Neo4j Testing (Part 2) #1129
Neo4j Testing (Part 2) #1129
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I have a couple tests in the example.js file now, that I would like to receive feedback on! The next couple tests need the Document API, I believe. I would also be interested in hearing about more basic edge cases I can make tests for . Right now all I have to test the basic addNode, addEdge and searchByGeneId functions and I am open to making more low level functions. I do have some functions that I use only for testing in the src/neo4j/test-functions.js file |
neo4j-test/example.js
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| it('Make AKT node', async function () { | ||
| expect(await getNumNodes()).equal(1); | ||
| await addNode('ncbigene:207', 'AKT'); | ||
| expect(await getGeneNameById('ncbigene:207')).equal('AKT'); |
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Should probably have helper functions along the lines of getGeneName(node) rather than getGeneNameById().
Things like getGeneName() would be useful generally, whereas getGeneNameById() seems like it's only useful for tests.
neo4j-test/example.js
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| let mapk6Relationships = mapk6.map(row => { | ||
| return row.get('r'); | ||
| }); |
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It would be useful to have some slightly higher level functions here, e.g. searchByGeneID() could directly return an array of edge JSONs.
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I've made two functions building off of searchByGeneId:
getNeighbouringNodes( id ): returns the array of nodes connected to/from the specified gene
getInteractions( id ): returns the array of edges/relationships leading from/towards the specified gene
Let me know what you think and please take a look at my other (rather small) amendments when you get the chance! Thank you so much for the feedback
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Re Docker: You can run both databases with |
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| export async function searchByGeneId(id) { |
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These exported functions should have some documentation (https://jsdoc.app/). There's probably an extension that would create most of this?
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e.g.
/**
* searchPubmed
* Query the PubMed database for matching UIDs.
*
* @param { String } q The query term
* @param { Object } opts EUTILS ESEARCH options
* @returns { Object } result The search results from PubMed
* @returns { Array } result.searchHits A list of PMIDs
* @returns { Number } result.count The number of searchHits containing PMIDs
* @returns { String } result.query_key See {@link https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch|EUTILS docs }
* @returns { String } result.webenv See {@link https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch|EUTILS docs }
*/
const searchPubmed = ( q, opts ) => eSearchPubmed( q, opts );
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I believe I'm done with this PR for the time being, if you could give it another once-over, I would appreciate it! |
Yes, right now the grounding id is the unique UUID every interaction in a factoid document has. I couldn't think of a more suitable one. If it was the two nodes the edge is connected to- then there can only be one edge between those two nodes ever, which does not make sense. That was the other grounding id(s) I was thinking about |
For writing Neo4j Tests (Part 2, after accidentally merging the first one)
Possible Tests (work in progress)