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Johan Viklund edited this page May 13, 2019 · 98 revisions

Until Autumn

  • Documentation - consolidate Documentation
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Bugfixing

Tuesday standups every other even week at 14.00.

Sprint 38

  • Documentation - consolidate Documentation
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Swefreq site
    • sFTP should use postgres database.
    • Bugfix, show variants when ALT=*
    • Merge develop into master
    • Make test deploy and rollback on dev
    • Deploy to production
  • Beacon
    • Deploy beacon to production
    • Update fi beacon-network and the other beacon network (double check whether new datasets show up)
    • Tests for BND, find some test-case.
    • How and when is access levels for more detailed information defined in the specification
  • Create user stories for derived and/or related datasets
    • HLA predictions
    • Structural variants
    • CYP
    • Or just plain same study on the same dataset

Sprint review 13 May, 2019, 13:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 37

  • Documentation - consolidate Documentation
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Keep all nucleotides in variants
22      20118621        .       TG      T,TGGG,TGGGG,TGG        172808

  • Beacon
    • Controlled access - sondera terrängen.
    • Tests for BND, find some test-case.
  • Use new beacon on swefreq
  • SFTP should use postgres database.
  • Change heading on population frequencies to dataset frequencies (including column header).
  • Ability to specify that a dataset don't need approval for downloads (still registered).

Sprint review 29 April, 2019, 14:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 36

  • Documentation - consolidate Documentation
    • Documentation about code in the repo and generated to read the docs!
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Database migration (Linus)
    • Merge feature/browser-postgres into develop.
  • Beacon
    • Handover mechanism
      • Code in beacon
      • URL handlers in browser
    • Controlled access - sondera terrängen.
    • Tests for BND, find some test-case.
  • Use new beacon on swefreq
  • SFTP should use postgres database.
  • Monitor request time in monitor with ⏰

Sprint review 15 April, 2019, 14:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 35

  • Documentation - consolidate
    • Documentation about code in the repo and generated to read the docs!
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Deploy before postgres migration
    • master merge
    • Deploy to production
  • Database migration (Linus)
    • Postgres migration (feature/postgres-database)
      • Reference genome in dataset_version table
      • Merge to develop
    • Browser migration to postgres
      • Create test datset
  • Beacon 1.0
    • Put Elixir Beacon nginx config in Ansible (JohanV)
    • Document what we support, what we don't support and what we are confused about. In docs/ subfolder.
      • Should include information about event types, what we have and how we support or not support them.

Sprint review 25 March, 2019, 13:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 34

  • Documentation - consolidate
    • Documentation about code in the repo and generated to read the docs!
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • RSID
  • Deploy before postgres migration
    • master merge
    • Deploy to production
  • Database migration (Linus)
    • Postgres migration (feature/postgres-database)
      • Reference genome in dataset_version table
      • Merge to develop
    • Browser migration to postgres
      • Test with complete datasets
  • Beacon 1.0
    • Column(s) signalling inclusion of dataset in beacon and/or browser
    • Put Elixir Beacon nginx config in Ansible (JohanV)
    • 0/1 coordinate transformation
    • More types of events, INV, DUP, MSNP(?)
      • Do we have these in our datasets?
      • Expand datamodel to include event type?

Sprint review 11 March, 2019, 11:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 33

  • Documentation - consolidate
    • Documentation about code in the repo and generated to read the docs and/or sphinx?
    • System and processes in swefreq-config, in docs subdirectory (JohanV)
  • Database migration (Linus)
    • Mongo migration
    • Parser for loading vcf-data
  • Beacon 1.0
    • Generate a dataset with nonsensitive data
      • Should support all currently supported types of queries (1.0)
    • Put Elixir Beacon nginx config in Ansible (JohanV)

Sprint review 25 February, 2019, 13:00 - E10:3314 https://sunet.zoom.us/j/435963356

