├── .dockerignore ├── .gitignore ├── INSTALL.org ├── LICENSE ├── Makefile ├── README.md ├── bin ├── README.md └── amigo.js ├── conf ├── .dummy_values.yaml ├── .initial_values.yaml ├── README.md ├── amigo2-apache.conf ├── context.yaml ├── examples │ ├── amigo.yaml.docker │ ├── amigo.yaml.jenkins-production-test │ ├── amigo.yaml.localhost │ ├── amigo.yaml.localhost-monarch │ ├── amigo.yaml.localhost-planteome │ ├── amigo.yaml.localhost_docker_loader │ ├── amigo.yaml.nakama │ ├── amigo.yaml.noctua │ ├── amigo.yaml.production │ ├── amigo.yaml.public │ ├── amigo.yaml.tomodachi │ ├── apache2.18_04.localhost_root.conf │ ├── apache2.localhost_root.conf │ └── apache2.ports.conf ├── go_solr_mirrors.yaml ├── go_sql_mirrors.yaml ├── grebe.yaml ├── handlers.yaml └── rte_resources.yaml ├── deployment └── ansible │ ├── README.md │ ├── ansible.cfg │ ├── golr-bulk-up.playbook.yaml │ ├── hosts │ └── tasks │ ├── env-golr.yaml │ ├── packages-golr.yaml │ ├── packages-std.yaml │ ├── rebuild-golr.yaml │ └── system-admin-std.yaml ├── docker-compose.yml ├── docker ├── Dockerfile ├── apache2 ├── console-capture-golr.xml ├── entrypoint.sh ├── java-golr-monit ├── libsql-tokenizer-perl_0.24-2_all.deb └── run-golr.sh ├── external ├── GO.xrf_abbs ├── README.org ├── db-xrefs.yaml ├── rte-1.xml ├── rte-2.xml └── test_mgi.mini.gaf ├── extra └── block │ ├── README.org │ ├── apache2-stanza.txt │ └── banned-hosts.txt ├── golr ├── Makefile ├── README.org ├── _test │ ├── mgi-limited-100.gaf │ └── mgi-limited.gaf ├── jetty │ ├── jetty │ ├── jetty-rewrite.xml │ ├── jetty.conf │ ├── jetty.xml │ └── no_access.html ├── solr │ ├── conf │ │ ├── schema.xml │ │ └── solrconfig.xml │ └── solr.war └── tools │ ├── golr-refresh.el │ ├── golr.el │ ├── lukeall-3.5.0.jar │ ├── one-offs │ ├── create-ev-agg-term-ids.pl │ ├── java │ │ ├── pom.xml │ │ ├── src │ │ │ └── main │ │ │ │ ├── java │ │ │ │ └── org │ │ │ │ │ └── bbop │ │ │ │ │ └── evaggxform │ │ │ │ │ └── EvAggXForm.java │ │ │ │ └── resources │ │ │ │ └── log4j.properties │ │ └── target │ │ │ └── classes │ │ │ ├── log4j.properties │ │ │ └── org │ │ │ └── bbop │ │ │ └── evaggxform │ │ │ └── EvAggXFormRun.class │ └── process-ieas.pl │ └── remove-schema-cruft.pl ├── gulpfile.js ├── install ├── javascript ├── bin │ ├── README.org │ ├── generate_general_statistics.js │ ├── generate_landing_statistics.js │ ├── generate_static_data.js │ ├── generate_statistics_for_plotly.js │ ├── generate_vals_statistics.js │ ├── golr-to-mongo.js │ ├── lego-listing.js │ ├── node_modules │ │ ├── .bin │ │ │ └── wepl │ │ ├── amigo2 │ │ │ ├── README.md │ │ │ ├── amigo2.js │ │ │ └── package.json │ │ ├── aws-sdk │ │ │ ├── .npmignore │ │ │ ├── CONTRIBUTING.md │ │ │ ├── LICENSE.txt │ │ │ ├── NOTICE.txt │ │ │ ├── README.md │ │ │ ├── UPGRADING.md │ │ │ ├── bower.json │ │ │ ├── index.js │ │ │ ├── lib │ │ │ │ ├── aws.js │ │ │ │ ├── browser.js │ │ │ │ ├── config.js │ │ │ │ ├── core.js │ │ │ │ ├── credentials.js │ │ │ │ ├── credentials │ │ │ │ │ ├── credential_provider_chain.js │ │ │ │ │ ├── ec2_metadata_credentials.js │ │ │ │ │ ├── environment_credentials.js │ │ │ │ │ ├── file_system_credentials.js │ │ │ │ │ ├── saml_credentials.js │ │ │ │ │ ├── shared_ini_file_credentials.js │ │ │ │ │ ├── temporary_credentials.js │ │ │ │ │ └── web_identity_credentials.js │ │ │ │ ├── event_listeners.js │ │ │ │ ├── http.js │ │ │ │ ├── http │ │ │ │ │ ├── node.js │ │ │ │ │ └── xhr.js │ │ │ │ ├── json │ │ │ │ │ ├── builder.js │ │ │ │ │ └── parser.js │ │ │ │ ├── metadata_service.js │ │ │ │ ├── model │ │ │ │ │ ├── api.js │ │ │ │ │ ├── collection.js │ │ │ │ │ ├── operation.js │ │ │ │ │ ├── paginator.js │ │ │ │ │ ├── resource_waiter.js │ │ │ │ │ └── shape.js │ │ │ │ ├── param_validator.js │ │ │ │ ├── protocol │ │ │ │ │ ├── json.js │ │ │ │ │ ├── query.js │ │ │ │ │ ├── rest.js │ │ │ │ │ ├── rest_json.js │ │ │ │ │ └── rest_xml.js │ │ │ │ ├── query │ │ │ │ │ └── query_param_serializer.js │ │ │ │ ├── region_config.js │ │ │ │ ├── region_config.json │ │ │ │ ├── request.js │ │ │ │ ├── resource_waiter.js │ │ │ │ ├── response.js │ │ │ │ ├── sequential_executor.js │ │ │ │ ├── service.js │ │ │ │ ├── services.js │ │ │ │ ├── services │ │ │ │ │ ├── cloudsearchdomain.js │ │ │ │ │ ├── cognitoidentity.js │ │ │ │ │ ├── dynamodb.js │ │ │ │ │ ├── ec2.js │ │ │ │ │ ├── elastictranscoder.js │ │ │ │ │ ├── glacier.js │ │ │ │ │ ├── route53.js │ │ │ │ │ ├── s3.js │ │ │ │ │ ├── sqs.js │ │ │ │ │ ├── sts.js │ │ │ │ │ └── swf.js │ │ │ │ ├── signers │ │ │ │ │ ├── presign.js │ │ │ │ │ ├── request_signer.js │ │ │ │ │ ├── s3.js │ │ │ │ │ ├── v2.js │ │ │ │ │ ├── v3.js │ │ │ │ │ ├── v3https.js │ │ │ │ │ └── v4.js │ │ │ │ ├── state_machine.js │ │ │ │ ├── util.js │ │ │ │ └── xml │ │ │ │ │ ├── browser_parser.js │ │ │ │ │ ├── builder.js │ │ │ │ │ └── node_parser.js │ │ │ ├── node_modules │ │ │ │ ├── aws-sdk-apis │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── LICENSE.txt │ │ │ │ │ ├── README.md │ │ │ │ │ ├── apis │ │ │ │ │ │ ├── autoscaling-2011-01-01.api.json │ │ │ │ │ │ ├── autoscaling-2011-01-01.paginators.json │ │ │ │ │ │ ├── cloudformation-2010-05-15.api.json │ │ │ │ │ │ ├── cloudformation-2010-05-15.paginators.json │ │ │ │ │ │ ├── cloudfront-2014-05-31.api.json │ │ │ │ │ │ ├── cloudfront-2014-05-31.paginators.json │ │ │ │ │ │ ├── cloudfront-2014-05-31.waiters.json │ │ │ │ │ │ ├── cloudsearch-2011-02-01.api.json │ │ │ │ │ │ ├── cloudsearch-2011-02-01.paginators.json │ │ │ │ │ │ ├── cloudsearch-2013-01-01.api.json │ │ │ │ │ │ ├── cloudsearch-2013-01-01.paginators.json │ │ │ │ │ │ ├── cloudsearchdomain-2013-01-01.api.json │ │ │ │ │ │ ├── cloudtrail-2013-11-01.api.json │ │ │ │ │ │ ├── cloudtrail-2013-11-01.paginators.json │ │ │ │ │ │ ├── cognito-identity-2014-06-30.api.json │ │ │ │ │ │ ├── cognito-sync-2014-06-30.api.json │ │ │ │ │ │ ├── datapipeline-2012-10-29.api.json │ │ │ │ │ │ ├── datapipeline-2012-10-29.paginators.json │ │ │ │ │ │ ├── directconnect-2012-10-25.api.json │ │ │ │ │ │ ├── directconnect-2012-10-25.paginators.json │ │ │ │ │ │ ├── dynamodb-2011-12-05.api.json │ │ │ │ │ │ ├── dynamodb-2011-12-05.paginators.json │ │ │ │ │ │ ├── dynamodb-2011-12-05.waiters.json │ │ │ │ │ │ ├── dynamodb-2012-08-10.api.json │ │ │ │ │ │ ├── dynamodb-2012-08-10.paginators.json │ │ │ │ │ │ ├── dynamodb-2012-08-10.waiters.json │ │ │ │ │ │ ├── ec2-2014-06-15.api.json │ │ │ │ │ │ ├── ec2-2014-06-15.paginators.json │ │ │ │ │ │ ├── ec2-2014-06-15.waiters.json │ │ │ │ │ │ ├── elasticache-2014-07-15.api.json │ │ │ │ │ │ ├── elasticache-2014-07-15.paginators.json │ │ │ │ │ │ ├── elasticbeanstalk-2010-12-01.api.json │ │ │ │ │ │ ├── elasticbeanstalk-2010-12-01.paginators.json │ │ │ │ │ │ ├── elasticloadbalancing-2012-06-01.api.json │ │ │ │ │ │ ├── elasticloadbalancing-2012-06-01.paginators.json │ │ │ │ │ │ ├── elasticmapreduce-2009-03-31.api.json │ │ │ │ │ │ ├── elasticmapreduce-2009-03-31.paginators.json │ │ │ │ │ │ ├── elastictranscoder-2012-09-25.api.json │ │ │ │ │ │ ├── elastictranscoder-2012-09-25.paginators.json │ │ │ │ │ │ ├── email-2010-12-01.api.json │ │ │ │ │ │ ├── email-2010-12-01.paginators.json │ │ │ │ │ │ ├── email-2010-12-01.waiters.json │ │ │ │ │ │ ├── glacier-2012-06-01.api.json │ │ │ │ │ │ ├── glacier-2012-06-01.paginators.json │ │ │ │ │ │ ├── glacier-2012-06-01.waiters.json │ │ │ │ │ │ ├── iam-2010-05-08.api.json │ │ │ │ │ │ ├── iam-2010-05-08.paginators.json │ │ │ │ │ │ ├── importexport-2010-06-01.api.json │ │ │ │ │ │ ├── importexport-2010-06-01.paginators.json │ │ │ │ │ │ ├── kinesis-2013-12-02.api.json │ │ │ │ │ │ ├── kinesis-2013-12-02.paginators.json │ │ │ │ │ │ ├── logs-2014-03-28.api.json │ │ │ │ │ │ ├── logs-2014-03-28.paginators.json │ │ │ │ │ │ ├── monitoring-2010-08-01.api.json │ │ │ │ │ │ ├── monitoring-2010-08-01.paginators.json │ │ │ │ │ │ ├── opsworks-2013-02-18.api.json │ │ │ │ │ │ ├── opsworks-2013-02-18.paginators.json │ │ │ │ │ │ ├── rds-2013-01-10.api.json │ │ │ │ │ │ ├── rds-2013-01-10.paginators.json │ │ │ │ │ │ ├── rds-2013-02-12.api.json │ │ │ │ │ │ ├── rds-2013-02-12.paginators.json │ │ │ │ │ │ ├── rds-2013-09-09.api.json │ │ │ │ │ │ ├── rds-2013-09-09.paginators.json │ │ │ │ │ │ ├── rds-2013-09-09.waiters.json │ │ │ │ │ │ ├── redshift-2012-12-01.api.json │ │ │ │ │ │ ├── redshift-2012-12-01.paginators.json │ │ │ │ │ │ ├── redshift-2012-12-01.waiters.json │ │ │ │ │ │ ├── route53-2013-04-01.api.json │ │ │ │ │ │ ├── route53-2013-04-01.paginators.json │ │ │ │ │ │ ├── route53domains-2014-05-15.api.json │ │ │ │ │ │ ├── s3-2006-03-01.api.json │ │ │ │ │ │ ├── s3-2006-03-01.paginators.json │ │ │ │ │ │ ├── s3-2006-03-01.waiters.json │ │ │ │ │ │ ├── sdb-2009-04-15.api.json │ │ │ │ │ │ ├── sdb-2009-04-15.paginators.json │ │ │ │ │ │ ├── sns-2010-03-31.api.json │ │ │ │ │ │ ├── sns-2010-03-31.paginators.json │ │ │ │ │ │ ├── sqs-2012-11-05.api.json │ │ │ │ │ │ ├── sqs-2012-11-05.paginators.json │ │ │ │ │ │ ├── storagegateway-2013-06-30.api.json │ │ │ │ │ │ ├── storagegateway-2013-06-30.paginators.json │ │ │ │ │ │ ├── sts-2011-06-15.api.json │ │ │ │ │ │ ├── support-2013-04-15.api.json │ │ │ │ │ │ ├── support-2013-04-15.paginators.json │ │ │ │ │ │ ├── swf-2012-01-25.api.json │ │ │ │ │ │ └── swf-2012-01-25.paginators.json │ │ │ │ │ ├── index.js │ │ │ │ │ ├── lib │ │ │ │ │ │ └── translator.js │ │ │ │ │ ├── metadata.json │ │ │ │ │ ├── package.json │ │ │ │ │ └── scripts │ │ │ │ │ │ └── translate-api │ │ │ │ ├── xml2js │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── .travis.yml │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── lib │ │ │ │ │ │ └── xml2js.