caleydo / ordino_product Goto Github PK

This repository builds Ordino Docker images from a collection of plugin repositories

License: BSD 3-Clause "New" or "Revised" License

JavaScript 84.64% Dockerfile 2.54% HTML 8.84% SCSS 3.83% Shell 0.15%

ordino_product's Introduction

Caleydo - Visualization for Molecular Biology

Caleydo is a visualization framework for molecular biology data. It is targeted at analyzing multiple heterogeneous but related tabular datasets (e.g., mRNA expression, copy number status and clinical variables), stratifications or clusters in these datasets and their relationships to biological pathways.

For user documentation please refer to the Caleydo Help. For general information and downloads based on binaries please use the Caleydo Website. This guide assumes that you want to install Caleydo from source.

Installation

Caleydo uses Java, OpenGL and the Eclipse Rich Client Platform (RCP). Things you need to install before being able to run Caleydo:

Eclipse Kepler for RCP and RAP Developers, which you can get from the eclipse download page. Other Eclipse versions won't work.
Install EGit in Eclipse using software updates.
Java SDK >= 1.7

To install Caleydo use EGit within Eclipse and clone the repository. Each directory in the caleydo-dev folder corresponds to an Eclipse project. Here is a good tutorial on how to import Eclipse projects from git.

If you want to use ssh (instead of https) for communicating with github out of eclipse follow these instructions. You will have to generate a new RSA key and save it to you ~/.ssh folder. Remeber to set a passphrase for you key. This will result in a file ida_rsa and ida_rsa.pub turning up in your ssh folder. Save your public rsa key with your eclipse account folder.

When cloning the repository follow the above tutorial. Don't change the username "git" to your username!

Team

Caleydo is an academic project currently developed by members of

Institute for Computer Graphics and Vision at Graz University of Technology, Austria
Institute of Computer Graphics at Johannes Kepler University Linz, Austria
Pfister Lab at the School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
Park Lab at Harvard Medical School, Boston, USA

Acknowledgements

Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

Bubble Sets - A Java implementation of the visualization technique.
CDK - The Chemistry Development Kit.
JGrahT - A graph library.
Jogl - Java bindings for OpenGL.
PathVisio - loading and parsing WikiPathways.
WordHoard - statistical utilities.

Bioinformatics Resources

David Bioinformatics Resources - Gene ID mapping.
KEGG - Pathways.
WikiPathways - Pathways.

Datasets

CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
TCGA - The Cancer Genome Atlas.

Resources

GitHub - Hosting our source code.
WebStorm - Free developer licenses for our web projects from JetBrains.

ordino_product's People

Contributors

Stargazers

Watchers

Forkers

blazhovsky

ordino_product's Issues

Depracted Travis Build Badge

There is a Travis Build Badge on top of the README, showing that the builds fail.

As we do not use travis for ordino, I guess we can remove/replace the badge... right?

Update circleci and use orbs

In order to fix the build, we need to update circleci to version 2.1 and use orbs.

Change _workspace.scss_ for compatibility with Bootstrap 5

Due to changes in the behaviour of variable defaults in Bootstrap 5, it is necessary to change the structure of the workspace.scss in order to be able to maintain the correct order of Bootstrap imports.

See https://github.com/datavisyn/visyn2025/issues/80#issuecomment-848708485

Update versions in starter branch

We should update all repos in phovea_product.json to the latest versions.

Update dependencies

We should update all dependencies to the latest accessible versions. As a first step, the following dependencies are excluded and will be done in a separate step:

all webpack dependencies
all test dependencies
vega, d3 and bootstrap

Update requirements and dependencies

We should use the latest versions both for requirements and dependencies.
Except for Typescript, tslint and d3 dependencies, which will be updated in a separate step.

Add 500.html and 404.html to the app

See phovea/generator-phovea#452

Update font family of the web templates in the deploy folder to Roboto

The web templates still use the Yantramanav font family

Cypress nightly builds on CircleCI are broken

The Cypress nightly builds on CircleCI are broken since 06.08.2022. The last successful build was 2516. All following builds are broken and never got fixed.