Sprint 32

  • Documentation - consolidate
    • Put information on the meta-documentation page.
  • LoF Annotation of ACpop - #486
  • Database migration
    • Mongo migration
    • Test PostgreSQL user credential against frontend on swefreq-dev
  • Elastic
  • Beacon 1.0
    • Generate a dataset with nonsensitive data
      • Talk with the beacon project
      • Should support all currently supported types of queries (1.0)
    • Put Elixir Beacon nginx config in Ansible

Sprint review 4 February, 2019, 13:00 - E10:3314
https://sunet.zoom.us/j/435963356

Sprint 31

  • Have new ACpop dataset privately visible in production web. #492
  • Method for completely new user to get sFTP credentials - #480
  • Beacon 1.0
    • Tests with randomised data
    • Support more of the data model
    • Join the Finnish network
  • Test PostgreSQL user credential against frontend on swefreq-dev

Sprint review 14 January, 2019, 13:00 - E10:3314
https://sunet.zoom.us/j/435963356

Sprint 30

  • Have new ACpop dataset visible in dev web. #492
  • Method for completely new user to get sFTP credentials - #480
  • Correct source IPs in tornado logs - #481
    • Into production.
  • Beacon 1.0
    • PostgreSQL database ready for beacon - #482
    • Swegen data in postgres database
    • Beacon running on hz
    • Exposed to the internet
  • Test PostgreSQL user credential against frontend

Sprint review 17 december, 13:00 - E10:3314
https://sunet.zoom.us/j/435963356

Sprint 29

  • Add new ACpop dataset - #475
    • Speed thinning
  • Method for completely new user to get sFTP credentials - #480
  • Correct source IPs in tornado logs - #481
    • Into production.
  • PostgreSQL database ready for beacon - #482
    • Finnish compatibility
    • Test beacon in dev container
  • Test PostgreSQL user credential against frontend

Sprint review 3 December 13:00 - E10:3314
https://sunet.zoom.us/j/435963356

Sprint 28

  • Add new ACpop dataset - #475
  • Method for completely new user to get sFTP credentials - #480
  • Correct source IPs in tornado logs - #481
  • PostgreSQL database ready for beacon - #482

Sprint review 19 November, 13:00 - E10:3314
https://sunet.zoom.us/j/435963356

Sprint 27

  • Finalize adding of ACpop dataset - #431
  • Browser integration tab in Prod - #362

Sprint review 13 August, 13:00 - E10:3309
https://sunet.zoom.us/j/435963356

Sprint 26

  • Adding of ACpop dataset - #431
    • SweFreq
    • GenomeBrowser
  • Browser integration tab - #362

Sprint review 21 June, 14:30 - E10:3309
https://sunet.zoom.us/j/435963356

Sprint 25

  • Demonstrate adding of second dataset - #431
    • SweFreq
    • GenomeBrowser
    • Checklist for adding a dataset
  • Browser integration tab - #362

Sprint review 1 June, 11:00 - E10:3309
https://sunet.zoom.us/j/435963356

Sprint 24

  • Demonstrate adding of second dataset - #431
    • SweFreq
    • GenomeBrowser
    • Checklist for adding a dataset
  • Browser integration tab - #362

Sprint review 18 May, 10:00 - E10:3309
https://sunet.zoom.us/j/435963356

Sprint 23

  • Demonstrate adding of second dataset - #431
    • SweFreq
    • GenomeBrowser
    • Documentation?
  • Update links in browser headers (auto-rendered) - #362

Sprint review 4 May, 14:30 - E10:3309
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 22

  • Release everything
    • #369 Set up sftp inbox
    • #434 New SweGen dataset release with corrected allele freq's on X & Y (US01:02 - Add dataset)
    • #435 & #436 Bioschemas markup for datasets and site (US14 - Bioschema markup of datasets)
    • #444 User account UI (upload credentials etc)
    • #437 Separate database field (and GUI rendering) for specified instructions and contact details (US02:05 Request access to individual data)
    • #449 Update the Elixir OIDC endpoint

Sprint review 13 April, 14:30 - E10:3309
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 21

