REST API: clean up for consistency

[julie-sullivan]

Some of these are for discussion:

• Is "get /{version}/{species}/feature/gene" a useful endpoint? Does it do anything? Can we remove? #485 - remove the unneeded default paths
• deprecate any query you can do via /search such as: /first, /list, /count
• Sort direction should be ASC, error if the user provides and invalid value. See Query sorting -- default descending or ascending? Also, should we error if invalid input? java-common-libs#42
• numberOfTotalResults - deprecate. Replaced by numMatches
• skipCount - delete. There is already a count boolean (defaults to FALSE) so this parameter serves no purpose.
• We should pick a case style and use it consistently throughout the API. Now we use a mixture of camelCase and snake_case.
• Having Variation and Variant end points is confusing, we should merge them into one. #487 merge Variant and Variation end points
• default limit 10 not 1000
• limit must be a valid number (this is true for all params)
• limit and count are independent
• limit can't be greater than 5000
• group by - the label isn't in the output
• group by - shouldn't have count, skip etc as valid options
• cadd - deprecate
• analysis end points (vs query end points) should be clearly by /run
• skip - default value should be 0 not -1
• aggregation stats in addition to group by that only returns count
• Make it easier to query for genome sequence. How?
• remove POST
• remove output format. it's only ever JSON

[julie-sullivan]

There are several classes that don't seem to be in use:

• Dot server
• Pathway
• Protein interactions
• Phenotype
• MiRNAGene
• MiRNAMature
• Utils

Can we delete? If we need to restore we can revive via git.

[julie-sullivan]

Caused by: java.lang.NumberFormatException: For input string: "a"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:580)
	at java.lang.Integer.valueOf(Integer.java:766)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.jersey.server.internal.inject.PrimitiveValueOfExtractor.getValue(PrimitiveValueOfExtractor.java:74)
	at org.glassfish.jersey.server.internal.inject.PrimitiveValueOfExtractor.extract(PrimitiveValueOfExtractor.java:91)
	at org.glassfish.jersey.server.internal.inject.QueryParamValueParamProvider$QueryParamValueProvider.apply(QueryParamValueParamProvider.java:78)
	... 72 more

[julie-sullivan]

Instead of " Please note that this parameter may not be enabled for all web services." only have valid web services for each end point.

This will cause duplication in the code however.

[julie-sullivan]

http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/#!/TFBS/getAllByTfbs

I'm having trouble with the cellType parameter.

• has no description. What should it be? "Type of cell, e.g. K562 or HepG2"
• it doesn't seem to work. The query outcome is the same, regardless of what I put in that field.

[julie-sullivan]

param	/info	/search	"redundant" path queries, e.g. gene/{id}/protein	distinct queries	/model	/sequence
exclude/include/sort	✓	✓	✓	-	-	-
count	-	✓	✓	-	-	-
limit,skip	-	✓	✓	-	-	-

[julie-sullivan]

If I include fields and don't explicitly mention id I get a null pointer exception:

2020-02-10 11:31:03 [qtp1127224355-9] INFO  connection:71 - Opened connection [connectionId{localValue:12, serverValue:2728}] to localhost:27017
java.lang.NullPointerException
	at org.opencb.cellbase.server.rest.feature.IdWSServer.getByFeatureIdInfo(IdWSServer.java:99)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

id is assumed to be present:

            List<CellBaseDataResult<Document>> dbNameList = xRefDBAdaptor.nativeGet(queries, queryOptions);
            for (int i = 0; i < dbNameList.size(); i++) {
                dbNameList.get(i).setId(list.get(i));
                for (Document document : dbNameList.get(i).getResults()) {
                    if (document.get("id").equals(list.get(i))) {

Therefore I removed include as the user shouldn't be changing this. See 1eddb92

[julie-sullivan]

The API description parameter is deprecated.

If you set the description properly using tags, it shows up in swagger like:

I think it makes the API harder to read.

@SwaggerDefinition(tags = {
        @Tag(name = "Species", description = "Species RESTful Web Services API")
}