Tests: Changed taxonomy manager test to use full sample file

- Taxonomy manager test now loads the `taxonomy.yml` file from the tests
folder and checks output against a snapshot.

Author: ZechyW

src/__tests__/__snapshots__/taxonomymanager.test.js.snap

@@ -0,0 +1,3 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`The TaxonomyManager should load an Odin taxonomy (yaml string) 1`] = `"[\\"Alias\\",\\"ModificationTrigger\\",\\"Site\\",{\\"Context\\":[\\"Species\\",\\"CellLine\\",\\"Organ\\",\\"CellType\\",\\"Cellular_component\\",\\"TissueType\\",\\"ContextDirection\\",\\"ContextLocation\\",\\"ContextPossessive\\"]},{\\"Modification\\":[\\"PTM\\",{\\"Mutant\\":[\\"GenericMutant\\",\\"SubstitutionMutant\\",\\"DeletionMutant\\",\\"DuplicationMutant\\",\\"InsertionMutant\\",\\"FrameshiftMutant\\"]},\\"EventSite\\",\\"Negation\\"]},{\\"PossibleController\\":[{\\"Event\\":[{\\"SimpleEvent\\":[\\"Binding\\",\\"Generic_event\\",\\"Translocation\\",{\\"Amount\\":[{\\"IncreaseAmount\\":[\\"Transcription\\"]},\\"DecreaseAmount\\"]},{\\"AdditionEvent\\":[\\"Acetylation\\",\\"Farnesylation\\",\\"Glycosylation\\",\\"Hydrolysis\\",\\"Hydroxylation\\",\\"Methylation\\",{\\"Phosphorylation\\":[\\"AutoPhosphorylation\\"]},\\"Ribosylation\\",\\"Sumoylation\\",\\"Ubiquitination\\"]},{\\"RemovalEvent\\":[\\"Deacetylation\\",\\"Defarnesylation\\",\\"Deglycosylation\\",\\"Dehydrolysis\\",\\"Dehydroxylation\\",\\"Demethylation\\",\\"Dephosphorylation\\",\\"Deribosylation\\",\\"Desumoylation\\",\\"Deubiquitination\\"]}]},{\\"ComplexEvent\\":[{\\"Regulation\\":[\\"Positive_regulation\\",\\"Negative_regulation\\"]},{\\"ActivationEvent\\":[\\"Positive_activation\\",\\"Negative_activation\\"]}]}]},{\\"Entity\\":[{\\"BioEntity\\":[\\"BioProcess\\",{\\"BioChemicalEntity\\":[\\"Generic_entity\\",\\"Simple_chemical\\",{\\"Equivalable\\":[\\"Family\\",{\\"MacroMolecule\\":[\\"Protein\\",\\"Gene_or_gene_product\\",\\"Complex\\",\\"GENE\\"]}]}]}]}]}]},{\\"Precedence\\":[\\"DirectConnection\\",\\"IndirectConnection\\",{\\"BetweenSentence\\":[\\"TimexAfter\\",\\"TimexBefore\\",\\"SentenceInitialEvent\\",\\"InterAfter\\",\\"InterBefore\\"]},{\\"TAM\\":[\\"Aux\\",{\\"Tense\\":[\\"PastTense\\",\\"PresentTense\\",\\"FutureTense\\"]},{\\"Aspect\\":[\\"Perfective\\",\\"Progressive\\"]}]}]}]"`;

src/__tests__/taxonomymanager.test.js

@@ -1,45 +1,25 @@
 /**
-* Test taxonomy manager
-*/
+ * Test taxonomy manager
+ */
 
-//import * as fs from "fs";
-
-// JS-YAML library
-//import * as yaml from "js-yaml";
+import * as fs from "fs";
 
 import TaxonomyManager from "../js/managers/taxonomy.js";
 import Config from "../js/config.js";
 
 describe("The TaxonomyManager", () => {
- it("should load an Odin taxonomy (yaml string)", () => {
-
-   // Pull the sample taxonomy file
-   //const yamlData = fs.readFileSync("./src/__tests__/data/taxonomy.yml", "utf8");
-
-   const yamlData = `
-- Alias
-- ModificationTrigger
-- Site
-- Context:
-   - Species
-   - CellLine
-   - Organ
-   - CellType
-   - Cellular_component
-   - TissueType
-   - ContextDirection
-   - ContextLocation
-   - ContextPossessive
-`
-   const conf = new Config();
-
-   // Initialize TaxonomyManager and load data
-   const taxman = new TaxonomyManager(conf);
-
-   taxman.loadTaxonomyYaml(yamlData);
-
-   const tree = taxman.getTaxonomyTree();
-
-   expect(tree[0]).toBe("Alias");
- });
+  it("should load an Odin taxonomy (yaml string)", () => {
+    const yamlData = fs.readFileSync("./src/__tests__/data/taxonomy.yml", "utf8");
+
+    const conf = new Config();
+
+    // Initialize TaxonomyManager and load data
+    const taxman = new TaxonomyManager(conf);
+
+    taxman.loadTaxonomyYaml(yamlData);
+
+    const tree = taxman.getTaxonomyTree();
+
+    expect(JSON.stringify(tree)).toMatchSnapshot();
+  });
 });