I checked the CircleCI logs and saw that a different base image was used:

Build 2516: cypress/base:10
Following builds (e.g., 2665): cimg/python:3.10.6-node

Looking at the git history the Docker images for the CircleCI job has been changed to executor: node-executor which uses the CircleCI base image with PR https://github.com/Caleydo/ordino_product/pull/74/files.

Previously:

    docker:
      - image: cypress/base:10
        environment:
          ## this enables colors in the output
          TERM: xterm

Now:

    executor: node-executor
    environment:
      CYPRESS_host: "https://ordino-daily.caleydoapp.org/"

Build failed due to missing `readable-stream` files

With PR Caleydo/tdp_publicdb#118 the package madge was removed from the dev dependencies.

Since then the Ordino product build fails with the following CircleCI build errors:

ERROR in ./node_modules/stream-browserify/index.js
Module not found: Error: Can't resolve 'readable-stream/duplex.js' in '/home/circleci/phovea/tmp0_ordin/node_modules/stream-browserify'
 @ ./node_modules/stream-browserify/index.js 30:16-52
 @ ./node_modules/cipher-base/index.js
 @ ./node_modules/create-hmac/browser.js
 @ ./node_modules/crypto-browserify/index.js
 @ ./node_modules/crypto-js/core.js
 @ ./node_modules/crypto-js/md5.js
 @ ./tdp_matomo/dist/app/Matomo.js
 @ ./tdp_matomo/dist/phovea.js
 @ ./tdp_matomo/phovea_registry.js
 @ ./phovea_registry.js
 @ multi ./phovea_registry.js ./ordino_public/dist/initialize.js

ERROR in ./node_modules/stream-browserify/index.js
Module not found: Error: Can't resolve 'readable-stream/passthrough.js' in '/home/circleci/phovea/tmp0_ordin/node_modules/stream-browserify'
 @ ./node_modules/stream-browserify/index.js 32:21-62
 @ ./node_modules/cipher-base/index.js
 @ ./node_modules/create-hmac/browser.js
 @ ./node_modules/crypto-browserify/index.js
 @ ./node_modules/crypto-js/core.js
 @ ./node_modules/crypto-js/md5.js
 @ ./tdp_matomo/dist/app/Matomo.js
 @ ./tdp_matomo/dist/phovea.js
 @ ./tdp_matomo/phovea_registry.js
 @ ./phovea_registry.js
 @ multi ./phovea_registry.js ./ordino_public/dist/initialize.js

ERROR in ./node_modules/stream-browserify/index.js
Module not found: Error: Can't resolve 'readable-stream/transform.js' in '/home/circleci/phovea/tmp0_ordin/node_modules/stream-browserify'
 @ ./node_modules/stream-browserify/index.js 31:19-58
 @ ./node_modules/cipher-base/index.js
 @ ./node_modules/create-hmac/browser.js
 @ ./node_modules/crypto-browserify/index.js
 @ ./node_modules/crypto-js/core.js
 @ ./node_modules/crypto-js/md5.js
 @ ./tdp_matomo/dist/app/Matomo.js
 @ ./tdp_matomo/dist/phovea.js
 @ ./tdp_matomo/phovea_registry.js
 @ ./phovea_registry.js
 @ multi ./phovea_registry.js ./ordino_public/dist/initialize.js

ERROR in ./node_modules/stream-browserify/index.js
Module not found: Error: Can't resolve 'readable-stream/writable.js' in '/home/circleci/phovea/tmp0_ordin/node_modules/stream-browserify'
 @ ./node_modules/stream-browserify/index.js 29:18-56
 @ ./node_modules/cipher-base/index.js
 @ ./node_modules/create-hmac/browser.js
 @ ./node_modules/crypto-browserify/index.js
 @ ./node_modules/crypto-js/core.js
 @ ./node_modules/crypto-js/md5.js
 @ ./tdp_matomo/dist/app/Matomo.js
 @ ./tdp_matomo/dist/phovea.js
 @ ./tdp_matomo/phovea_registry.js
 @ ./phovea_registry.js
 @ multi ./phovea_registry.js ./ordino_public/dist/initialize.js

Investigating the problem shows that removing the madge dependency switched the version of readable-stream from version 2.x to version 3.x in the node_modules root. Instead the version 2.x dependencies of multiple packages got nested and resulting in broken imports.

