TC conference call - 02. February 2016

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TC conference call - 02. February 2016
Title TC conference call
Location Google Hangout
Date Start 2016/02/02
Date End 2016/02/02


  • General progress on GitHub and discussions...
  • New repo dw-collections-ui - Carl is joining us to work on the front-end
  • New repo dw-dmail - portable email server (hello dmail, bye gmail)
  • Update on dw-classifications - information about the docker container, including some new Python and R scripts that convert Dyntaxa XML to CSV - can Kessy help with converting the load script to use CSV instead of XML when loading data into the module?
  • Update on dw-cco - complex collections object docker packaging with support for postgres, mysql and SQLite3? Next steps to make the DINA-Specify API run against this?
  • Update on seqdb - progress update from Satpal


Attending: Thomas Stjernegaard Jeppesen and David Konrad (DEN), James Macklin (CAN), Rob Cubey (UK), Kessy Abarenkov and Allan Zirk (EST), Markus Skyttner, Ida Li, Ingimar Erlingsson, Carl Claesson (SWE).

First Carl was introduced to the people on the call as working with the front-end development of the Collection Manager for half a year onwards.

Report from SWE

New repos at GitHub/DINA-Web

  • dw-collections-ui (Calle is putting the Collection Manager front-end stuff here).
  • dw-dmail (portable email server using Docker, might be interesting as alternative to dependencies on third party email services).

Progress on some other repos

  • dw-classifications - scripts for converting Dyntaxa XML to CSV and removing cycles were added since last meeting, a request for help from Kessy with load script for CSV data and recommendations around how to speed up loading was made but EST team is pretty busy right now with infrastructure work so she cannot spend much time on this right now.
  • dw-collections - providing the DINA Specify REST API - various improvements made to documentation (based on input from Alan Jones, Calle, Ida) and some minor fixes.

In general we are adding .travis.yml files to the repos which cause Travis CI to build projects and the repo can then display a green badge to indicate that it is in a state that can be built. We also started use uploading of build files to GitHub Releases which enables a fully cloud-based packaging of all the components of the DINA-Web system.

  • Markus S aims to suggest a "Release Guidelines" document to the meeting next time for adoption.
  • Ingimar reported progress on the deployment of SeqDB at NRM, where progress is being made and Satpal plan to deliver a new Vagrant packaging of SeqDB with some customizations requested from the users at NRM.

Report from DEN

  • Martin is working on the data migration and Thomas is currently focusing on another project.
  • Thomas has outlined a referential integrity use case and shared this with Glen N. It seems the necessary components to do a POC based on this scenario appears to already exist (dw-collections and dw-classifications) so this topic should be possible to revisit in the next meeting.

Report from CAN

  • James reported that he and Paul is getting ready to submit a manuscript describing the Complex Collections Object data model.
  • James suggested setting up a meeting to coordinate further steps regarding the suggested new data model captured in the dw-cco repo.

Report from EST

  • No big news to report, busy on infrastructure road map preparations.
  • Work progresses on the Classifications (aka Taxonomy) module and Kessy gave a presentation of the front-end used in Pluto-F earlier in the week to a group of people in the SWE team. Since then, the SWE team has a document listing a set of use cases intended for testing this module within the context of the new DINA-Web Collections Manager.

Action points

  • Work on "referential use case", Markus to send email with suggested setup for a POC adressing this scenario.
  • Issue "Release Guidelines" draft for review at next meeting (Markus).
  • Set up meeting discussing next steps for "Complex Collection Objects" and usage of "dw-cco" (Ingimar).

Next meeting 23. Feb 2016, 13.00 UCT

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