@apollo-annotation/jbrowse-plugin-apollo 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +76 -0
- package/dist/index.esm.js +10248 -0
- package/dist/index.esm.js.map +1 -0
- package/dist/index.js +7 -0
- package/dist/jbrowse-plugin-apollo.cjs.development.js +10298 -0
- package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -0
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js +2 -0
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -0
- package/dist/jbrowse-plugin-apollo.umd.development.js +46957 -0
- package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -0
- package/dist/jbrowse-plugin-apollo.umd.production.min.js +2 -0
- package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -0
- package/package.json +130 -0
- package/src/ApolloInternetAccount/addMenuItems.ts +94 -0
- package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +121 -0
- package/src/ApolloInternetAccount/components/LoginButtons.tsx +62 -0
- package/src/ApolloInternetAccount/components/LoginIcons.tsx +74 -0
- package/src/ApolloInternetAccount/configSchema.ts +26 -0
- package/src/ApolloInternetAccount/index.ts +2 -0
- package/src/ApolloInternetAccount/model.ts +448 -0
- package/src/ApolloJobModel.ts +117 -0
- package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +186 -0
- package/src/ApolloSequenceAdapter/configSchema.ts +12 -0
- package/src/ApolloSequenceAdapter/index.ts +21 -0
- package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx +12 -0
- package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +692 -0
- package/src/ApolloSixFrameRenderer/configSchema.ts +7 -0
- package/src/ApolloSixFrameRenderer/index.ts +3 -0
- package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +64 -0
- package/src/ApolloTextSearchAdapter/configSchema.ts +24 -0
- package/src/ApolloTextSearchAdapter/index.ts +18 -0
- package/src/BackendDrivers/BackendDriver.ts +31 -0
- package/src/BackendDrivers/CollaborationServerDriver.ts +318 -0
- package/src/BackendDrivers/DesktopFileDriver.ts +170 -0
- package/src/BackendDrivers/InMemoryFileDriver.ts +76 -0
- package/src/BackendDrivers/index.ts +4 -0
- package/src/ChangeManager.ts +148 -0
- package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +248 -0
- package/src/LinearApolloDisplay/components/index.ts +1 -0
- package/src/LinearApolloDisplay/configSchema.ts +16 -0
- package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +422 -0
- package/src/LinearApolloDisplay/glyphs/CanonicalGeneGlyph.ts +1191 -0
- package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +151 -0
- package/src/LinearApolloDisplay/glyphs/Glyph.ts +382 -0
- package/src/LinearApolloDisplay/glyphs/ImplicitExonGeneGlyph.ts +697 -0
- package/src/LinearApolloDisplay/glyphs/index.ts +4 -0
- package/src/LinearApolloDisplay/index.ts +2 -0
- package/src/LinearApolloDisplay/stateModel/base.ts +146 -0
- package/src/LinearApolloDisplay/stateModel/getGlyph.ts +39 -0
- package/src/LinearApolloDisplay/stateModel/glyphs.ts +45 -0
- package/src/LinearApolloDisplay/stateModel/index.ts +20 -0
- package/src/LinearApolloDisplay/stateModel/layouts.ts +230 -0
- package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +513 -0
- package/src/LinearApolloDisplay/stateModel/rendering.ts +441 -0
- package/src/LinearApolloDisplay/stateModel/trackHeightMixin.ts +43 -0
- package/src/LinearApolloDisplay/types.ts +1 -0
- package/src/OntologyManager/OntologyStore/__snapshots__/fulltext.test.ts.snap +208 -0
- package/src/OntologyManager/OntologyStore/__snapshots__/index.test.ts.snap +18846 -0
- package/src/OntologyManager/OntologyStore/fulltext-stopwords.ts +137 -0
- package/src/OntologyManager/OntologyStore/fulltext.test.ts +94 -0
- package/src/OntologyManager/OntologyStore/fulltext.ts +264 -0
- package/src/OntologyManager/OntologyStore/index.test.ts +130 -0
- package/src/OntologyManager/OntologyStore/index.ts +526 -0
- package/src/OntologyManager/OntologyStore/indexeddb-schema.ts +89 -0
- package/src/OntologyManager/OntologyStore/indexeddb-storage.ts +180 -0
- package/src/OntologyManager/OntologyStore/obo-graph-json-schema.ts +110 -0
- package/src/OntologyManager/OntologyStore/prefixes.ts +35 -0
- package/src/OntologyManager/index.ts +173 -0
- package/src/SixFrameFeatureDisplay/components/TrackLines.tsx +19 -0
- package/src/SixFrameFeatureDisplay/components/index.ts +1 -0
- package/src/SixFrameFeatureDisplay/configSchema.ts +21 -0
- package/src/SixFrameFeatureDisplay/index.ts +2 -0
- package/src/SixFrameFeatureDisplay/stateModel.ts +413 -0
- package/src/TabularEditor/HybridGrid/ChangeHandling.ts +88 -0
- package/src/TabularEditor/HybridGrid/Feature.tsx +346 -0
- package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +34 -0
- package/src/TabularEditor/HybridGrid/Highlight.tsx +40 -0
- package/src/TabularEditor/HybridGrid/HybridGrid.tsx +138 -0
- package/src/TabularEditor/HybridGrid/NumberCell.tsx +77 -0
- package/src/TabularEditor/HybridGrid/ToolBar.tsx +59 -0
- package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +119 -0
- package/src/TabularEditor/HybridGrid/index.ts +1 -0
- package/src/TabularEditor/TabularEditorPane.tsx +34 -0
- package/src/TabularEditor/index.ts +3 -0
- package/src/TabularEditor/model.ts +44 -0
- package/src/TabularEditor/types.ts +3 -0
- package/src/components/AddAssembly.tsx +464 -0
- package/src/components/AddChildFeature.tsx +247 -0
- package/src/components/AddFeature.tsx +252 -0
- package/src/components/CopyFeature.tsx +328 -0
- package/src/components/DeleteAssembly.tsx +185 -0
- package/src/components/DeleteFeature.tsx +90 -0
- package/src/components/Dialog.tsx +47 -0
- package/src/components/DownloadGFF3.tsx +213 -0
- package/src/components/ImportFeatures.tsx +295 -0
- package/src/components/ManageChecks.tsx +280 -0
- package/src/components/ManageUsers.tsx +218 -0