Reading about the functionality of npm's dependency resolution, I found this quote:

The key is to remember that install order matters.

With this in mind our build was previously succeeding because madge uses readable stream in version 2.x (and set this version as default). The package-lock.json (with just installing madge as dependency) confirms this theory.

Taking a closer look at the workspace package-lock.json shows that the version 3.x is introduced by webpack:

[email protected]
[email protected]
[email protected]
[email protected]
[email protected] deduped

The only option to fix this build error is to explicitly add readable-stream in version 2.x to one of our plugins. Since the error points to the tdp_matomo repository, I'd suggest to add it there. In my local tests the webpack build succeeds, once readable-stream@^2.0.0 is added as dev dependency to the workspace.

Reset phovea generator version

TODO for the future: currently the phovea generator version is hardcoded by commit hash in the package.json of the touruíng branch

This should be changed back once a new generator version is released

Error when setting up the workspace: `You are in 'detached HEAD' state.`

Release number or git hash: master
Web browser version and OS: Windows (tested by me) and Linux (tested by @anita-steiner)
Environment (local or deployed): local

Steps to reproduce

Open CMD
yo phovea:setup-workspace ordino_product

Observed behavior

? SSH clone No
create directory: ordino
clone repository: git clone -b master --depth 1 https://github.com/Caleydo/ordino_product.git
Cloning into 'ordino_product'...
remote: Counting objects: 16, done.
remote: Compressing objects: 100% (15/15), done.
remote: Total 16 (delta 0), reused 9 (delta 0), pack-reused 0
Unpacking objects: 100% (16/16), done.
clone repository: git clone -b v3.1.0 https://github.com/Caleydo/ordino_public.git
Cloning into 'ordino_public'...
remote: Counting objects: 360, done.
remote: Compressing objects: 100% (12/12), done.
Receiving objects:  93% (335/360)   12 (delta 5), pack-reused 343 eceiving objects:  89% (321/360)
Receiving objects: 100% (360/360), 147.69 KiB | 0 bytes/s, done.
Resolving deltas: 100% (193/193), done.
Note: checking out 'c93e62cfc7b330470a429a5c652609ba6715842b'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

clone repository: git clone -b v3.1.0 https://github.com/Caleydo/tdp_gene.git
Cloning into 'tdp_gene'...
remote: Counting objects: 2480, done.
remote: Compressing objects: 100% (10/10), done.
Receiving objects: 100% (2480/2480), 566.99 KiB | 0 bytes/s, done.0eceiving objects:  61% (1513/2480)
Resolving deltas: 100% (1736/1736), done.

Note: checking out '5df9bd96dc3c6b937aacd2c7ffbd57cb40621bb9'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

�[94mclone repository:�[39m git clone -b v3.1.0 https://github.com/Caleydo/tdp_publicdb.git
Cloning into 'tdp_publicdb'...
remote: Counting objects: 3579, done.
remote: Compressing objects: 100% (15/15), done.
remote: Total 3579 (delta 4), reused 4 (delta 1), pack-reused 3563
Receiving objects: 100% (3579/3579), 2.00 MiB | 847.00 KiB/s, done.
Resolving deltas: 100% (2486/2486), done.
Note: checking out 'bd6dbc1c1b248b0d6bc9dd8157162e58688a329e'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

