check; nothing to update. Note: some packages have been updated with minor version changes since I updated the dev server. npm audit fix // fix 2 security vulnerabilities npm install typescript@">=3.4.0 <3.5.0" --save-dev --save-exact // downgrade to TS 3.4.5; incompatible with Angular 8 compiler

3. Temporary fix, to allow Biothings POST methodology to work properly:

vim ~/cvisb/pyenv/lib/python3.5/site-packages/biothings/web/api/es/query.py line :query_kwargs.pop('version') #####TEMP FIX 20191114 by Chunlei Wu


4. Restarted Tornado: `./restart_tornado`
5. Cleared:
- `/dataset`
- `/datadownload`
- `/experiment`
6. Uploaded new versions of:
- `/datacatalog`
- HLA, Ebola Virus Seq, Lassa Virus Seq, Systems Serology `/dataset`
- HLA, Ebola Virus Seq, Lassa Virus Seq `/datadownload`
- HLA, Ebola Virus Seq, Lassa Virus Seq, Systems Serology `/experiment`
- Ebola Virus Seq `/patient`


### v 0.1: 2019-09-13
- created version 0.1 with Angular 6.1.10

### 2019-06-05
- schema rebuilt (v. 0.1 for all)
- python requirements updated to include pyparsing
- updated to latest version of Biothings, which includes nested facets
- auth list updated
- dev merged to master
- all indices wiped and recreated

# Dev
### 2021-12-15
* Updated npm to 8.3.0: `sudo npm install -g npm@latest`
* Upgraded to Angular 13.1.1 via local --> package.json update, wipe of `node_modules` and `npm install`. Also ran `npm audit fix` sequentially to clear security audits.
* Upgraded node to higher version (14.15.4; latest had dependency issues.): `sudo n 14.15.4`

### 2021-12-14
* Upgraded to Angular 12.2.14 via local --> package.json update, wipe of `node_modules` and `npm install`. Also ran `npm audit fix`
* Upgraded to Angular 11.2.15 via local --> package.json update, wipe of `node_modules` and `npm install`

### 2021-11-23
* rebuilt schemas.

### 2021-11-22: Upgrade to Angular 10
* `npm uninstall @angular/cli` --> remove local version of angular client
* `npm uninstall -g @angular/cli` --> remove global version of angular clientw
* `sudo n 12.22.7` --> update Node to node-v12.22.7
* Still installed; find symlinked file with
  * `which ng` --> /usr/bin/ng
  * ls -lh | grep ng within the folder to find the symlinks --> `../lib/node_modules/@angular/cli/bin/ng`
https://stackoverflow.com/questions/43070441/cannot-uninstall-angular-cli?rq=1
* `sudo rm -rf /lib/node_modules/@angular`
* `sudo rm -rf /usr/bin/ng`
* `sudo npm install -g @angular/cli@10.2.3`

npm ERR! Your cache folder contains root-owned files, due to a bug in npm ERR! previous versions of npm which has since been addressed. npm ERR! npm ERR! To permanently fix this problem, please run: npm ERR! sudo chown -R 1000:1000 "/home/ubuntu/.npm"

* git commit package.json changes
* `npx @angular/cli@10 update @angular/material@10 --force`


* `ng update`



### 2020-09-15
* Ran into disk space issues; released 2GB from the swapfile
* Removed, reinstalled, and `npm audit fix`'d `node_modules`

