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core

A REST API and other components for the Pixlise project, supporting the Pixlise UI.

https://github.com/pixlise/core

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    4 of 8 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

A REST API and other components for the Pixlise project, supporting the Pixlise UI.

Basic Info
  • Host: GitHub
  • Owner: pixlise
  • License: apache-2.0
  • Language: Go
  • Default Branch: development
  • Size: 207 MB
Statistics
  • Stars: 4
  • Watchers: 5
  • Forks: 2
  • Open Issues: 3
  • Releases: 29
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

Pixlise Core

DOI

Open in Gitpod

build build build

What is it?

PIXLISE Core is the API and data management processes for the PIXLISE platform.

PIXLISE is deployed to https://www.pixlise.org

Building

The core package is written in Golang and contains a number of components required for deplyoment of the PIXLISE platform. The simplest way to build the code is to run

shell make build

within the project root directory. This will build a number of binary files that are then located in the _out directory. The main API is called pixlise-api-xxx where xxx is the target architecture. By default we build for Mac, Linux and Windows.

Code Generation

  • go install github.com/favadi/protoc-go-inject-tag@latest
  • Run ./genproto.sh

Run-time Configuration

Executing the API requires several environment variables to be set. These include ones related to AWS (see below). A config file is also read. It's path can be specified with a command line argument: customConfigPath. This config specifies buckets and other configuration parameters to allow the API to execute containers and log errors, etc.

To see the configuration JSON structure, look at the APIConfig structure in /api/config/config.go

Docker / Kubernetes

TODO

Required Environment Variables

  • AWSACCESSKEY_ID
  • AWSSECRETACCESS_KEY
  • AWS_REGION=us-west-1

Developing in Gitpod

If you're wondering what the Gitpod button above is and would like to get a development environment up and running easily, visit the documentation here for more info.

Debugging in VS Code

  • Download the source.

  • Add a new configuration to your .vscode/launch.json file with program set to internal/api, which supplies the following to start debugger: "env": { "AWS_ACCESS_KEY_ID":"<<< LOOK THIS UP! >>>", "AWS_SECRET_ACCESS_KEY":"<<< LOOK THIS UP! >>>", "AWS_DEFAULT_REGION":"us-east-1", "AWS_S3_US_EAST_1_REGIONAL_ENDPOINT":"regional", ... Any other env variables as needed },

  • Start a local mongo DB in docker: run local-mongo/startdb.sh. On startup the DB is seeded with data from JSON files. This container can be stopped and will be deleted at that point.

  • Hit debug for the config in VS Code

You may encounter errors related to having an old Go version. At time of writing PIXLISE Core requires Go version 1.21. VS Code may also want to install some plugins for Go development.

The API takes a few seconds to start up. Watch the Debug Console in VS Code! You will see: - A dump of the configuration the API started with - Mongo DB connection status - A listing of all API endpoints and what permission they require - "INFO: API Started..." signifying the API is ready to accept requests

Local Mongo database access

Download "MongoDB Compass" and when the docker container is running locally (in docker), connect to it with this connection string: mongodb://mongoadmin:secret@localhost:27888/?authMechanism=DEFAULT

Example CLI flags

-quantExecutor docker - this tells the API to use local docker as the quant executor, meaning PIQUANT jobs will start on your local development machine.

Documentation

Given this is written in Go, it supports godoc! Being a public repository, documentation automatically is pulled into the online Go documentation site, but to view documentation locally, you can run godoc -http=:6060 and to export to a zip file you can create a directory and run godoc-static --destination=./doctest ./. That last parameter being the current directory - if it's missed, then all go packages are documented (and somehow the ones in this project are not!)

Owner

  • Name: Pixlise
  • Login: pixlise
  • Kind: organization

Pixlise Open Source Spectroscopy Analysis

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Delete event: 26
  • Push event: 222
  • Pull request review event: 5
  • Pull request review comment event: 8
  • Pull request event: 189
  • Fork event: 1
  • Create event: 110
Last Year
  • Issues event: 1
  • Watch event: 1
  • Delete event: 26
  • Push event: 222
  • Pull request review event: 5
  • Pull request review comment event: 8
  • Pull request event: 189
  • Fork event: 1
  • Create event: 110

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 934
  • Total Committers: 8
  • Avg Commits per committer: 116.75
  • Development Distribution Score (DDS): 0.398
Past Year
  • Commits: 428
  • Committers: 3
  • Avg Commits per committer: 142.667
  • Development Distribution Score (DDS): 0.131
Top Committers
Name Email Commits
Peter Nemere p****e@q****u 562
Tom Barber t****m@s****k 206
RyanStonebraker r****r@g****m 52
Ryan Stonebraker r****r@j****v 43
Michael Fedell m****l@j****v 39
Barber b****r@M****v 23
Michael Fedell m****4@g****m 6
Peter Nemere s****d@g****m 3
Committer Domains (Top 20 + Academic)
jpl.nasa.gov: 2 mt-306070.jpl.nasa.gov: 1 spicule.co.uk: 1 qut.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 172
  • Average time to close issues: N/A
  • Average time to close pull requests: about 19 hours
  • Total issue authors: 0
  • Total pull request authors: 5
  • Average comments per issue: 0
  • Average comments per pull request: 0.01
  • Merged pull requests: 161
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 45
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 minutes
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pnemere (3)
Pull Request Authors
  • pnemere (305)
  • RyanStonebraker (34)
  • michaelfedell (6)
  • buggtb (5)
  • mojafa (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 4
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 330
proxy.golang.org: github.com/pixlise/core/v2
  • Versions: 35
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Forks count: 9.0%
Average: 9.0%
Dependent repos count: 9.3%
Stargazers count: 10.9%
Last synced: 6 months ago
proxy.golang.org: github.com/pixlise/core
  • Versions: 0
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Forks count: 9.0%
Average: 9.0%
Dependent repos count: 9.3%
Stargazers count: 10.9%
Last synced: 6 months ago
proxy.golang.org: github.com/pixlise/core/v4
  • Versions: 257
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 8.7%
Average: 9.3%
Dependent repos count: 9.8%
Last synced: 6 months ago
proxy.golang.org: github.com/pixlise/core/v3
  • Versions: 38
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 8.1%
Dependent repos count: 9.3%
Average: 11.9%
Forks count: 13.6%
Stargazers count: 16.6%
Last synced: 6 months ago