�[94mclone repository:�[39m git clone -b v3.1.0 https://github.com/datavisyn/tdp_uploaded_data.git
Cloning into 'tdp_uploaded_data'...
remote: Repository not found.
fatal: repository 'https://github.com/datavisyn/tdp_uploaded_data.git/' not found
{ status: 128,
  signal: null,
  output: [ null, null, null ],
  pid: 19348,
  stdout: null,
  stderr: null,
  envPairs:
   [ 'ALLUSERSPROFILE=C:\\ProgramData',
     'APPDATA=C:\\Users\\Holger Stitz\\AppData\\Roaming',
     'CommonProgramFiles=C:\\Program Files\\Common Files',
     'CommonProgramFiles(x86)=C:\\Program Files (x86)\\Common Files',
     'CommonProgramW6432=C:\\Program Files\\Common Files',
     'COMPUTERNAME=DESKTOP-0DE31SV',
     'ComSpec=C:\\WINDOWS\\system32\\cmd.exe',
     'DEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection',
     'FPS_BROWSER_APP_PROFILE_STRING=Internet Explorer',
     'FPS_BROWSER_USER_PROFILE_STRING=Default',
     'GIT_LFS_PATH=C:\\Program Files\\Git LFS',
     'GYP_MSVS_VERSION=2015',
     'HOMEDRIVE=C:',
     'HOMEPATH=\\Users\\Holger Stitz',
     'LOCALAPPDATA=C:\\Users\\Holger Stitz\\AppData\\Local',
     'LOGONSERVER=\\\\DESKTOP-0DE31SV',
     'NUMBER_OF_PROCESSORS=4',
     'OneDrive=C:\\Users\\Holger Stitz\\OneDrive',
     'OS=Windows_NT',
     'Path=C:\\Program Files\\Docker\\Docker\\Resources\\bin;C:\\Python27\\;C:\\Python27\\Scripts;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\HashiCorp\\Vagrant\\bin;C:\\Program Files (x86)\\GitExtensions\\;C:\\Program Files\\PostgreSQL\\9.5\\bin;C:\\Program Files\\Git\\cmd;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;D:\\Users\\Holger Stitz\\Downloads\\programme\\ffmpeg-20161204-1f5630a-win64-static\\bin\\;C:\\Program Files (x86)\\Skype\\Phone\\;C:\\Program Files\\Amazon\\AWSCLI\\;C:\\Program Files (x86)\\Windows Kits\\8.1\\Windows Performance Toolkit\\;C:\\Program Files\\nodejs\\;C:\\Program Files\\Git LFS;C:\\Users\\Holger Stitz\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Holger Stitz\\AppData\\Local\\atom\\bin;C:\\Users\\Holger Stitz\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Holger Stitz\\AppData\\Roaming\\npm;C:\\Users\\Holger Stitz\\AppData\\Local\\rodeo\\app-2.5.2\\bin;C:\\Program Files\\Microsoft VS Code\\bin',
     'PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JSE;.WSF;.WSH;.MSC;.CPL',
     'PROCESSOR_ARCHITECTURE=AMD64',
     'PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 60 Stepping 3, GenuineIntel',
     'PROCESSOR_LEVEL=6',
     'PROCESSOR_REVISION=3c03',
     'ProgramData=C:\\ProgramData',
     'ProgramFiles=C:\\Program Files',
     'ProgramFiles(x86)=C:\\Program Files (x86)',
     'ProgramW6432=C:\\Program Files',
     'PROMPT=$P$G',
     'PSModulePath=D:\\Users\\Holger Stitz\\Documents\\WindowsPowerShell\\Modules;C:\\Program Files\\WindowsPowerShell\\Modules;C:\\WINDOWS\\system32\\WindowsPowerShell\\v1.0\\Modules',
     'PUBLIC=C:\\Users\\Public',
     'SESSIONNAME=Console',
     'SystemDrive=C:',
     'SystemRoot=C:\\WINDOWS',
     'TEMP=C:\\Users\\HOLGER~1\\AppData\\Local\\Temp',
     'TMP=C:\\Users\\HOLGER~1\\AppData\\Local\\Temp',
     'USERDOMAIN=DESKTOP-0DE31SV',
     'USERDOMAIN_ROAMINGPROFILE=DESKTOP-0DE31SV',
     'USERNAME=Holger Stitz',
     'USERPROFILE=C:\\Users\\Holger Stitz',
     'VBOX_MSI_INSTALL_PATH=C:\\Program Files\\Oracle\\VirtualBox\\',
     'VS140COMNTOOLS=C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\Common7\\Tools\\',
     'VSEDEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection',
     'windir=C:\\WINDOWS' ],
  options:
   { cwd: 'ordino',
     stdio: [ [Object], [Object], [Object] ],
     file: 'git',
     args:
      [ 'git',
        'clone',
        '-b',
        'v3.1.0',
        'https://github.com/datavisyn/tdp_uploaded_data.git' ],
     envPairs:
      [ 'ALLUSERSPROFILE=C:\\ProgramData',
        'APPDATA=C:\\Users\\Holger Stitz\\AppData\\Roaming',
        'CommonProgramFiles=C:\\Program Files\\Common Files',
        'CommonProgramFiles(x86)=C:\\Program Files (x86)\\Common Files',
        'CommonProgramW6432=C:\\Program Files\\Common Files',
        'COMPUTERNAME=DESKTOP-0DE31SV',
        'ComSpec=C:\\WINDOWS\\system32\\cmd.exe',
        'DEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection',
        'FPS_BROWSER_APP_PROFILE_STRING=Internet Explorer',
        'FPS_BROWSER_USER_PROFILE_STRING=Default',
        'GIT_LFS_PATH=C:\\Program Files\\Git LFS',
        'GYP_MSVS_VERSION=2015',
        'HOMEDRIVE=C:',
        'HOMEPATH=\\Users\\Holger Stitz',
        'LOCALAPPDATA=C:\\Users\\Holger Stitz\\AppData\\Local',
        'LOGONSERVER=\\\\DESKTOP-0DE31SV',
        'NUMBER_OF_PROCESSORS=4',
        'OneDrive=C:\\Users\\Holger Stitz\\OneDrive',
        'OS=Windows_NT',
