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Commit 14c6a55

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Hernan Morales
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Add BioDatabases, BioOntology and Features Viewer
BioPathway enhacements.
1 parent c40850b commit 14c6a55

38 files changed

Lines changed: 8381 additions & 20 deletions

‎repository/BaselineOfBioSmalltalk/BaselineOfBioSmalltalk.class.st‎

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@@ -248,7 +248,8 @@ BaselineOfBioSmalltalk >> baselineTestsGroup: spec [
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'BioClassifierTests'
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"'BioProjectTests'"
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'BioArlequin-Tests'
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'BioSummarizedExperiment-Tests' )
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'BioSummarizedExperiment-Tests'
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'BioPlots-Tests' )
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]
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{ #category : 'baselines' }

‎repository/BioDatabases-Tests/BioDatabasesTest.class.st‎

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Class {
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#name : 'BioDatabasesTest',
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#superclass : 'BioAbstractTest',
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#category : 'BioDatabases-Tests',
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#package : 'BioDatabases-Tests'
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}
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{ #category : 'tests' }
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BioDatabasesTest >> testAddAndRemoveDatabase [ | db testDB | db := BioDatabases new. testDB := BioDatabase type: #tertiary category: 'Test' name: 'TestDB' description: 'Test'. db addDatabase: testDB. self assert: db size equals: 1. db removeDatabase: testDB. self assert: db size equals: 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testAllDatabases [ | db | db := BioDatabases withAllDatabases. self assert: db size > 300. self assert: db size = 654
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testBioDatabaseCreation [ | db | db := BioDatabase type: #primary category: 'Test' name: 'TestDB' description: 'A test database'. self assert: db type equals: #primary. self assert: db category equals: 'Test'. self assert: db name equals: 'TestDB'. self assert: db description equals: 'A test database'. self assert: db url isNil. self assert: db status isNil
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testBioDatabasePrintOn [ | db str | db := BioDatabase type: #primary category: 'Test' name: 'MyDB' description: 'Desc'. str := String streamContents: [ :s | db printOn: s ]. self assert: (str includesSubstring: 'MyDB')
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testCategories [ | db | db := BioDatabases withAllDatabases. self assert: db categories size >= 30. self assert: (db categories includes: 'Protein'). self assert: (db categories includes: 'Immunogenetics')
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testCategorySelectors [ | sels | sels := BioDatabases categorySelectors. self assert: sels size >= 30. self assert: (sels includes: #proteinDatabases). self assert: (sels includes: #immunogeneticsDatabases). self deny: (sels includes: #allDatabases)
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testDatabaseUrls [ "All databases should have a URL." | db | db := BioDatabases withAllDatabases. db databases do: [ :d | self assert: d url notNil. self assert: d url notEmpty ]
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testFilterByCategories [ | db | db := BioDatabases withAllDatabases. self assert: (db byCategories: #('Protein' 'RNA')) size >= 40. self assert: (db byCategories: #('Nonexistent')) size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testFilterByCategory [ | db | db := BioDatabases withAllDatabases. self assert: (db byCategory: 'Protein') size >= 25. self assert: (db byCategory: 'RNA') size >= 15. self assert: (db byCategory: 'Nonexistent') size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testFilterByType [ | db | db := BioDatabases withAllDatabases. self assert: (db byType: #primary) size > 400. self assert: (db byType: #secondary) size > 100. self assert: (db byType: #tertiary) size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testFilterByTypes [ | db | db := BioDatabases withAllDatabases. self assert: ((db byTypes: #(primary secondary)) size) = db size. self assert: (db byTypes: #(tertiary)) size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testPrimaryDatabases [ | db | db := BioDatabases withPrimaryDatabases. self assert: db size > 400. self assert: (db databases allSatisfy: [ :d | d type = #primary ])
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testSearchByKeyword [ | db | db := BioDatabases withAllDatabases. self assert: (db searchKeyword: 'malaria') size >= 1. self assert: (db searchKeyword: 'Malaria') size >= 1. self assert: (db searchKeyword: 'nonexistent') size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testSearchByName [ | db | db := BioDatabases withAllDatabases. self assert: (db searchName: 'PDB') size >= 1. self assert: (db byName: 'PDB') size >= 1. self assert: (db searchName: 'zzzzzzzzzzz') size = 0
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testSecondaryDatabases [ | db | db := BioDatabases withSecondaryDatabases. self assert: db size > 100. self assert: (db databases allSatisfy: [ :d | d type = #secondary ])
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]
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{ #category : 'tests' }
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BioDatabasesTest >> testTypes [ | db | db := BioDatabases withAllDatabases. self assert: (db types includes: #primary). self assert: (db types includes: #secondary)
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]

‎repository/BioDatabases-Tests/package.st‎

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Package { #name : 'BioDatabases-Tests' }

‎repository/BioDatabases/BioDatabase.class.st‎

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Class {
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#name : 'BioDatabase',
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#superclass : 'Object',
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#instVars : [
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'type',
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'category',
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'name',
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'description',
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'url',
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'status'
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],
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#category : 'BioDatabases',
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#package : 'BioDatabases'
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}
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{ #category : 'as yet unclassified' }
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BioDatabase class >> type: aType category: aCat name: aName description: aDesc [
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^ self new
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type: aType;
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category: aCat;
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name: aName;
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description: aDesc;
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yourself
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]
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{ #category : 'as yet unclassified' }
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BioDatabase class >> type: aType category: aCat name: aName description: aDesc url: aUrl [ ^ self new type: aType; category: aCat; name: aName; description: aDesc; url: aUrl; yourself
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]
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{ #category : 'accessing' }
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BioDatabase >> category [
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^ category
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]
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{ #category : 'accessing' }
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BioDatabase >> category: aString [
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category := aString
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]
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{ #category : 'accessing' }
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BioDatabase >> description [
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^ description
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]
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{ #category : 'accessing' }
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BioDatabase >> description: aString [
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description := aString
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]
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{ #category : 'accessing' }
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BioDatabase >> name [
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^ name
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]
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{ #category : 'accessing' }
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BioDatabase >> name: aString [
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name := aString
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]
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{ #category : 'printing' }
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BioDatabase >> printOn: aStream [
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super printOn: aStream.
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aStream nextPutAll: ' ('.
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name ifNotNil: [ aStream nextPutAll: name ].
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aStream nextPutAll: ')'
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]
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{ #category : 'accessing' }
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BioDatabase >> status [ ^ status
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]
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{ #category : 'accessing' }
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BioDatabase >> status: anObject [
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status := anObject
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]
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{ #category : 'accessing' }
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BioDatabase >> type [
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^ type
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]
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{ #category : 'accessing' }
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BioDatabase >> type: aSymbol [
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type := aSymbol
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]
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{ #category : 'accessing' }
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BioDatabase >> url [
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^ url
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]
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{ #category : 'accessing' }
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BioDatabase >> url: aString [
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url := aString
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]

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