Searching for full or partial concept accessions is not working, eg TO:0000286

[KeywanHP]

The example below should only show paths between gene:TraesCS2B02G184100 and TO:0020057
http://knetminer.rothamsted.ac.uk/wheatknet/genepage?keyword=0020057&list=TraesCS2B02G184100

But it shows many other paths...

It works fine if instead of the the TO accession, the TO name is used:
http://knetminer.rothamsted.ac.uk/wheatknet/genepage?keyword=leaf%20AND%20rust%20AND%20response&list=TraesCS2B02G184100

[KeywanHP]

I just checked that TO is included in the list of Accession Data Sources to be searched, and yes it is there:

knetminer/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java

Line 616 in 30ea3ee

String[] datasources = {"PFAM", "IPRO", "UNIPROTKB", "EMBL", "KEGG", "EC", "GO", "TO", "NLM", "TAIR",

So maybe the Lucene search is doing something funny with digits:

knetminer/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java

Line 696 in 30ea3ee

for (String dsAc : dsAcc) {

[AjitPS]

We have internally deployed KnetMiner:master (2 weeks ago) for testing Arabidopsis on http://babvs72.rothamsted.ac.uk:8091/client/

Querying with a gene and TO term: http://babvs72.rothamsted.ac.uk:8091/ws/araknet/genepage?keyword=0002616&list=AT2G25930 shows gene plus 235 other (visible) concepts out of total: 419; with various Phenotype & 7 visible Trait nodes (1 of which is TO:0002616)

[KeywanHP]

Checked the Lucene index with Luke and spotted a tiny typo which meant the KnetMiner search was not considering concept accessions.

[AjitPS]

Still does not highlight TO term when, e.g., TO:0002616 or 0002616, used in keyword.

also, http://localhost:9090/ws/aratiny/genepage?keyword=%22plant%20height%22&list= throws this new error:
[qtp293108580-22] ERROR rres.knetminer.datasource.ondexlocal.OndexServiceProvider - Lucene search failed
java.lang.IllegalStateException: field "ConceptAccession_IPRO" was indexed without position data; cannot run PhraseQuery (phrase=ConceptAccession_IPRO:"plant height")
at org.apache.lucene.search.PhraseQuery$PhraseWeight.scorer(PhraseQuery.java:411) ~[lucene-core-6.6.0.jar:6.6.0 5c7a7b65d2aa7ce5ec96458315c661a18b320241

[KeywanHP]

The fix had unlocked another issue with the way concept accessions were indexed in Lucene. It has now been resolved in Ondex LuceneEnv. Following queries are now working as expected:

ws/aratiny/genepage?keyword="TO:0000286"&list=AT1G13180
ws/aratiny/genepage?keyword=0000286&list=AT1G13180