        'Path=C:\\Program Files\\Docker\\Docker\\Resources\\bin;C:\\Python27\\;C:\\Python27\\Scripts;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\HashiCorp\\Vagrant\\bin;C:\\Program Files (x86)\\GitExtensions\\;C:\\Program Files\\PostgreSQL\\9.5\\bin;C:\\Program Files\\Git\\cmd;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;D:\\Users\\Holger Stitz\\Downloads\\programme\\ffmpeg-20161204-1f5630a-win64-static\\bin\\;C:\\Program Files (x86)\\Skype\\Phone\\;C:\\Program Files\\Amazon\\AWSCLI\\;C:\\Program Files (x86)\\Windows Kits\\8.1\\Windows Performance Toolkit\\;C:\\Program Files\\nodejs\\;C:\\Program Files\\Git LFS;C:\\Users\\Holger Stitz\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Holger Stitz\\AppData\\Local\\atom\\bin;C:\\Users\\Holger Stitz\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\Holger Stitz\\AppData\\Roaming\\npm;C:\\Users\\Holger Stitz\\AppData\\Local\\rodeo\\app-2.5.2\\bin;C:\\Program Files\\Microsoft VS Code\\bin',
        'PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JSE;.WSF;.WSH;.MSC;.CPL',
        'PROCESSOR_ARCHITECTURE=AMD64',
        'PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 60 Stepping 3, GenuineIntel',
        'PROCESSOR_LEVEL=6',
        'PROCESSOR_REVISION=3c03',
        'ProgramData=C:\\ProgramData',
        'ProgramFiles=C:\\Program Files',
        'ProgramFiles(x86)=C:\\Program Files (x86)',
        'ProgramW6432=C:\\Program Files',
        'PROMPT=$P$G',
        'PSModulePath=D:\\Users\\Holger Stitz\\Documents\\WindowsPowerShell\\Modules;C:\\Program Files\\WindowsPowerShell\\Modules;C:\\WINDOWS\\system32\\WindowsPowerShell\\v1.0\\Modules',
        'PUBLIC=C:\\Users\\Public',
        'SESSIONNAME=Console',
        'SystemDrive=C:',
        'SystemRoot=C:\\WINDOWS',
        'TEMP=C:\\Users\\HOLGER~1\\AppData\\Local\\Temp',
        'TMP=C:\\Users\\HOLGER~1\\AppData\\Local\\Temp',
        'USERDOMAIN=DESKTOP-0DE31SV',
        'USERDOMAIN_ROAMINGPROFILE=DESKTOP-0DE31SV',
        'USERNAME=Holger Stitz',
        'USERPROFILE=C:\\Users\\Holger Stitz',
        'VBOX_MSI_INSTALL_PATH=C:\\Program Files\\Oracle\\VirtualBox\\',
        'VS140COMNTOOLS=C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\Common7\\Tools\\',
        'VSEDEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection',
        'windir=C:\\WINDOWS' ] },
  args:
   [ 'git',
     'clone',
     '-b',
     'v3.1.0',
     'https://github.com/datavisyn/tdp_uploaded_data.git' ],
  file: 'git',
  error: null }
�[94mclone repository:�[39m git clone -b develop https://github.com/phovea/phovea_server.git
Cloning into 'phovea_server'...
remote: Counting objects: 2073, done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 2073 (delta 2), reused 2 (delta 0), pack-reused 2066R
Receiving objects: 100% (2073/2073), 407.69 KiB | 0 bytes/s, done.
Resolving deltas: 100% (1386/1386), done.
�[94mclone repository:�[39m git clone -b develop https://github.com/phovea/phovea_security_flask.git
Cloning into 'phovea_security_flask'...
remote: Counting objects: 477, done.
Rremote: Total 477 (delta 0), reused 0 (delta 0), pack-reused 477                     % (363/477)
Receiving objects: 100% (477/477), 85.68 KiB | 0 bytes/s, done.
Resolving deltas: 100% (282/282), done.
�[94mclone repository:�[39m git clone -b develop https://github.com/phovea/phovea_data_redis.git
Cloning into 'phovea_data_redis'...
remote: Counting objects: 444, done.
Rremote: Total 444 (delta 0), reused 0 (delta 0), pack-reused 444
Receiving objects: 100% (444/444), 64.70 KiB | 0 bytes/s, done.
Resolving deltas: 100% (258/258), done.
�[94mclone repository:�[39m git clone -b develop https://github.com/phovea/phovea_data_mongo.git
Cloning into 'phovea_data_mongo'...
remote: Counting objects: 352, done.
Rremote: Total 352 (delta 0), reused 0 (delta 0), pack-reused 352                     % (222/352)
Receiving objects: 100% (352/352), 55.50 KiB | 0 bytes/s, done.
Resolving deltas: 100% (186/186), done.
�[94mclone repository:�[39m git clone -b develop https://github.com/phovea/phovea_clue.git
Cloning into 'phovea_clue'...
remote: Counting objects: 3823, done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 3823 (delta 5), reused 10 (delta 3), pack-reused 3808
Receiving objects: 100% (3823/3823), 920.68 KiB | 808.00 KiB/s, done.
Resolving deltas: 100% (2721/2721), done.
�[94mclone repository:�[39m git clone -b v3.1.0 https://github.com/datavisyn/tdp_core.git
Cloning into 'tdp_core'...
remote: Counting objects: 6783, done.
remote: Compressing objects: 100% (68/68), done.
remote: Total 6783 (delta 54), reused 53 (delta 25), pack-reused 6690
Receiving objects: 100% (6783/6783), 1.06 MiB | 808.00 KiB/s, done.
Resolving deltas: 100% (4972/4972), done.
Note: checking out 'a542a20538d1a4991a67c0bbe53c497e3f921fa6'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

