Software Group Progress Report Q2 2014: Difference between revisions
Jump to navigation
Jump to search
(→Noctua) |
|||
Line 71: | Line 71: | ||
* Authentication | * Authentication | ||
* Semi-permanent layout | * Semi-permanent layout | ||
* | * Undo (push to Q4?) | ||
* Showing inference | * Showing inference | ||
* Improved front-end | * Improved front-end |
Revision as of 20:00, 6 June 2014
Progress Report Q2
Website
- Drupal
- Drupal Content: migration complete (Moni, Seth, Rama, ...)
- Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) JIRA GO-106
- AmiGO
- AmiGO 2.0 released in March (Seth)
- AmiGO 2.1 in testing May (Seth, Rama)
- Term Enrichment
- Panther services integrated (Anushya, Seth)
Authentication / Authorization
- Gathering requirements at CalTech hackathon
- Implementing Persona authentication into Noctua
GO MME: Noctua/Barista/Minerva
- Implemented prototype system, 3 components:
- Noctua: client component
- Barista: messaging/session layer
- Minerva: OWLServer
- CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua noctua-51
- Implemented v1 of LEGO->GPAD/GAF in OWLTools JIRA GO-288
Transition to OWL and ontology support
Top-level ticket: GO-222
- Berkeley OWL hackathon (with David and Tanya): gathered requirements, tested roundtripping, reasoning etc
- Added import catalogs to OE (this allowed us to add all logical defs to main ontology)
- oboeditor plugin for Protege v0.1 (Heiko, Simon J)
- Fixes to obo/owl converter for never_in_taxon links
- TG templates (HEIKO TO ADD)
- ...
GPAD/GPI
- GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS)
- Added 2-way converters to OWLTools (Heiko)
- GPI exports direct from MGI (Mary)
Retire GO Mine
- Done? (SETH/KALPANA)
PAINT
- Paint v1.0 release (Suzi)
- JsPAINT prototype (Mitch, Seth)
Priorities for Q3
Website
- Attempt further virtualization/distribution of AmiGO 2 client
- Image deployment at production?
- Test feasibility of AmiGO 2 client running in in hosted or PaaS?
- PaaS may require rewrite of some high-level bits
- AmiGO AmiGO_2#Timeline
- Selenium test framework (Mary, JuanCarlos)
- AmiGO 2.2 July
- AmiGO 2.3 Oct
GO MME
Top-level ticket: GO-255
Milestone in github: Q3
Noctua
- Authorization
- Authentication
- Semi-permanent layout
- Undo (push to Q4?)
- Showing inference
- Improved front-end
- Species selector for new models & Filter search for appropriate genes/proteins
- Dev instance up and running at CalTech (JuanCarlos, Raymond)
- OA-type editor in Noctua (Juancarlos)
Minerva
- Import from Reactome (Chris)
- Pipeline for GAF/GPAD output (Heiko)
Paper Viewer
- Capella->Noctua integration noctua-51 pushed to Q4
Infrastructure
- Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
- Refactor GOlr loading (Seth, Heiko, Chris)
- Migrate crons to Jenkins JIRA GO-99 (Heiko, Mike)
- GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4
MySQL retirement
- Replace go-db-perl code with OWLTools code (Kalpana) JIRA GO-282
Transition to OWL
- oboeditor plugin v0.2
- prototype of solution for caching inferred links (Heiko, DavidOS)
- Progress towards automation of integration with RHEA GO-190 -- not enough resources to complete in Q3
- Progress towards automation of integration with IPR/PFAM -- not enough resources to complete in Q3