- package/src/components/ModifyFeatureAttribute.tsx +457 -0
- package/src/components/OntologyTermAutocomplete.tsx +240 -0
- package/src/components/OntologyTermMultiSelect.tsx +349 -0
- package/src/components/OpenLocalFile.tsx +178 -0
- package/src/components/ViewChangeLog.tsx +208 -0
- package/src/components/ViewCheckResults.tsx +151 -0
- package/src/components/index.ts +12 -0
- package/src/config.ts +10 -0
- package/src/declare.d.ts +3 -0
- package/src/extensions/annotationFromPileup.ts +208 -0
- package/src/extensions/index.ts +1 -0
- package/src/index.ts +394 -0
- package/src/makeDisplayComponent.tsx +244 -0
- package/src/session/ClientDataStore.ts +282 -0
- package/src/session/index.ts +1 -0
- package/src/session/session.ts +373 -0
- package/src/types.ts +10 -0
- package/src/util/index.ts +31 -0
- package/src/util/loadAssemblyIntoClient.ts +291 -0
package/README.md
ADDED
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# jbrowse-plugin-apollo
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## Testing with cypress
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These notes setup cypress and run tests. These notes are likely to change.
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- One time step: **Outside** the Apollo dev container
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[install cypress](https://docs.cypress.io/guides/getting-started/installing-cypress).
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E.g. on your OS terminal (not vscode) run:
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```
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yarn --cwd packages/jbrowse-plugin-apollo add cypress --dev
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yarn --cwd packages/jbrowse-plugin-apollo add cypress-mongodb --dev
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```
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Add these lines to the `packageExtensions` section of `.yarnrc.yml`:
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```
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cypress-mongodb@*:
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dependencies:
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bson: "*"
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```
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Then run `yarn` again.
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---
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- Start [jbrowse](https://github.com/GMOD/jbrowse-components): You may want to
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pull the latest code to be consistent with the GitHub workflow
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```
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cd /path/to/jbrowse-components
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git pull
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yarn --cwd products/jbrowse-web start
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```
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- Start Apollo server. Within the docker container (_i.e_ within vscode) and in
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distinct terminals run:
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```
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yarn --cwd packages/apollo-shared start
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```
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```
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yarn --cwd packages/apollo-collaboration-server run cypress:start
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```
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```
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yarn --cwd packages/jbrowse-plugin-apollo start
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```
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If above you change the name for the test database (`apolloTestDb`), change
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accordingly in `commands.ts`
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- Open cypress in the testing directory, _i.e._ where yo have the relevant
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`package.json`. Typically (again outside the dev container/vscode):
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```
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yarn --cwd packages/jbrowse-plugin-apollo run cypress open --config baseUrl=http://localhost:3000
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```
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- For end-to-end testing, click "E2E Testing" `->` Chrome `->`
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`Start E2E Testing`. Click on one of the available test scripts.
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To run tests locally in headless mode:
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```
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yarn --cwd packages/jbrowse-plugin-apollo run cypress run \
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--browser chrome \
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--config '{"baseUrl": "http://localhost:3000",
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"screenshotOnRunFailure": true,
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"video": true,
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"videoCompression": false,
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"retries": {"runMode": 0}}' \
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--spec cypress/e2e/editFeature.cy.ts
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```
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