BioThings Studio 0.2b

Docker images

All BioThings docker images are now available Docker Hub, and can be fetched using docker pull command:

• BioThings Studio 0.2b: docker pull biothings/biothings-studio:0.2b
• Studio4MyGene 0.2b: docker pull biothings/studio4mygene:0.2b
• Studio4MyVariant 0.2b: docker pull biothings/studio4myvariant:0.2b
• Studio4MyChem 0.2b: docker pull biothings/studio4mychem:0.2b

Tutorial

http://docs.biothings.io/en/latest/doc/studio.html

Changelog

• Autohub feature integrated, allowing to manage data releases from the same Hub.
• Upgrade feature to monitor new commits available on the remote github repo, and pull latest code
• Data plugin can now be defined as "advanced" plugin, where repo contains python code defining dumper and uploader(s). Advanced data plugins are registered the same through the webapp.
• New "hooks" feature, allowing to define custom commands for the Hub console
• Ability to expose a read-only Hub API, default port is 7081
• Added code-server, running on port 60080, to easily allow code edit without having to enter container

BioThings Studio 0.2a

Docker image:

Docker images

All BioThings docker images are now available Docker Hub, and can be fetched using docker pull command:

• BioThings Studio 0.2a: docker pull biothings/biothings-studio:0.2a
• Studio4MyGene 0.2a: docker pull biothings/studio4mygene:0.2a
• Studio4MyVariant 0.2a: docker pull biothings/studio4myvariant:0.2a
• Studio4MyChem 0.2a: docker pull biothings/studio4mychem:0.2a

Tutorial

http://docs.biothings.io/en/latest/doc/studio.html

Changelog

• updated to BioThings SDK 0.6.0, which provides all functionalities to create and publish data release (full & incremental).

BioThings Studio 0.1f

Docker image:

Docker images

• BioThings Studio 0.1f: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/biothings_studio:0.1f.docker
• Studio4MyGene 0.1f: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4mygene:0.1f.docker
• Studio4MyVariant 0.1f: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4myvariant:0.1f.docker
• Studio4MyChem 0.1f: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4mychem:0.1f.docker

Tutorial

http://docs.biothings.io/en/latest/doc/studio.html

Changelog

System & Docker

• docker image based on Ubtun 18.04, using python 3.7
• updated to BioThings SDK 0.3.x, Oracle Java 12, MongoDB 4.0.10

Plugins

• export plugins code to plain python code in order to access more features from BioThings SDK (dumper, uploader, mapping code can be exported)
• specify requirements (dependencies) in plugin's manifest file

http://docs.biothings.io/en/latest/doc/studio_guide.html#data-plugin-architecture-and-specifications

Webapp

• display diff (json-diff format) between mapping generated from inspection and registered mapping to easily track changes
• sample/limit options for data inspection allowing to partially and/or randomly inspect a subset of data
• delete Hub API connections now possible from connection widget
• new build configuration form including new LinkDataBuilder, which allows to create build from a single datasource without having to fully copy the data to the merged collection (saves time and disk-space)
• more mapping editing features (field type, and manual specification)
• more sanity check when registering a plugin

Misc

• CPU activity not tracked anymore to due to hub getting slow with blocking calls

List of Studio's issues specifically addressed in this releases: https://github.com/biothings/biothings_studio/milestone/3?closed=1

BioThings Studio 0.1e

Docker image:

Docker images

• BioThings Studio 0.1e: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/biothings_studio:0.1e.docker
• Studio4MyGene 0.1e: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4mygene:0.1e.docker
• Studio4MyVariant 0.1e: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4myvariant:0.1e.docker
• Studio4MyChem 0.1e: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/studio4mychem:0.1e.docker

Tutorial

http://docs.biothings.io/en/latest/doc/studio.html

Changelog

(lost...)

System & Docker

• docker image based on Ubtun 18.04, using python 3.6
• updated to BioThings SDK 0.2.3, Tornado 5.1, SockJS 1.0.6

http://docs.biothings.io/en/latest/doc/studio_guide.html#data-plugin-architecture-and-specifications

List of Studio's issues specifically addressed in this releases: https://github.com/biothings/biothings_studio/milestone/1?closed=1

BioThings Studio 0.1d

Docker image available at: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/biothings_studio:0.1d.docker

Tutorial available at: http://docs.biothings.io/en/latest/doc/studio.html

• /status and /whatsnew improved endpoints
• documents inspected using parallelization (faster ES mapping generation)
• loading indicator to improve UI feedback
• misc UI improvements/fixes

BioThings Studio 0.1c

Docker image available at: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/biothings_studio_0.1c.docker

Tutorial available at: http://docs.biothings.io/en/latest/doc/studio.html

• add reloader to automatically restart the Hub when a source file has changed in data sources and data plugins
• add new Hub API endpoints /status and /whatnew
• webapp home page now displays status and newly updated data sources
• add new dump_plugin command to manager data plugin source code from the Hub
• add new restart/stop commands
• publish events in realtime, about sources/builds/... changes occurring in the Hub, through the websocket
• add connection creation widget to connect webapp to multiple Hub API
• bug fixes and UI improvements...

Biothings Studio 0.1b

Docker image available at: http://biothings-containers.s3-website-us-west-2.amazonaws.com/biothings_studio/biothings_studio_0.1b.docker

• use websocket
• use reloader to reload dumpers/uploaders when a source file changes
• fix requirements installation while booting the studio
• add SSH server running in docker image to connect using "biothings" user, in case tmux can't be accessed through "docker exec" due to terminal misconfiguration, which depends on docker host (workaround)
• add utf8 encoding to prevent ascii decoding error