�[31mError: failed: git - status code: 128�[39m
events.js:165
      throw err;
      ^

Error: Uncaught, unspecified "error" event. (failed: git - status code: 128)
    at Generator.emit (events.js:163:17)
    at Immediate.<anonymous> (D:\dev\repos\phovea\generator-phovea\node_modules\yeoman-generator\lib\base.js:446:16)
    at runCallback (timers.js:672:20)
    at tryOnImmediate (timers.js:645:5)
    at processImmediate [as _immediateCallback] (timers.js:617:5)

Expected behavior

The setup should finish without errors.

Add `injectVersion` to CircleCI config

The most recent build.js file supports the flag injectVersion which injects the product version into the package.json of the built component (e.g., web, server). We can add the CircleCI config to activate this behavior.

Add actual usage instructions to readme

Inlcude that this product can be used to setup a workspace:

prerequisites:

npm install -g yo github:phovea/generator-phovea

create workspace:

yo phovea:setup-workspace ordino_product

Also remove npm test , as there are no tests.

Probably remove Building as i think only CircleCI will do that.

Update build.js

See phovea/generator-phovea#461

Remove tdp_uploaded_data from product

I don't know who has access to datavisyn/tdp_uploaded_data, but i think we should remove it from this (Caleydo) repo and probably make a second (private) repo in datavisyn's organiztaion as it breaks the workspace setup.

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