Difference between revisions of "WebDev 2010.05.19-Agenda and Minutes"
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== 1. Administration update (Todd; 5 minutes) == | == 1. Administration update (Todd; 5 minutes) == | ||
+ | |||
+ | * almost all services now migrated to OICR | ||
+ | * servers giving good performance | ||
+ | * leaner architecture | ||
== 2. modENCODE status (Xiaoqi; 10 minutes) == | == 2. modENCODE status (Xiaoqi; 10 minutes) == | ||
+ | |||
+ | * slow software, try 2.08 version (LS) | ||
+ | * test in dev | ||
+ | * try MySQL optimization | ||
== 3. Biomart progress (Abby; 10 minutes) == | == 3. Biomart progress (Abby; 10 minutes) == | ||
+ | |||
+ | * Biomart WS210 building, slow | ||
+ | * Port 80 for the Biomart site -- problematic; works with 8080 | ||
+ | * To discuss issues with folks @ OICR, esp. Joseph. | ||
== 4. WS214 status & WS215 pipeline goals (Norie; 10 minutes) == | == 4. WS214 status & WS215 pipeline goals (Norie; 10 minutes) == | ||
+ | |||
+ | * position matrix restore for WS214 | ||
+ | * for WS215: GFF-MySQL, additional ontology search data | ||
== 5. API progress (Xiaoqi, Norie, Todd, 5 minutes) == | == 5. API progress (Xiaoqi, Norie, Todd, 5 minutes) == | ||
+ | |||
+ | * Strains, Interactions developed and tested; working on Anatomy_ontology, Gene_ontology, Person (NBC) | ||
+ | * DB connectivity, evidence method (XS) | ||
+ | * Variation (nearly done) and Paper (25%) (TH) | ||
== 6. Open table == | == 6. Open table == | ||
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Made changes to Bio::Graphics::Browser2::Region.pm | Made changes to Bio::Graphics::Browser2::Region.pm | ||
− | + | * wasn't searching through automatic classes for exact search - failing for Bio::DB::GFF. | |
− | + | * changed in dev, aligner and exact search work there | |
− | |||
==== Search demo (Abby) ==== | ==== Search demo (Abby) ==== |
Latest revision as of 16:42, 19 May 2010
Contents
Agenda
1. Administration update (Todd; 5 minutes)
- almost all services now migrated to OICR
- servers giving good performance
- leaner architecture
2. modENCODE status (Xiaoqi; 10 minutes)
- slow software, try 2.08 version (LS)
- test in dev
- try MySQL optimization
3. Biomart progress (Abby; 10 minutes)
- Biomart WS210 building, slow
- Port 80 for the Biomart site -- problematic; works with 8080
- To discuss issues with folks @ OICR, esp. Joseph.
4. WS214 status & WS215 pipeline goals (Norie; 10 minutes)
- position matrix restore for WS214
- for WS215: GFF-MySQL, additional ontology search data
5. API progress (Xiaoqi, Norie, Todd, 5 minutes)
- Strains, Interactions developed and tested; working on Anatomy_ontology, Gene_ontology, Person (NBC)
- DB connectivity, evidence method (XS)
- Variation (nearly done) and Paper (25%) (TH)
6. Open table
Aligner and exact search problem in gbrowse2 (Abby)
Made changes to Bio::Graphics::Browser2::Region.pm
- wasn't searching through automatic classes for exact search - failing for Bio::DB::GFF.
- changed in dev, aligner and exact search work there
Search demo (Abby)
http://dev.wormbase.org:9010/ --home page
http://dev.wormbase.org:9010/search/gene/lin-5* --multiple hit example
If there's time and/or you want explanations of code I added:
- Search box triggers action to Search controller:
http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/Web/Controller/Search.pm
- Controller accesses Search object from API:
http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API.pm
http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/Search.pm
- Search object returns list of Search::Result objects:
http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/Search/Result.pm
- results.tt2 template renders the Search::Result objects:
http://bitbucket.org/tharris/wormbase/src/tip/root/templates/search/results.tt2