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • #431 Add test dataset
    • #432 Scripts or checklists (procedures) for loading vcf data to genome browser instance
  • #433 New browser release not showing allele freq's (US06 - Browse datasets)
    • #434 New SweGen dataset release w/o "allele freq" (US01:02 - Add dataset)
  • #435 & #436 Bioschemas markup for datasets and site (US14 - Bioschema markup of datasets)
  • #444 User account UI (upload credentials etc)

Sprint review 29 March, 9:00 - E10:2309
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 20

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • #431 Add test dataset
    • #432 Scripts or checklists (procedures) for loading vcf data to genome browser instance
  • #433 New browser release not showing allele freq's (US06 - Browse datasets)
    • #434 New SweGen dataset release w/o "allele freq" (US01:02 - Add dataset)
  • #435 & #436 Bioschemas markup for datasets and site (US14 - Bioschema markup of datasets)
  • #444 User account UI (upload credentials etc)

Sprint review 15 March, 14:30 - E10:3309
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 19

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • #431 Add test dataset
    • #432 Scripts or checklists (procedures) for loading vcf data to genome browser instance
  • #433 New browser release not showing allele freq's (US06 - Browse datasets)
    • #434 New SweGen dataset release w/o "allele freq" (US01:02 - Add dataset)
  • #435 & #436 Bioschemas markup for datasets and site (US14 - Bioschema markup of datasets)
  • #437 Separate database field (and GUI rendering) for specified instructions and contact details (US02:05 Request access to individual data)

Sprint review 26 February, 10:00 - E10:2309
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 18

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • UI for inbox credentials
    • Add new dataset(s) - dependent on receiving files
  • User interface for converting Google login users to ELIXIR ID.
  • Exclude estimated allele frequencies from SweGen dataset => new dataset release
  • New browser release not showing allele freq's
  • Re-prioritise user stories

Sprint review 9 February, 10:00 - E10:3314
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 17

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • Add new dataset(s) - dependent on receiving files
    • #393 Implement using only one copy of reference datasets in Browser
  • User interface for converting Google login users to ELIXIR ID.
  • Investigate support for GRChg38 datasets - Browser etc
  • Exclude estimated allele frequencies from SweGen dataset => new release

Sprint review 25 January, 13:00 - E10:
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 16

  • Adding a new dataset (US01:02 - Add dataset)
    • #369 Set up sftp inbox
    • Add new dataset(s) - dependent on receiving files
    • #393 Implement using only one copy of reference datasets in Browse
  • #306 Use ELIXIR AAI instead of Google (US01:03 - Clear interface, US04 - Data access control)
  • #394Test checklist for Browser (US01:03 - Clear interface, US04 - Data access control)

Sprint review 15 January, 15:00 - E10:3314
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/435963356

Sprint 15

  • Adding a new dataset (US01:02 - Add dataset)
    • #241 Scripts for metadata in SweFreq (US02 - Describe a dataset)
      • Document process
    • #369 Set up sftp inbox
    • Add new dataset(s) - dependent on sftp inbox
    • #384 Investigate possibility to avoid loading reference datasets more than once in Browser
  • #306 Use ELIXIR AAI instead of Google (US01:03 - Clear interface, US04 - Data access control)

Sprint review 6 December, 15:30 - E10:2314
Join from PC, Mac, Linux, iOS or Android: https://sunet.zoom.us/j/103790390

Sprint 14

  • #30 Temporary links to datasets (US01 - Share a dataset, US05 - Download whole dataset)
  • #345 Refactor angular and backend architecture (US01 - Share a dataset, US05 - Download whole dataset)
  • Adding a new dataset (US01:02 - Add dataset)
    • #241 Scripts for metadata in SweFreq (US02 - Describe a dataset)
    • Document process
  • #306 ELIXIR AAI support design - dependent on response from ELIXIR (US01:03 - Clear interface, US04 - Data access control)
  • #352 Investigate possibility to get Swedish ExAC data into SweFreq (US01 - Share a dataset)

