BridgeDb
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bridgedb
The BridgeDb Library source code
To use the webservice.bridgedb.org HTTP API, a client library needs copies of these files from the BridgeDb webservice JAR: * [organisms](https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.txt) * [datasources_headers](https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/resources/org/bridgedb/bio/datasources_headers.txt) * [datasources](https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt) In the Swagger docs, there...
Currently, when attempt to load a linkset file into IMS, if the linkset file is empty an Exception is thrown and the load terminates. *emty* means there are zero links...
Should http://data.bridgedb.org/ be directed to http://bridgedb.org/data/? Analogous to new data.wikipathways.org...
To make the webservice easier to use, let's look into supporting aliases for `systemCode` for the webservice. This can be broken into two parts: 1. [ ] support conventionalName (e.g.,...
It is suggested to have bridgedb.org serve more information about the data sources, in particularly, give access to datasources.txt. I propose the webservice should do that.
In situations where a value might not exist, generally preferable to return values wrapped with a Java `Optional` rather than a `null`. It's more self documenting, and generally easier to...
I still can't get my head around why we have so much duplication of data sources in `org.bridgedb.bio` vs `org.bridgedb.rdf`: - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/BioDataSource.ttl - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/DataSource.ttl - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt - https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl...
Moving [this issue](https://github.com/PathVisio/pathvisio/issues/48) from pathvisio github to BridgeDB. DeniseSl22 commented on Jul 31 Hi all, (again about the library, sorry about that ;)....) In the Pathvisio library, secondary identifiers of...
See https://travis-ci.org/bridgedb/BridgeDb#L4544-L4549
under `org.bridgedb.webservice.synergizer` we include `lib/synergizer.jar` as a `system` dependency, so anyone using this module would also need to add synergizer.jar to their own class path. I tried to find the...