Software Group Progress Report Q2 2014: Difference between revisions
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* Drupal | * Drupal | ||
** Drupal Content: migration complete (Moni, Seth, Rama, ...) | ** Drupal Content: migration complete (Moni, Seth, Rama, ...) | ||
** Drupal Rollout: migrated to | ** Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) [https://www.ebi.ac.uk/panda/jira/browse/GO-106 JIRA GO-106] | ||
* AmiGO | * AmiGO | ||
** AmiGO 2.0 released in March (Seth) | ** AmiGO 2.0 released in March (Seth) | ||
Line 11: | Line 11: | ||
** Panther services integrated (Anushya, Seth) | ** Panther services integrated (Anushya, Seth) | ||
=== Authentication / | === Authentication / Authorization === | ||
* Gathering requirements at CalTech hackathon | * Gathering requirements at CalTech hackathon | ||
* Implementing | * Implementing Persona authentication into Noctua | ||
=== Noctua === | === LEGO: Noctua/Barista/Minerva === | ||
* Implemented | * Implemented prototype system, 3 components: | ||
** Noctua: client component | ** Noctua: client component | ||
** Barista: | ** Barista: messaging/session layer | ||
** Minerva: OWLServer | ** Minerva: OWLServer | ||
* CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51] | * CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51] | ||
* Implemented v1 of LEGO->GPAD/GAF in OWLTools [https://www.ebi.ac.uk/panda/jira/browse/GO-288 JIRA GO-288] | * Implemented v1 of LEGO->GPAD/GAF in OWLTools [https://www.ebi.ac.uk/panda/jira/browse/GO-288 JIRA GO-288] | ||
=== Transition to OWL === | === Transition to OWL and ontology support === | ||
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-222 GO-222] | Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-222 GO-222] | ||
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* oboeditor plugin for Protege v0.1 (Heiko, Simon J) | * oboeditor plugin for Protege v0.1 (Heiko, Simon J) | ||
* Fixes to obo/owl converter for never_in_taxon links | * Fixes to obo/owl converter for never_in_taxon links | ||
* TG templates (HEIKO TO ADD) | |||
* ... | |||
=== GPAD/GPI === | === GPAD/GPI === | ||
Line 46: | Line 48: | ||
== Priorities for Q3 == | == 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]] | * AmiGO [[AmiGO_2#Timeline]] | ||
** Selenium test framework (Mary, JuanCarlos) | ** Selenium test framework (Mary, JuanCarlos) | ||
** AmiGO 2.2 July | ** AmiGO 2.2 July | ||
** AmiGO 2.3 Oct | ** AmiGO 2.3 Oct | ||
** Matrix improvements | |||
=== | === LEGO === | ||
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255] | Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255] | ||
* | Milestone in github: [https://github.com/kltm/go-mme/issues?milestone=3&page=1&state=open 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) | * Dev instance up and running at CalTech (JuanCarlos, Raymond) | ||
* OA-type editor in Noctua | * OA-type editor in Noctua (Juancarlos) | ||
* Pipeline for GAF/GPAD output | |||
==== Minerva ==== | |||
* Import from Reactome (Chris) | |||
* Pipeline for GAF/GPAD output (Heiko) | |||
=== Paper Viewer === | === Paper Viewer === | ||
* Capella-Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4 | |||
* Capella->Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4 | |||
=== Infrastructure === | === Infrastructure === | ||
* Migrate MGI GAF->GPAD scripts to OWLTools (Mary) | * Migrate MGI GAF->GPAD scripts to OWLTools (Mary) | ||
* Refactor | * Refactor GOlr loading (Seth, Heiko, Chris) | ||
* Migrate crons to Jenkins [https://www.ebi.ac.uk/panda/jira/browse/GO-99 JIRA GO-99] | * Migrate crons to Jenkins [https://www.ebi.ac.uk/panda/jira/browse/GO-99 JIRA GO-99] (Heiko, Mike) | ||
* GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4 | |||
=== MySQL retirement === | === MySQL retirement === | ||
* Replace go-db-perl code with | * Replace go-db-perl code with OWLTools code (Kalpana) [https://www.ebi.ac.uk/panda/jira/browse/GO-282 JIRA GO-282] | ||
=== Transition to OWL === | === Transition to OWL === | ||
* oboeditor plugin v0.2 | * oboeditor plugin v0.2 | ||
* prototype of solution for caching inferred links (Heiko, DavidOS) | * prototype of solution for caching inferred links (Heiko, DavidOS) |
Latest revision as of 10:58, 18 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
LEGO: 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
- Matrix improvements
LEGO
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