Export BEL Nanopubs in search result to a file.

[wshayes]

Expanding upon the initial issue to support a CSV export:

We should allow export of the search results (total set after facets selected) to any file format supported by the OpenBEL API. We will then make CSV export a supported BEL Nanopub format.

This is a more useful, general solution that allows BEL Manager to export to all core file formats (e.g. BEL Script, XBEL, JSON) as well as user-added formats (e.g. SIF).

This work would involve:

• Add an export option to the search page that allows a user to pick a file format supported by the OpenBEL API (see API route to retrieve supported translators openbel-api#104). A CSV format will be supported (see search results export as CSV openbel-api#81).
• When the user selects the file format and exports then a file will be prompted for download by the browser. This will be driven by the /api/evidence endpoint using Accept header or format query parameter.

Example:

Export at most 5000 BEL Nanopubs to a BEL Script file:

http://next.belframework.org/api/evidence?size=5000&format=bel

Export BEL Nanopubs filtered to Human to an XBEL file:

http://next.belframework.org/api/evidence?size=5000&filter={%22category%22:%22experiment_context%22,%22name%22:%22Species%22,%22value%22:%229606%22}&format=xbel

[kellymccann91]

The Export button has been added on the top right of the search results.

Questions:
-What should it say? Is 'Export (+ icon)' meaningful enough for users to know that it refers to search results?
-Is the location alright now? As a user is that where you'd look?
-Aurelia.dialog - @wshayes: I should have pestered you about this yesterday. I have the plugin configured, but I'm struggling to actually call the code. I'll keep trying. Then I may need your help to retrieve and download the search results in Excel/CSV format.

[wshayes]

Tony - can you provide an API endpoint that will accept a search query and provide an export as either BEL Script, XBEL or Evidence JSON as you did with the Dataset exports?

After that, please assign this back to Kelly so she can redo the Export button to allow a dropdown to select the export format.

[abargnesi]

Can do. I can add the Accept header and format query parameter option to GET /api/evidence to export the whole, or filtered set, of the evidence_collection resource to a download.

[abargnesi]

OpenBEL API 0.6.1 added retrieving BEL Nanopubs in any supported file format.

I have improved the solution in the issue description above, @kellymccann91 please take a look.

[wshayes]

Tony shared the following on the API enhancement:

The /api/evidence and /api/datasets/{id}/evidence endpoints will respect the "Accept" request header and "format" query parameter. The "format" query parameter is preferred when both are provided.

Example:

Accept: application/xml
/api/evidence?start=0&size=1000&filter={...}

OR

/api/evidence?start=0&size=1000&filter={...}&format=xbel

---

The OpenBEL API provides the following by default:

• id: bel, name: "BEL Script Translator", media_type: application/bel, extension: bel
• id: xbel, name: "XBEL Translator", media_type: application/xml, extension: xbel
• id: json_evidence, name: "JSON Evidence Translator", media_type: application/json, extension: json
• id: jgf, name: "JSON Graph Format Translator", media_type: application/vnd.jgf+json, extension: jgf.json
• id: nquads, name: "N-quads RDF Translator", media_type: application/n-quads, extension: nq
• id: turtle, name: "Turtle RDF Translator", media_type: application/turtle OR application/x-turtle, extension: ttl

There are some other RDF formats supported but they can wait for 104.