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ └── sax │ │ │ │ │ │ │ ├── AUTHORS │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── examples │ │ │ │ │ │ │ ├── big-not-pretty.xml │ │ │ │ │ │ │ ├── example.js │ │ │ │ │ │ │ ├── get-products.js │ │ │ │ │ │ │ ├── hello-world.js │ │ │ │ │ │ │ ├── not-pretty.xml │ │ │ │ │ │ │ ├── pretty-print.js │ │ │ │ │ │ │ ├── shopping.xml │ │ │ │ │ │ │ ├── strict.dtd │ │ │ │ │ │ │ ├── switch-bench.js │ │ │ │ │ │ │ ├── test.html │ │ │ │ │ │ │ └── test.xml │ │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ └── sax.js │ │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ │ └── test │ │ │ │ │ │ │ ├── buffer-overrun.js │ │ │ │ │ │ │ ├── case.js │ │ │ │ │ │ │ ├── cdata-chunked.js │ │ │ │ │ │ │ ├── cdata-end-split.js │ │ │ │ │ │ │ ├── cdata-fake-end.js │ │ │ │ │ │ │ ├── cdata-multiple.js │ │ │ │ │ │ │ ├── cdata.js │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ ├── issue-23.js │ │ │ │ │ │ │ ├── issue-30.js │ │ │ │ │ │ │ ├── issue-35.js │ │ │ │ │ │ │ ├── issue-47.js │ │ │ │ │ │ │ ├── issue-49.js │ │ │ │ │ │ │ ├── parser-position.js │ │ │ │ │ │ │ ├── script.js │ │ │ │ │ │ │ ├── self-closing-child-strict.js │ │ │ │ │ │ │ ├── self-closing-child.js │ │ │ │ │ │ │ ├── self-closing-tag.js │ │ │ │ │ │ │ ├── stray-ending.js │ │ │ │ │ │ │ ├── trailing-non-whitespace.js │ │ │ │ │ │ │ ├── unquoted.js │ │ │ │ │ │ │ ├── xmlns-issue-41.js │ │ │ │ │ │ │ ├── xmlns-rebinding.js │ │ │ │ │ │ │ ├── xmlns-strict.js │ │ │ │ │ │ │ ├── xmlns-unbound.js │ │ │ │ │ │ │ ├── xmlns-xml-default-ns.js │ │ │ │ │ │ │ ├── xmlns-xml-default-prefix-attribute.js │ │ │ │ │ │ │ ├── xmlns-xml-default-prefix.js │ │ │ │ │ │ │ └── xmlns-xml-default-redefine.js │ │ │ │ │ └── package.json │ │ │ │ └── xmlbuilder │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── README.md │ │ │ │ │ ├── lib │ │ │ │ │ ├── XMLBuilder.js │ │ │ │ │ ├── XMLFragment.js │ │ │ │ │ └── index.js │ │ │ │ │ └── package.json │ │ │ ├── package.json │ │ │ ├── scripts │ │ │ │ └── console │ │ │ └── testem.json │ │ ├── bbop │ │ │ ├── README.md │ │ │ ├── bbop.js │ │ │ ├── bin │ │ │ │ └── web-repl.js │ │ │ └── package.json │ │ ├── express │ │ │ ├── .npmignore │ │ │ ├── History.md │ │ │ ├── LICENSE │ │ │ ├── Readme.md │ │ │ ├── index.js │ │ │ ├── lib │ │ │ │ ├── application.js │ │ │ │ ├── express.js │ │ │ │ ├── middleware │ │ │ │ │ ├── init.js │ │ │ │ │ └── query.js │ │ │ │ ├── request.js │ │ │ │ ├── response.js │ │ │ │ ├── router │ │ │ │ │ ├── index.js │ │ │ │ │ ├── layer.js │ │ │ │ │ ├── match.js │ │ │ │ │ └── route.js │ │ │ │ ├── utils.js │ │ │ │ └── view.js │ │ │ ├── node_modules │ │ │ │ ├── accepts │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ ├── mime-types │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── .travis.yml │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── SOURCES.md │ │ │ │ │ │ │ ├── component.json │ │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ │ ├── custom.json │ │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ │ ├── mime.json │ │ │ │ │ │ │ │ └── node.json │ │ │ │ │ │ │ └── package.json │ │ │ │ │ │ └── negotiator │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ ├── charset.js │ │ │ │ │ │ │ ├── encoding.js │ │ │ │ │ │ │ ├── language.js │ │ │ │ │ │ │ ├── mediaType.js │ │ │ │ │ │ │ └── negotiator.js │ │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ │ └── readme.md │ │ │ │ │ └── package.json │ │ │ │ ├── buffer-crc32 │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── .travis.yml │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── package.json │ │ │ │ │ └── tests │ │ │ │ │ │ └── crc.test.js │ │ │ │ ├── cookie-signature │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── cookie │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── debug │ │ │ │ │ ├── .jshintrc │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── browser.js │ │ │ │ │ ├── component.json │ │ │ │ │ ├── debug.js │ │ │ │ │ ├── node.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ └── ms │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ └── package.json │ │ │ │ │ └── package.json │ │ │ │ ├── depd │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── escape-html │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── component.json │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── finalhandler │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── HISTORY.md │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── fresh │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── media-typer │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── HISTORY.md │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── merge-descriptors │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── README.md │ │ │ │ │ ├── component.json │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── methods │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── package.json │ │ │ │ │ └── test │ │ │ │ │ │ └── methods.js │ │ │ │ ├── parseurl │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── HISTORY.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── path-to-regexp │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── component.json │ │ │ │ │ ├── index.js │ │ │ │ │ ├── package.json │ │ │ │ │ └── test.js │ │ │ │ ├── proxy-addr │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ └── ipaddr.js │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── Cakefile │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── ipaddr.min.js │ │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ └── ipaddr.js │ │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ │ ├── src │ │ │ │ │ │ │ └── ipaddr.coffee │ │ │ │ │ │ │ └── test │ │ │ │ │ │ │ └── ipaddr.test.coffee │ │ │ │ │ └── package.json │ │ │ │ ├── qs │ │ │ │ │ ├── .jshintignore │ │ │ │ │ ├── .jshintrc │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── .travis.yml │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── lib │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ ├── parse.js │ │ │ │ │ │ ├── stringify.js │ │ │ │ │ │ └── utils.js │ │ │ │ │ ├── package.json │ │ │ │ │ └── test │ │ │ │ │ │ ├── parse.js │ │ │ │ │ │ └── stringify.js │ │ │ │ ├── range-parser │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── send │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── lib │ │ │ │ │ │ ├── send.js │ │ │ │ │ │ └── utils.