Adding search API at /search to minerva #234
Merged
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
added 20 commits
June 25, 2019 13:28
though note it currently give multiple responses per model if a single gene class is used on more than one instance within that model.
e.g. query: http://127.0.0.1:6800/search/?gene_product_class_uri=http://identifiers.org/mgi/MGI:1328355&gene_product_class_uri=http://identifiers.org/mgi/MGI:87986 response: { "n": 1, "models": [ { "id": "gomodel:5ce58dde00001215", "date": "2019-06-26", "title": "Mouse-Aatf-antiapoptosis", "state": "production", "contributors": [ "http://orcid.org/0000-0001-7476-6306" ], "query_match": { "http://identifiers.org/mgi/MGI:1328355": [ "http://model.geneontology.org/5ce58dde00001215/5ce58dde00001312", "http://model.geneontology.org/5ce58dde00001215/5ce58dde00001229" ], "http://identifiers.org/mgi/MGI:87986": [ "http://model.geneontology.org/5ce58dde00001215/5ce58dde00001217" ] } } ] }
works for requests for genes, goterms. Could be generalized further in terms of input parameters - e.g. a generic 'type=.." instead of goterm, gene_product etc.
Not much difference really. All tests in minerva server pass. Local testing with Noctua stack is working without error. Note that there is no longer a way to set conf.requestBufferSize . See here for info. on the upgrade.
Added parameter to API and sparql template. Updgraded jetty dependency to 9.2.3.v20140905 . (from 7). Note that jetty 9.4 will break it.
still leaving as union in the query.
returns models more recent than the requested date. Date must be in 10 character format: yyyy-mm-dd e.g. 2019-03-05
Allows client to iterate through result blocks of arbitrary size. Client decides how many to add to a 'page' in their context. e.g. to iterate through results 2 at a time, query like this, in order: http://127.0.0.1:6800/search/?date=2019-03-06&offset=0&limit=2 http://127.0.0.1:6800/search/?date=2019-03-06&offset=2&limit=2 etc. you will get the same thing you would get from the following request, but in two steps instead of one. http://127.0.0.1:6800/search/?date=2019-03-06&offset=0&limit=4
not all models have provided_by or modelstate annotations. This really impacts the text search service. By making these fields optional, made the searches with text much faster. Works nicely even on full noctua-dev model set.
|
Clean merge! |
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.
No description provided.