Gene ws server v2 #120
Merged
Gene ws server v2 #120
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
andresfsilva
requested changes
Jul 16, 2019
| public GeneWSServerV2() { | ||
| } | ||
|
|
||
| @GetMapping(value = "/{geneIds}") |
There was a problem hiding this comment.
the idea is to return the variants in the specified genes instead of returning the gene's coordinates. So change this to /v2/genes/{geneIds}/variants and return the variants using the coordinates
junaidnz97
force-pushed
the
GeneWSServerV2
branch
from
b1f7f3e
to
85a48c2
Compare
jmmut
requested changes
Jul 26, 2019
| MultiMongoDbFactory.setDatabaseNameForCurrentThread(DBAdaptorConnector.getDBName(species + "_" + assembly)); | ||
| List<FeatureCoordinates> featureCoordinates = service.findAllByGeneIdsOrGeneNames(geneIds, geneIds); | ||
| if (featureCoordinates.size() == 0) { | ||
| return new ResponseEntity(featureCoordinates, HttpStatus.NOT_FOUND); |
There was a problem hiding this comment.
in my opinion, an empty list is more a "204 no content" than a "404 not found"
There was a problem hiding this comment.
Okay :)
Fixed 👍
| return new ResponseEntity(featureCoordinates, HttpStatus.NOT_FOUND); | ||
| } | ||
| String regions = ""; | ||
| for (int i = 0; i < featureCoordinates.size(); i++) { |
There was a problem hiding this comment.
instead of this loop, use
String regions = featureCoordinates.stream().map(this::getRegionString).collect(Collectors.joining(","));
I prefer the stream version not only for being shorter and with less redundancy, but also because conditions like if (i != featureCoordinates.size() - 1) are confusing and prone to bugs.
andresfsilva
requested changes
Jul 29, 2019
eva-server/src/main/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2.java
Outdated
Show resolved
Hide resolved
…2.java Co-Authored-By: andresfsilva <afsilva04@gmail.com>
junaidnz97
force-pushed
the
GeneWSServerV2
branch
from
7ee0bdd
to
57cf989
Compare
andresfsilva
requested changes
Aug 1, 2019
eva-server/src/test/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2Test.java
Outdated
Show resolved
Hide resolved
eva-server/src/test/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2Test.java
Outdated
Show resolved
Hide resolved
eva-server/src/test/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2Test.java
Show resolved
Hide resolved
eva-server/src/test/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2Test.java
Outdated
Show resolved
Hide resolved
| variantList.forEach(variant -> { | ||
| chromosomes.add(variant.getChromosome()); | ||
| }); | ||
| return chromosomes; |
There was a problem hiding this comment.
This method is called testGetVariantsGeneHelper but is returning chromosomes. This should return variants
eva-server/src/test/java/uk/ac/ebi/eva/server/ws/GeneWSServerV2Test.java
Show resolved
Hide resolved
Co-Authored-By: andresfsilva <afsilva04@gmail.com>
jmmut
approved these changes
Aug 2, 2019
andresfsilva
approved these changes
Aug 5, 2019
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The purpose of this PR is to add an endpoint "/v2/genes/{geneIds}" which retrieves a list of
FeatureCoordinatesfor the given geneIds.