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ ├── finished │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── HISTORY.md │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ ├── node_modules │ │ │ │ │ │ │ │ └── ee-first │ │ │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ │ │ │ └── test.js │ │ │ │ │ │ │ └── package.json │ │ │ │ │ │ ├── mime │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── mime.js │ │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ │ ├── test.js │ │ │ │ │ │ │ └── types │ │ │ │ │ │ │ │ ├── mime.types │ │ │ │ │ │ │ │ └── node.types │ │ │ │ │ │ └── ms │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ └── package.json │ │ │ │ │ └── package.json │ │ │ │ ├── serve-static │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── Readme.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ ├── type-is │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── HISTORY.md │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ └── mime-types │ │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ │ ├── .travis.yml │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── SOURCES.md │ │ │ │ │ │ │ ├── component.json │ │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ ├── custom.json │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ ├── mime.json │ │ │ │ │ │ │ └── node.json │ │ │ │ │ │ │ └── package.json │ │ │ │ │ └── package.json │ │ │ │ ├── utils-merge │ │ │ │ │ ├── .travis.yml │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ │ └── vary │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── History.md │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── index.js │ │ │ │ │ └── package.json │ │ │ └── package.json │ │ ├── minimist │ │ │ ├── .travis.yml │ │ │ ├── LICENSE │ │ │ ├── example │ │ │ │ └── parse.js │ │ │ ├── index.js │ │ │ ├── package.json │ │ │ ├── readme.markdown │ │ │ └── test │ │ │ │ ├── all_bool.js │ │ │ │ ├── bool.js │ │ │ │ ├── dash.js │ │ │ │ ├── default_bool.js │ │ │ │ ├── dotted.js │ │ │ │ ├── long.js │ │ │ │ ├── num.js │ │ │ │ ├── parse.js │ │ │ │ ├── parse_modified.js │ │ │ │ ├── short.js │ │ │ │ └── whitespace.js │ │ ├── mongodb │ │ │ ├── .gitmodules │ │ │ ├── .travis.yml │ │ │ ├── CONTRIBUTING.md │ │ │ ├── LICENSE │ │ │ ├── Makefile │ │ │ ├── Readme.md │ │ │ ├── index.js │ │ │ ├── lib │ │ │ │ └── mongodb │ │ │ │ │ ├── admin.js │ │ │ │ │ ├── aggregation_cursor.js │ │ │ │ │ ├── auth │ │ │ │ │ ├── mongodb_cr.js │ │ │ │ │ ├── mongodb_gssapi.js │ │ │ │ │ ├── mongodb_plain.js │ │ │ │ │ ├── mongodb_sspi.js │ │ │ │ │ └── mongodb_x509.js │ │ │ │ │ ├── collection.js │ │ │ │ │ ├── collection │ │ │ │ │ ├── aggregation.js │ │ │ │ │ ├── batch │ │ │ │ │ │ ├── common.js │ │ │ │ │ │ ├── ordered.js │ │ │ │ │ │ └── unordered.js │ │ │ │ │ ├── commands.js │ │ │ │ │ ├── core.js │ │ │ │ │ ├── geo.js │ │ │ │ │ ├── index.js │ │ │ │ │ ├── query.js │ │ │ │ │ └── shared.js │ │ │ │ │ ├── command_cursor.js │ │ │ │ │ ├── commands │ │ │ │ │ ├── base_command.js │ │ │ │ │ ├── db_command.js │ │ │ │ │ ├── delete_command.js │ │ │ │ │ ├── get_more_command.js │ │ │ │ │ ├── insert_command.js │ │ │ │ │ ├── kill_cursor_command.js │ │ │ │ │ ├── query_command.js │ │ │ │ │ └── update_command.js │ │ │ │ │ ├── connection │ │ │ │ │ ├── base.js │ │ │ │ │ ├── connection.js │ │ │ │ │ ├── connection_pool.js │ │ │ │ │ ├── connection_utils.js │ │ │ │ │ ├── mongos.js │ │ │ │ │ ├── read_preference.js │ │ │ │ │ ├── repl_set │ │ │ │ │ │ ├── ha.js │ │ │ │ │ │ ├── options.js │ │ │ │ │ │ ├── repl_set.js │ │ │ │ │ │ ├── repl_set_state.js │ │ │ │ │ │ └── strategies │ │ │ │ │ │ │ ├── ping_strategy.js │ │ │ │ │ │ │ └── statistics_strategy.js │ │ │ │ │ ├── server.js │ │ │ │ │ ├── server_capabilities.js │ │ │ │ │ └── url_parser.js │ │ │ │ │ ├── cursor.js │ │ │ │ │ ├── cursorstream.js │ │ │ │ │ ├── db.js │ │ │ │ │ ├── gridfs │ │ │ │ │ ├── chunk.js │ │ │ │ │ ├── grid.js │ │ │ │ │ ├── gridstore.js │ │ │ │ │ └── readstream.js │ │ │ │ │ ├── index.js │ │ │ │ │ ├── mongo_client.js │ │ │ │ │ ├── responses │ │ │ │ │ └── mongo_reply.js │ │ │ │ │ ├── scope.js │ │ │ │ │ └── utils.js │ │ │ ├── node_modules │ │ │ │ ├── bson │ │ │ │ │ ├── .travis.yml │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── README.md │ │ │ │ │ ├── binding.gyp │ │ │ │ │ ├── browser_build │ │ │ │ │ │ ├── bson.js │ │ │ │ │ │ └── package.json │ │ │ │ │ ├── build │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── Release │ │ │ │ │ │ │ ├── .deps │ │ │ │ │ │ │ │ └── Release │ │ │ │ │ │ │ │ │ ├── bson.node.d │ │ │ │ │ │ │ │ │ └── obj.target │ │ │ │ │ │ │ │ │ ├── bson.node.d │ │ │ │ │ │ │ │ │ └── bson │ │ │ │ │ │ │ │ │ └── ext │ │ │ │ │ │ │ │ │ └── bson.o.d │ │ │ │ │ │ │ ├── bson.node │ │ │ │ │ │ │ ├── linker.lock │ │ │ │ │ │ │ └── obj.target │ │ │ │ │ │ │ │ ├── bson.node │ │ │ │ │ │ │ │ └── bson │ │ │ │ │ │ │ │ └── ext │ │ │ │ │ │ │ │ └── bson.o │ │ │ │ │ │ ├── binding.Makefile │ │ │ │ │ │ ├── bson.target.mk │ │ │ │ │ │ └── config.gypi │ │ │ │ │ ├── build_browser.js │ │ │ │ │ ├── builderror.log │ │ │ │ │ ├── ext │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── bson.cc │ │ │ │ │ │ ├── bson.h │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ ├── win32 │ │ │ │ │ │ │ ├── ia32 │ │ │ │ │ │ │ │ └── bson.node │ │ │ │ │ │ │ └── x64 │ │ │ │ │ │ │ │ └── bson.node │ │ │ │ │ │ └── wscript │ │ │ │ │ ├── lib │ │ │ │ │ │ └── bson │ │ │ │ │ │ │ ├── binary.js │ │ │ │ │ │ │ ├── binary_parser.js │ │ │ │ │ │ │ ├── bson.js │ │ │ │ │ │ │ ├── bson_new.js │ │ │ │ │ │ │ ├── code.js │ │ │ │ │ │ │ ├── db_ref.js │ │ │ │ │ │ │ ├── double.js │ │ │ │ │ │ │ ├── float_parser.js │ │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ │ ├── long.js │ │ │ │ │ │ │ ├── max_key.js │ │ │ │ │ │ │ ├── min_key.js │ │ │ │ │ │ │ ├── objectid.js │ │ │ │ │ │ │ ├── symbol.js │ │ │ │ │ │ │ └── timestamp.js │ │ │ │ │ ├── node_modules │ │ │ │ │ │ └── nan │ │ │ │ │ │ │ ├── .dntrc │ │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── build │ │ │ │ │ │ │ └── config.gypi │ │ │ │ │ │ │ ├── include_dirs.js │ │ │ │ │ │ │ ├── nan.h │ │ │ │ │ │ │ └── package.json │ │ │ │ │ ├── package.json │ │ │ │ │ └── tools │ │ │ │ │ │ ├── gleak.js │ │ │ │ │ │ └── jasmine-1.1.0 │ │ │ │ │ │ ├── MIT.LICENSE │ │ │ │ │ │ ├── jasmine-html.js │ │ │ │ │ │ ├── jasmine.css │ │ │ │ │ │ ├── jasmine.js │ │ │ │ │ │ └── jasmine_favicon.png │ │ │ │ ├── kerberos │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── binding.gyp │ │ │ │ │ ├── build │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── Release │ │ │ │ │ │ │ ├── .deps │ │ │ │ │ │ │ │ └── Release │ │ │ │ │ │ │ │ │ ├── kerberos.node.d │ │ │ │ │ │ │ │ │ └── obj.target │ │ │ │ │ │ │ │ │ └── kerberos.node.d │ │ │ │ │ │ │ ├── kerberos.node │ │ │ │ │ │ │ ├── linker.lock │ │ │ │ │ │ │ └── obj.target │ │ │ │ │ │ │ │ └── kerberos.node │ │ │ │ │ │ ├── binding.Makefile │ │ │ │ │ │ ├── config.gypi │ │ │ │ │ │ └── kerberos.target.mk │ │ │ │ │ ├── builderror.log │ │ │ │ │ ├── index.js │ │ │ │ │ ├── lib │ │ │ │ │ │ ├── auth_processes │ │ │ │ │ │ │ └── mongodb.js │ │ │ │ │ │ ├── base64.c │ │ │ │ │ │ ├── base64.h │ │ │ │ │ │ ├── kerberos.cc │ │ │ │ │ │ ├── kerberos.h │ │ │ │ │ │ ├── kerberos.js │ │ │ │ │ │ ├── kerberos_context.cc │ │ │ │ │ │ ├── kerberos_context.h │ │ │ │ │ │ ├── kerberosgss.c │ │ │ │ │ │ ├── kerberosgss.h │ │ │ │ │ │ ├── sspi.js │ │ │ │ │ │ ├── win32 │ │ │ │ │ │ │ ├── base64.c │ │ │ │ │ │ │ ├── base64.h │ │ │ │ │ │ │ ├── kerberos.cc │ │ │ │ │ │ │ ├── kerberos.h │ │ │ │ │ │ │ ├── kerberos_sspi.c │ │ │ │ │ │ │ ├── kerberos_sspi.h │ │ │ │ │ │ │ ├── worker.cc │ │ │ │ │ │ │ ├── worker.h │ │ │ │ │ │ │ └── wrappers │ │ │ │ │ │ │ │ ├── security_buffer.cc │ │ │ │ │ │ │ │ ├── security_buffer.h │ │ │ │ │ │ │ │ ├── security_buffer.js │ │ │ │ │ │ │ │ ├── security_buffer_descriptor.cc │ │ │ │ │ │ │ │ ├── security_buffer_descriptor.h │ │ │ │ │ │ │ │ ├── security_buffer_descriptor.js │ │ │ │ │ │ │ │ ├── security_context.cc │ │ │ │ │ │ │ │ ├── security_context.h │ │ │ │ │ │ │ │ ├── security_context.js │ │ │ │ │ │ │ │ ├── security_credentials.cc │ │ │ │ │ │ │ │ ├── security_credentials.h │ │ │ │ │ │ │ │ └── security_credentials.js │ │ │ │ │ │ ├── worker.cc │ │ │ │ │ │ └── worker.h │ │ │ │ │ ├── package.json │ │ │ │ │ └── test │ │ │ │ │ │ ├── kerberos_tests.js │ │ │ │ │ │ ├── kerberos_win32_test.js │ │ │ │ │ │ └── win32 │ │ │ │ │ │ ├── security_buffer_descriptor_tests.js │ │ │ │ │ │ ├── security_buffer_tests.js │ │ │ │ │ │ └── security_credentials_tests.js │ │ │ │ └── readable-stream │ │ │ │ │ ├── .npmignore │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.md │ │ │ │ │ ├── duplex.js │ │ │ │ │ ├── lib │ │ │ │ │ ├── _stream_duplex.js │ │ │ │ │ ├── _stream_passthrough.js │ │ │ │ │ ├── _stream_readable.js │ │ │ │ │ ├── _stream_transform.js │ │ │ │ │ └── _stream_writable.js │ │ │ │ │ ├── node_modules │ │ │ │ │ ├── core-util-is │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── float.patch │ │ │ │ │ │ ├── lib │ │ │ │ │ │ │ └── util.js │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ └── util.js │ │ │ │ │ ├── inherits │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── inherits.js │ │ │ │ │ │ ├── inherits_browser.js │ │ │ │ │ │ ├── package.json │ │ │ │ │ │ └── test.js │ │ │ │ │ ├── isarray │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── build │ │ │ │ │ │ │ └── build.js │ │ │ │ │ │ ├── component.json │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ └── package.json │ │ │ │ │ └── string_decoder │ │ │ │ │ │ ├── .npmignore │ │ │ │ │ │ ├── LICENSE │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ ├── index.js │ │ │ │ │ │ └── package.json │ │ │ │ │ ├── package.json │ │ │ │ │ ├── passthrough.js │ │ │ │ │ ├── readable.js │ │ │ │ │ ├── transform.js │ │ │ │ │ └── writable.js │ │ │ └── package.json │ │ └── mustache │ │ │ ├── .gitmodules │ │ │ ├── .jshintrc │ │ │ ├── .npmignore │ │ │ ├── .travis.yml │ │ │ ├── CHANGES │ │ │ ├── LICENSE │ │ │ ├── README.md │ │ │ ├── Rakefile │ │ │ ├── bower.json │ │ │ ├── mustache.js │ │ │ ├── mustache.js.nuspec │ │ │ ├── package.json │ │ │ └── wrappers │ │ │ ├── dojo │ │ │ ├── mustache.js.post │ │ │ └── mustache.js.pre │ │ │ ├── jquery │ │ │ ├── mustache.js.post │ │ │ └── mustache.js.pre │ │ │ ├── mootools │ │ │ ├── mustache.js.post │ │ │ └── mustache.js.pre │ │ │ ├── qooxdoo │ │ │ ├── mustache.js.post │ │ │ └── mustache.js.pre │ │ │ └── yui3 │ │ │ ├── mustache.js.post │ │ │ └── mustache.js.pre │ ├── ringo-example.js │ └── ringo-opensearch.js ├── docs │ └── .naturaldocs_project │ │ ├── Languages.txt │ │ ├── Menu.txt │ │ └── Topics.txt ├── lib │ ├── amigo │ │ ├── api.js │ │ ├── api.js.tests │ │ ├── commonjs-modules_1_0-bbop.js │ │ ├── commonjs-modules_1_0-shim.js │ │ ├── data │ │ │ ├── README.org │ │ │ ├── context.js │ │ │ ├── definitions.js │ │ │ ├── dispatch.js │ │ │ ├── golr.js │ │ │ ├── server.js │ │ │ ├── statistics.js │ │ │ ├── statistics.js.tests │ │ │ ├── xrefs.js │ │ │ └── xrefs.js.hidden_tests │ │ ├── handler.js │ │ ├── handler.js.tests │ │ ├── handlers │ │ │ ├── alternate_id.js │ │ │ ├── echo.js │ │ │ ├── owl_class_expression.js │ │ │ ├── owl_class_expression.js.tests │ │ │ └── qualifiers.js │ │ ├── linker.js │ │ ├── linker.js.tests │ │ ├── ui │ │ │ ├── css │ │ │ │ └── widgets.css │ │ │ ├── interactive.js │ │ │ ├── rollup.js │ │ │ └── widgets.js │ │ ├── version.js │ │ └── version.js.tests │ └── jquery-ui-1.10.3.custom.min.js ├── npm │ ├── amigo2-instance-data │ │ ├── README.md │ │ ├── generation-templates │ │ │ ├── context.js.tmpl │ │ │ ├── definitions.js.tmpl │ │ │ ├── dispatch.js.tmpl │ │ │ ├── golr.js.tmpl │ │ │ ├── server.js.tmpl │ │ │ └── xrefs.js.tmpl │ │ ├── gulpfile.js │ │ ├── lib │ │ │ ├── amigo2-instance-data.js │ │ │ ├── data │ │ │ │ └── README.md │ │ │ ├── handler.js │ │ │ └── linker.js │ │ ├── package-lock.json │ │ ├── package.json │ │ └── tests │ │ │ ├── amigo2-instance-data.tests.js │ │ │ ├── handler.tests.js │ │ │ ├── linker.tests.js │ │ │ ├── static.tests.js │ │ │ └── trivial.tests.js │ └── bbop-widget-set │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── gulpfile.js │ │ ├── lib │ │ ├── autocomplete_simple.js │ │ ├── browse.js │ │ ├── bundle.js │ │ ├── display.js │ │ ├── generators.js │ │ ├── graph_tools.js │ │ ├── html.js │ │ ├── jquery-ui-1.10.3.custom.min.js │ │ ├── live_filters.js │ │ ├── live_geospatial.js │ │ ├── live_pager.js │ │ ├── live_results.js │ │ ├── repl.js │ │ └── set.js │ │ ├── package-lock.json │ │ ├── package.json │ │ └── tests │ │ ├── bracket.test.js │ │ ├── clickable_object.test.js │ │ ├── html.test.js │ │ └── trivial.test.js ├── staging │ └── README.org └── web │ ├── AmiGOBioView.js │ ├── AmiGOCytoView.js │ ├── AmiGOOntView.js │ ├── BaseStatistics.js │ ├── Browse.js │ ├── BulkSearch.js │ ├── CytoDraw.js │ ├── DDBrowse.js │ ├── DrillExp.js │ ├── FacetMatrix.js │ ├── FreeBrowse.js │ ├── GOCAMWidgetLoader.js │ ├── GOOSE.js │ ├── GPDetails.js │ ├── Gannet.js │ ├── GeneralSearchForwarding.js │ ├── Grebe.js │ ├── LandingGraphs.js │ ├── LiveSearchGOlr.js │ ├── LoadDetails.js │ ├── Matrix.js │ ├── Medial.js │ ├── ModelDetails.js │ ├── PANTHERTree.js │ ├── PTHR10170.js │ ├── PhyloExp.js │ ├── PhyloGraph.js │ ├── REPL.js │ ├── ReferenceDetails.js │ ├── Schema.js │ ├── TEBase.js │ └── TermDetails.js ├── metadata ├── ann-config.browse.yaml ├── ann-config.yaml ├── ann_ev_agg-config.yaml ├── bio-config.browse.yaml ├── bio-config.yaml ├── complex-ann-config.yaml ├── general-config.yaml ├── model-ann-config.yaml ├── noctua-model-meta-config.yaml ├── ont-config.yaml ├── protein-family-config.yaml └── term-autocomplete-config.yaml ├── package.json ├── perl ├── bin │ ├── amigo │ ├── amigo_exp │ ├── aserve │ ├── aserve_exp │ ├── facet_matrix │ ├── gaffer │ ├── gannet │ ├── goose │ ├── grebe │ ├── matrix │ ├── pgraph │ ├── repl │ ├── rte │ ├── static │ ├── tebase │ ├── visualize │ └── xrefs ├── docs │ └── .naturaldocs_project │ │ ├── Languages.txt │ │ └── Topics.txt └── lib │ ├── AmiGO.pm │ ├── AmiGO │ ├── Aid.pm │ ├── Aid │ │ └── ReferenceGenome.pm │ ├── CSS.pm │ ├── ChewableGraph.pm │ ├── External.pm │ ├── External │ │ ├── GOLD.pm │ │ ├── GOLD │ │ │ ├── Query.pm │ │ │ └── Status.pm │ │ ├── HTML.pm │ │ ├── HTML │ │ │ ├── Wiki.pm │ │ │ └── Wiki │ │ │ │ ├── BBOPJS.pm │ │ │ │ ├── GOLD.pm │ │ │ │ ├── GOlr.pm │ │ │ │ └── LEAD.pm │ │ ├── JSON.pm │ │ ├── JSON │ │ │ ├── AmiGO.pm │ │ │ ├── Solr.pm │ │ │ └── Solr │ │ │ │ ├── GOlr.pm │ │ │ │ └── GOlr │ │ │ │ ├── BulkSearch.pm │ │ │ │ ├── Document.pm │ │ │ │ ├── SafeQuery.pm │ │ │ │ ├── Search.pm │ │ │ │ └── Status.pm │ │ ├── LEAD.pm │ │ ├── LEAD │ │ │ ├── Query.pm │ │ │ └── Status.pm │ │ ├── QuickGO │ │ │ ├── OntGraphics.pm │ │ │ └── Term.pm │ │ ├── Raw.pm │ │ ├── XML.pm │ │ ├── XML │ │ │ └── GONUTS.pm │ │ ├── XMLFast.pm │ │ └── XMLFast │ │ │ └── RemoteTermEnrichment.pm │ ├── GraphViz.pm │ ├── Input.pm │ ├── JSON.pm │ ├── JavaScript.pm │ ├── KVStore.pm │ ├── KVStore │ │ ├── Filesystem.pm │ │ ├── Filesystem │ │ │ └── QuickGO.pm │ │ └── QuickGO.pm │ ├── SVG.pm │ ├── SVGRewrite.pm │ ├── Sanitize.pm │ ├── WebApp.pm │ ├── WebApp │ │ ├── FacetMatrix.pm │ │ ├── GOOSE.pm │ │ ├── Gaffer.pm │ │ ├── Gannet.pm │ │ ├── Grebe.pm │ │ ├── HTMLClient.pm │ │ ├── HTMLClient │ │ │ └── Dispatch.pm │ │ ├── HTMLClientExp.pm │ │ ├── Matrix.pm │ │ ├── PGraph.pm │ │ ├── REPL.pm │ │ ├── RTE.pm │ │ ├── Services.pm │ │ ├── Static.pm │ │ ├── Static │ │ │ └── Dispatch.pm │ │ ├── TEBase.pm │ │ ├── VisualizeServer.pm │ │ └── Xrefs.pm │ ├── Worker.pm │ └── Worker │ │ ├── ColorRange.pm │ │ ├── GOlr.pm │ │ ├── GOlr │ │ ├── Closure.pm │ │ ├── ComplexAnnotationGroup.pm │ │ ├── ComplexAnnotationUnit.pm │ │ ├── GeneProduct.pm │ │ ├── IC.pm │ │ ├── ModelAnnotation.pm │ │ └── Term.pm │ │ ├── Gaffer.pm │ │ ├── PGraph.pm │ │ └── Visualize.pm │ ├── GO │ ├── SQLite3.pm │ └── SQLite3 │ │ └── KVStore.pm │ ├── README.txt │ └── t │ ├── 01_amigo_chewablegraph.t │ ├── 02_amigo_chewablegraph.t │ ├── 05_trivial_client_use.t │ ├── 10_simple_solr_query.t │ ├── 15_gaffer_xform.t │ └── 20_parsing_panther_output.t ├── provision ├── PROVISION_AWS_README.md ├── PROVISION_README.md ├── ansible │ ├── amigo-golr-setup.yml │ ├── hosts.amigo │ ├── roles │ │ ├── amigo-golr │ │ │ ├── files │ │ │ │ └── libsql-tokenizer-perl_0.24-2_all.deb │ │ │ ├── tasks │ │ │ │ └── main.yml │ │ │ └── templates │ │ │ │ ├── amigo-go-public.yaml │ │ │ │ ├── amigo-go.yaml │ │ │ │ ├── amigo-index.html │ │ │ │ ├── amigo-obo.yaml │ │ │ │ ├── amigo2-apache.conf │ │ │ │ └── etc-default-jetty9 │ │ ├── get-wildcard-certs │ │ │ └── tasks │ │ │ │ └── main.yml │ │ ├── standard-distribution-jammy-aws │ │ │ └── tasks │ │ │ │ └── main.yml │ │ ├── webserver-apache-proxy-ssl │ │ │ ├── tasks │ │ │ │ └── main.yml │ │ │ └── templates │ │ │ │ └── proxy-ssl.conf │ │ ├── webserver-apache-proxy │ │ │ ├── tasks │ │ │ │ └── main.yml │ │ │ └── templates │ │ │ │ └── proxy.conf │ │ └── webserver-apache │ │ │ └── tasks │ │ │ └── main.yml │ └── wildcard-setup.yaml ├── aws │ └── main.tf ├── build_images.yaml ├── down_services.yaml ├── files │ ├── qos-noop.conf │ └── robots.txt ├── production │ ├── README.md │ ├── backend.tf.sample │ ├── config-instance.yaml.sample │ ├── config-stack.yaml.sample │ └── go-aws-credentials.sample ├── qos-vars.yaml ├── stage.yaml ├── start_services.yaml ├── templates │ ├── 001-inline-amigo.conf │ ├── amigo-ssl.yaml │ ├── amigo.yaml │ ├── apache2 │ ├── apache2.ports.conf │ ├── console-capture-golr.xml │ ├── docker-compose-production.yaml │ ├── docker-compose.yaml │ ├── httpd-vhosts-amigo-redirect.conf │ ├── httpd-vhosts-amigo-ssl.conf │ ├── httpd-vhosts-amigo.conf │ ├── httpd-vhosts-golr-ssl.conf │ ├── httpd-vhosts-golr.conf │ ├── java-golr-monit │ └── qos.conf └── vars.yaml ├── scripts ├── ListDependencies.pm ├── README.org ├── amigo-create-base-stats-cache.js ├── amigo-data-demo-02.js ├── amigo-data-demo.js ├── amigo-runner ├── backport-xrefs.js ├── benchmark.pl ├── blank-kvetch.pl ├── build-cpan-env.pl ├── clean-filesystem.pl ├── global-message.pl ├── golr-enrich-load-with-geospatial.js ├── json-to-graphviz.pl ├── make-gnuplot-stacked-histogram.pl ├── make-gnuplot-vals.pl ├── produce-xrefs.pl ├── schema-match.js ├── schema.yaml ├── simulate.pl ├── svgs2gifs ├── validate-xrefs.js ├── version.pl ├── w3c-validate.pl └── web-bowser.js ├── staging └── README.org ├── static ├── css │ ├── amigo.css │ ├── bbop.css │ ├── bootstrap-theme.css │ ├── bootstrap-theme.css.map │ ├── bootstrap-theme.min.css │ ├── bootstrap.css │ ├── bootstrap.css.map │ ├── bootstrap.min.css │ ├── formatting.css │ └── iefix.css ├── fonts │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ └── glyphicons-halflings-regular.woff ├── images │ ├── browse-icon.50.png │ ├── browse-icon.png │ ├── capable_of.gif │ ├── capable_of.svg │ ├── current_term.gif │ ├── dd-browse.50.png │ ├── dd-browse.png │ ├── develops_from.gif │ ├── develops_from.svg │ ├── dot-graph.50.png │ ├── dot-graph.png │ ├── down.png │ ├── error.png │ ├── formula.50.png │ ├── galaxy-icon.png │ ├── gannet-1.50.png │ ├── gannet-1.png │ ├── go-logo-favicon.ico │ ├── go-logo-icon.mini.png │ ├── go-logo-icon.png │ ├── go-logo-icon.small.png │ ├── go-logo-icon.small.sans.png │ ├── go-logo.import.png │ ├── go-logo.large.png │ ├── go-logo.mini.png │ ├── go-logo.pdf │ ├── go-logo.png │ ├── go-logo.small.png │ ├── gonuts.jpg │ ├── gonuts.link.jpg │ ├── goose-1.50.png │ ├── goose-1.png │ ├── grebe.50.png │ ├── grebe.png │ ├── has_component.gif │ ├── has_component.svg │ ├── has_function.gif │ ├── has_function.svg │ ├── has_process.gif │ ├── has_process.svg │ ├── info-jump.png │ ├── info-jump.svg │ ├── info.gif │ ├── info.svg │ ├── is_a.gif │ ├── is_a.svg │ ├── library.50.png │ ├── library.svg │ ├── logo-amigolabs-sm.png │ ├── logo-sm.png │ ├── logo_panther.jpg │ ├── magnifying-glass.50.png │ ├── magnifying-glass.png │ ├── negatively_regulates.gif │ ├── negatively_regulates.svg │ ├── notice.png │ ├── notice.xcf │ ├── occurs_in.gif │ ├── occurs_in.svg │ ├── part_of.gif │ ├── part_of.svg │ ├── positively_regulates.gif │ ├── positively_regulates.svg │ ├── question.icon.png │ ├── question.png │ ├── regulates.gif │ ├── regulates.svg │ ├── related_to.gif │ ├── related_to.svg │ ├── reorder.gif │ ├── repl-icon.50.png │ ├── repl-icon.png │ ├── results_in_maturation_of.gif │ ├── stats-generic.50.png │ ├── stats-generic.png │ ├── term-enrichment-graph.50.png │ ├── term-enrichment-graph.png │ ├── term-enrichment-graph.svg │ ├── term-enrichment.50.png │ ├── term-enrichment.png │ ├── term_lineage_wedge.png │ ├── term_subset_wedge.png │ ├── tools.50.png │ ├── tools.png │ ├── waiting_ac.gif │ ├── waiting_ajax.gif │ ├── waiting_poll.gif │ ├── wand.png │ ├── warning.png │ ├── wikipedia.link.png │ └── wikipedia.png ├── js │ ├── com │ │ ├── README.txt │ │ ├── bootstrap.js │ │ ├── bootstrap.min.js │ │ ├── jquery-1.5.1.min.js │ │ ├── jquery-1.8.0.js │ │ ├── jquery-1.8.0.min.js │ │ ├── jquery-1.9.1.js │ │ ├── jquery-1.9.1.min.js │ │ ├── jquery-ui-1.10.3.custom.js │ │ ├── jquery-ui-1.10.3.custom.min.js │ │ ├── jquery-ui-1.8.13.custom.min.js │ │ ├── jquery-ui-1.8.23.custom.min.js │ │ ├── jquery.jsPlumb-1.5.5.js │ │ ├── jquery.tablesorter.min.js │ │ ├── jquery │ │ │ └── css │ │ │ │ ├── jqamigo-1.10.3 │ │ │ │ ├── images │ │ │ │ │ ├── animated-overlay.gif │ │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ │ ├── ui-bg_flat_100_f5f8f9_40x100.png │ │ │ │ │ ├── ui-bg_flat_100_ffffff_40x100.png │ │ │ │ │ ├── ui-bg_flat_55_e9effa_40x100.png │ │ │ │ │ ├── ui-bg_flat_55_fbec88_40x100.png │ │ │ │ │ ├── ui-bg_flat_75_d0ffee_40x100.png │ │ │ │ │ ├── ui-bg_flat_85_d3dff5_40x100.png │ │ │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ │ │ ├── ui-icons_000000_256x240.png │ │ │ │ │ ├── ui-icons_217bc0_256x240.png │ │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ │ ├── ui-icons_3875d7_256x240.png │ │ │ │ │ └── ui-icons_cd0a0a_256x240.png │ │ │ │ ├── jquery-ui-1.10.3.custom.css │ │ │ │ └── jquery-ui-1.10.3.custom.min.css │ │ │ │ ├── jqamigo-1.8.13 │ │ │ │ ├── images │ │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ │ ├── ui-bg_flat_100_f5f8f9_40x100.png │ │ │ │ │ ├── ui-bg_flat_100_ffffff_40x100.png │ │ │ │ │ ├── ui-bg_flat_55_e9effa_40x100.png │ │ │ │ │ ├── ui-bg_flat_55_fbec88_40x100.png │ │ │ │ │ ├── ui-bg_flat_75_d0ffee_40x100.png │ │ │ │ │ ├── ui-bg_flat_85_d3dff5_40x100.png │ │ │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ │ │ ├── ui-icons_000000_256x240.png │ │ │ │ │ ├── ui-icons_217bc0_256x240.png │ │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ │ ├── ui-icons_3875d7_256x240.png │ │ │ │ │ └── ui-icons_cd0a0a_256x240.png │ │ │ │ └── jquery-ui-1.8.13.custom.css │ │ │ │ └── jqamigo-1.8.23 │ │ │ │ ├── images │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ ├── ui-bg_flat_100_f5f8f9_40x100.png │ │ │ │ ├── ui-bg_flat_100_ffffff_40x100.png │ │ │ │ ├── ui-bg_flat_55_e9effa_40x100.png │ │ │ │ ├── ui-bg_flat_55_fbec88_40x100.png │ │ │ │ ├── ui-bg_flat_75_d0ffee_40x100.png │ │ │ │ ├── ui-bg_flat_85_d3dff5_40x100.png │ │ │ │ ├── ui-bg_glass_95_fef1ec_1x400.png │ │ │ │ ├── ui-icons_000000_256x240.png │ │ │ │ ├── ui-icons_217bc0_256x240.png │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ ├── ui-icons_3875d7_256x240.png │ │ │ │ └── ui-icons_cd0a0a_256x240.png │ │ │ │ └── jquery-ui-1.8.23.custom.css │ │ ├── jstree │ │ │ ├── 32px.png │ │ │ ├── 40px.png │ │ │ ├── jstree.min.js │ │ │ ├── style.min.css │ │ │ └── throbber.gif │ │ └── raphael-min.js │ ├── ly │ │ └── plotly.min.js │ └── org │ │ ├── cytoscape.js │ │ ├── d3.v3.js │ │ └── d3.v3.min.js ├── robots.txt └── staging ├── templates └── html │ └── bs3 │ ├── common │ ├── abstract_help_link.tmpl │ ├── annotation_search.tmpl │ ├── autocomplete_explanation.tmpl │ ├── autocomplete_help_link.tmpl │ ├── body_open.tmpl │ ├── content_close.tmpl │ ├── content_open.tmpl │ ├── content_title.tmpl │ ├── footer.tmpl │ ├── grebe_entry.tmpl │ ├── grebe_entry_container_close.tmpl │ ├── grebe_entry_container_open.tmpl │ ├── head_close.tmpl │ ├── head_open.tmpl │ ├── header.tmpl │ ├── header_search.tmpl │ ├── info_rollup_end.tmpl │ ├── info_rollup_start.tmpl │ ├── landing_item.tmpl │ ├── landing_search_form.tmpl │ ├── load_detail_list.tmpl │ ├── mq_message.tmpl │ ├── noscript_js_limited.tmpl │ ├── noscript_js_limited_search.tmpl │ ├── noscript_js_necessary.tmpl │ ├── simple_search_form.tmpl │ ├── simple_search_results.tmpl │ ├── term_details_community.tmpl │ ├── term_details_entry.tmpl │ ├── term_details_graphics.tmpl │ ├── term_details_lineage.tmpl │ ├── term_details_main.tmpl │ ├── term_details_neighborhood.tmpl │ ├── term_details_neighborhood_head.tmpl │ ├── term_details_re_row.tmpl │ ├── term_details_search.tmpl │ ├── term_details_sentences.tmpl │ └── term_details_xrefs.tmpl │ └── pages │ ├── base_statistics.tmpl │ ├── browse.tmpl │ ├── bulk_search.tmpl │ ├── complex_annotation_details.tmpl │ ├── dd_browse.tmpl │ ├── error.tmpl │ ├── facet_matrix.tmpl │ ├── free_browse.tmpl │ ├── gannet.tmpl │ ├── gene_product_details.tmpl │ ├── goose.tmpl │ ├── grebe.tmpl │ ├── landing.tmpl │ ├── live_search_golr.tmpl │ ├── load_details.tmpl │ ├── matrix.tmpl │ ├── medial_search.tmpl │ ├── message_generic.tmpl │ ├── model_biology.tmpl │ ├── model_details.tmpl │ ├── not_found_generic.tmpl │ 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