Automate bridgedb webservices

What HumDay can do in bridgedb webservices

2 documented operations change something in bridgedb webservices.

• POSTReturns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism./{organism}/xrefsBatch
• POSTReturns a list of xrefs, that maps to a given list of identifiers to a given data source and organism./{organism}/xrefsBatch/{systemCode}

What HumDay can read from bridgedb webservices

These are the operations a schedule or a trigger can watch.

• GETReturns a list of xrefs with identifiers that contain the query string for a given organism./{organism}/search/{query}
• GETReturns true or false based on whether or not /{organism}/search/{query} is supported for a given organism./{organism}/isFreeSearchSupported
• GETReturns a list of xrefs and associated attributes that contain the query string for a given organism./{organism}/attributeSearch/{query}
• GETReturns the list of properties available for a given organism/{organism}/properties
• GETReturns a list of data sources available as xref sources for a given organism./{organism}/sourceDataSources
• GETReturns a list of data sources available as xref targets for a given organism./{organism}/targetDataSources
• GETReturns the supported attributes to the given Organism./{organism}/attributeSet
• GETReturns a list of xrefs that map to a given identifier, data source, and organism./{organism}/xrefs/{systemCode}/{identifier}
• GETReturns true or false based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given a {sourceSystemCode} query./{organism}/isMappingSupported/{sourceSystemCode}/{targetSystemCode}
• GETReturns the attributes for a given identifier, data source, organism./{organism}/attributes/{systemCode}/{identifier}
• GETReturns true or false based on whether or not an xref exists in the database given an identifier, data source, and organism./{organism}/xrefExists/{systemCode}/{identifier}

How automating bridgedb webservices works

1. Describe the outcome. Say what you want to happen, in your own words. No node graphs, no field mapping.
2. Approve the contract. HumDay writes down exactly what it will do, what it will touch, and what it will never do. You approve it before anything is built.
3. See it proven. The program runs and shows you the result before it is allowed near your live bridgedb webservices account.
4. Grant access, then go live. You approve the specific bridgedb webservices operations it may use — and only those.

Questions about bridgedb webservices automation

Can HumDay connect to bridgedb webservices?

Yes. HumDay reads bridgedb webservices's own published API description and derives the operations from it, so there is no hand-built connector to wait for. 13 operations are documented.

Do I need to write code to automate bridgedb webservices?

No. You describe the outcome you want in plain words. HumDay agrees a contract with you, writes the program, and shows you a test run before anything touches your bridgedb webservices account.

What can HumDay do in bridgedb webservices?

2 of the 13 documented operations change something in bridgedb webservices, and 11 read from it. HumDay only ever uses the specific operations your approved contract needs.

Is my bridgedb webservices account safe?

Your credentials are stored encrypted and are never shown in chat, code, or logs. Every run is limited to the operations you explicitly approved, and anything that writes to bridgedb webservices is held behind that approval.

Where this came from

The operations above are read from a published API description for bridgedb webservices at bridgedb.github.io/swagger/swagger.json. Descriptions are the provider’s own words, not ours. Last published 2023-03-06.