Sprint review 22 November, 14:00 - E10:2309
Web browser: https://vconf.kth.se/. Set SciLifeLab2 as conference room. Pincode: 8800;
SIP/H323: connect to [email protected]

Sprint 13

  • Temporary links to datasets (US01 - Share a dataset, US05 - Download whole dataset)
  • Refactor angular and backend architecture (US01 - Share a dataset, US05 - Download whole dataset)
  • Adding a new dataset (US01:02 - Add dataset)
    • Load to genome browser (US06 - Browse datasets)
    • Scripts for metadata (US02 - Describe a dataset)
    • Document process
  • ELIXIR AAI support design - dependent on response from ELIXIR (US01:03 - Clear interface, US04 - Data access control)
  • Investigate possibility to get Swedish ExAC data into SweFreq (US01 - Share a dataset)

Sprint review 6 November, 15:00 - E10:3314
Web browser: https://vconf.kth.se/. Set SciLifeLab as conference room. Pincode: 8800;
SIP/H323: connect to [email protected]

Sprint 12

  • Refactor angular and backend architecture (US01 - Share a dataset, US05 - Download whole dataset)
  • Schema changes for logging (US08 - Dataset statistics)
  • Test adding a new dataset (US01:02 - Add dataset)
    • Load to genome browser (US06 - Browse datasets)
    • Scripts for metadata (US02 - Describe a dataset)
    • Document process
  • ELIXIR AAI support design - dependent on response from ELIXIR (US01:03 - Clear interface, US04 - Data access control)

Sprint review 23 October, 15:00 - E10:2314
Web browser: https://vconf.kth.se/. Set SciLifeLab as conference room. Pincode: 8800;
SIP/H323: connect to [email protected]

Sprint 11

  • ELIXIR AAI support - design process, also handling old Google ID logins (US01:03 - Clear interface, US04 - Data access control)
  • Dataset version interface (US05 - Download whole datasets)
  • Test adding a new dataset (US01:02 - Add dataset)
    • Load to genome browser (US06 - Browse datasets)
    • Scripts for metadata (US02 - Describe a dataset)
    • Document process

Sprint review 10 October, 14:00 - E10:3102

Sprint 10

  • Beacon for each dataset
  • Remodel dataset metadata (Sample set cardinality, Sample Collection, ...)
  • New layout to Production server

Sprint review 26 September, 14:30 - E10:3102

Sprint 9

  • Make a dataset page template
  • Finalize rebuild of the swefreq start page
  • Extend db schema for private datasets
  • Extend db schema for temporary file links

Sprint review 11 September, 15:00 - E10:3314

Sprint 8

  • Make a dataset page template
    • Include a second "fake" dataset
  • Rebuild the swefreq start page
  • Investigate vcf-miner (& Gnomad)

Sprint review 28 August, 10:00 - E10:2314

Sprint 7

  • Reproduce current site dataset info with data held in new schema
  • User survey
  • Study and dataset metadata specifications
  • Investigate vcf-miner

Sprint review 28 June, 10:00 - E10:3314

Sprint 6

  • Merge local Exac changes to gnomad code base
  • Fix download response delay
  • Reproduce current site dataset info with data held in new schema
  • User survey
  • Study and dataset metadata specifications

Sprint review 7 June, 14:00 - E10:3314

Sprint 5

  • Reproduce current site user management with data held in new schema (done)
  • Merge local Exac changes to gnomad code base
  • Move data to right location for off-site backup (done)
  • Study and dataset metadata specifications
  • User survey

Sprint review 16 May, 14:00 - E10:3314

Sprint 4

  • New database schema to support new site
  • Start migrating to new schema -> reproduce current site with data held in new schema (instead of hardcoded pages)
  • Investigate gnomad browser as replacement for Exac
  • Sort out backup of Hertz and mysql database

Sprint review 28 April, 11:00

  • Introduce Study and relevant metadata to the db schema
    • Johan R to provide relevant field
  • First step: user login
  • gnomad should work
  • backup
    • user db backed up every hour
    • off-site backup at UU IT - TSM
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