### 2020-02-18: Angular 9 install
1. cleaned up a few random things
- Added json import to `tsconfig.json`
- Updated material modules to direct import the specific mod
- Added `import '@angular/compiler'` to `main.ts`
- remove hammer.js from package
- remove import  'hammerjs' calls
- removed `entryComponents` import
- removed `ModuleMapLoaderModule` from `sample-viewer/src/app/app.server.module.ts`
- Forced a few d3-geo-projections typing conflicts that Angular 8 was okay with: `let minLon = d3.geoBounds(gin as any)[0][0]`
- `sudo npm install -g npm@latest`: update latest version of node from 6.4.1 to 6.13.7
- `npm install`
- `npm audit fix`
- `sudo npm install n -g`: install n to update node
- `sudo n stable`: update node from 10.12 to 12.16.0
- `ng update @angular/core@8 @angular/cli@8 --create-commits` : make sure v. 8 at latest
- `ng update @angular/cli @angular/core --create-commits`: install v. 9
- `ng update @angular/material --force`
- `ng update @nguniversal/express-engine`
- `ng update` --> `ng update rxjs`
- `npm uninstall webpack-cli`
- ```
rm -rf node_modules
npm install

for some reason to get SSR to compile, had to move server.ts from the root directory to inside /src and update the references to that file in angular.json
new SSR error: "refused to set unsafe header cookie" via angular/angular#15730 (comment) (XHR2 bypass)
committed, pushed to GH, pulled locally.
on average, .js bundles decreased by ~9%. looks like a big portion may be due to cross-use of modules; getting thrown into main.js since they have to be re-used. not sure if that can be worked around.

2019-12-09

installed Angular FontAwesome module

2019-11-14

temp fix: in Biothings package, modify POST arguments to .pop version from query_kwargs in ne ~/cvisb/pyenv/lib/python3.5/site-packages/biothings/web/api/es/query.py
schema rebuilt, auth list updated.

2019-10-23/24

Upgraded to Angular 8 and updated all packages (from package.json)

rm package-lock.json
npm install
npm audit fix
npm uninstall @angular-devkit/build-angular
npm install @angular-devkit/build-angular

ng update --all --force // to get Angular Universal updated
downgrade to typescript 3.4.5: npm install typescript@">=3.4.0 <3.5.0" --save-dev --save-exact

After syncing dev/local versions, did a final removal of package-lock.json and npm install on both sides

2019-06-05

schema rebuilt
auth list updated

Local

2021-12-15: Upgrade Angular 12.2.14 to Angular 13.1.1

npx @angular/cli@13 update @angular/core@13 @angular/cli@13 --force npx @angular/cli@13 update @angular/material@13 --force ng update @nguniversal/common@10 --force ng update @nguniversal/common@11 --force ng update @nguniversal/common@12 --force ng update @nguniversal/common@13 --force npm audit fix

2021-12-14: Upgrade Angular 11.2.15 to Angular 12.2.14

npx @angular/cli@12 update @angular/core@12 @angular/cli@12 --force npx @angular/cli@12 update @angular/material@12 --force ng update --> npm install --> ng update npm audit fix

fixed error in choropleth.component.ts: file import
fixed typescript error in MyHttpClient extension

2021-12-14: Upgrade Angular 10.2.3 to Angular 11.2.15

npx @angular/cli@11 update @angular/core@11 @angular/cli@11 --force npx @angular/cli@11 update @angular/material@11 --force ng update --> npm install --> ng update

2020-02-13+

Upgraded to Angular 9, updated all packages.
followed https://update.angular.io/#8.0:9.0l3

updated all Material import calls

remove hammer.js from package
remove import 'hammerjs' calls

ng update @angular/core@8 @angular/cli@8 --create-commits
ng update @angular/cli @angular/core --create-commits

ng update @angular/material --force
ng update @nguniversal/express-engine
ng update --> ng update rxjs

rm -rf node_modules
npm install

If you depend on many Angular libraries you may consider speeding up your build by invoking the ngcc (Angular Compatibility Compiler) in an npm postinstall script via small change to your package.json. If you have specified any entryComponents in your NgModules or had any uses of ANALYZE_FOR_ENTRY_COMPONENTS, you can remove them. They are no longer required with the Ivy compiler and runtime.

Some notes on the Angular 9 problems:

Had to import Material modules individually; Angular CLI was supposed to do automatically, but that didn't happen.

core.js:5845 ERROR Error: Uncaught (in promise): TypeError: Cannot read property 'ngModule' of undefined
TypeError: Cannot read property 'ngModule' of undefined
    at isModuleWithProviders

In main.ts:

import '@angular/compiler';

https://stackoverflow.com/questions/60183056/ionic-5-with-angular-9-angular-jit-compilation-failed-angular-compiler-not

error TS2306: File '/Users/laurahughes/GitHub/cvisb_data/sample-viewer/node_modules/@angular/material/index.d.ts' is not a module.

8 import { MatExpansionModule } from '@angular/material/';

Had to force a few d3-geo-projections typing conflicts that Angular 8 was okay with.

let minLon = d3.geoBounds(gin as any)[0][0],

In tsconfig.json:

"compilerOptions": {
  "resolveJsonModule": true,
}

https://mariusschulz.com/blog/importing-json-modules-in-typescript

ERROR
Cannot find module '../../assets/geo/naturalearth_africa.json'. Consider using '--resolveJsonModule' to import module with '.json' extension

2019-10-23

Upgraded to Angular 8 and updated all packages (from package.json)

rm package-lock.json
npm install
npm audit fix
npm uninstall @angular-devkit/build-angular
npm install @angular-devkit/build-angular

ng update --all --force // to get Angular Universal updated
downgrade to typescript 3.4.5: npm install typescript@">=3.4.0 <3.5.0" --save-dev --save-exact
// Not necessary to do on dev...
Changing from "@angular-devkit/build-angular": "^0.802.1"
to "@angular-devkit/build-angular": "^0.13.9",
https://github.com/akveo/ngx-admin/issues/2138#issuecomment-522264613
npm install
npm install --save core-js@^2.5.0 https://stackoverflow.com/questions/55398923/error-cant-resolve-core-js-es7-reflect-in-node-modules-angular-devkit-bui

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2021-12-15: Upgrade Angular 12.2.14 to Angular 13.1.1

2021-12-14: Upgrade Angular 11.2.15 to Angular 12.2.14

2021-12-14: Upgrade Angular 10.2.3 to Angular 11.2.15

2019-10-23

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2020-11-17 / 2020-11-18

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2021-12-14: Upgrade Angular 11.2.15 to Angular 12.2.14

2021-12-14: Upgrade Angular 10.2.3 to Angular 11.2.15

2019-10-23