=== Interactive development

• Startup:

  % rm -rf classes % lein repl (require '[appengine-magic.core :as ae]) (require '[rvar.core :as rvar] :reload-all) (ae/serve rvar/rvar-app)

• Whenever you edit, do:

  (require '[rvar.core :as rvar] :reload-all)

• Memcache clear:

  (require '[appengine-magic.services.memcache :as mc]) (mc/clear-all!)

=== Local server

% lein appengine-prepare
% ~/install/gae/appengine-java-sdk-1.4.0/bin/dev_appserver.sh resources

=== Data file generation

• Hand edit scripts/data/phenotypes.csv specifying health traits of interest and references at Ensembl and SNPedia.
• lein run scripts/ensembl_phenotypes.clj scripts/data
• python2.6 scripts/snpedia_to_disease.py scripts/data
• lein run scripts/ensembl_transcripts.clj scripts/data
• python2.6 scripts/merge_phenotype_data.py scripts/data
• python2.6 scripts/publication_summary.py scripts/data
• lein run scripts/pub_refine_keywords.clj scripts/data
• lein run scripts/rate_variants.clj scripts/data
• lein run scripts/provider_variations.clj ../genomes/provider_details.csv scripts/data
• lein run scripts/group_variations.clj scripts/data

=== Upload

• python2.6 scripts/upload_data_to_gae.py scripts/data localhost:8080 [email protected] ""

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --filename=data/phenotypes.csv --url=http://localhost:8080/remote_api --application=our-var --kind Phenotype

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --kind Gene --filename=data/genes.csv

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --kind VariationTranscript --filename=data/tx-variation.csv

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --filename=data/variation-lit.csv --kind VariationLit

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --filename=data/variation-providers.csv --kind VariationProviders

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --filename=data/variation-scores.csv --kind VariationScore

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --url=http://localhost:8080/remote_api --application=our-var --filename=data/variation-groups.csv --kind VariationGroup

• ~/install/gae/google_appengine/appcfg.py upload_data --config_file=bulkloader.yaml --filename=data/variation-phenotypes.csv --url=http://localhost:8080/remote_api --application=our-var --kind VariationPhenotype