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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
4 stars 2 forks source link

quick search function #298

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago 

<https://www.github.com/superphy#isFoundIn> | <https://www.github.com/superphy#4cc0b917d6af3f3ae1d6fe2d36b453070a16f563> |  
-- | -- | --
<https://www.github.com/superphy#isFoundIn> | <https://www.github.com/superphy#spfy1> |  
<https://www.github.com/superphy#isFoundIn> | <https://www.github.com/superphy#4cc0b917d6af3f3ae1d6fe2d36b453070a16f563/contigs> |  
rdf:type | <http://www.biointerchange.org/gfvo#Contig> |  
kevinkle commented 6 years ago 

ERROR WITH JOB: 3c008708-3daf-4a22-baff-0fae7b3ea4b3
Traceback (most recent call last): File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job rv = job.perform() File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform self._result = self.func(*self.args, **self.kwargs) File "./middleware/decorators.py", line 188, in func_wrapper query = func(*args, **kwargs) File "./middleware/decorators.py", line 178, in func_wrapper query = func(*args, **kwargs) File "./modules/dbsearch/search_queries.py", line 33, in query_db_accession """.format(recordid) KeyError: '\n ?spfyIdObject ge'```
kevinkle commented 6 years ago 
Jump to content
ERROR WITH JOB: 4b7a8246-5b3d-4fb4-88e2-8c2f7fabd4e3
Traceback (most recent call last): File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job rv = job.perform() File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform self._result = self.func(*self.args, **self.kwargs) File "./middleware/decorators.py", line 193, in func_wrapper results = sparql.query().convert() File "/opt/conda/envs/backend/lib/python2.7/site-packages/SPARQLWrapper/Wrapper.py", line 567, in query return QueryResult(self._query()) File "/opt/conda/envs/backend/lib/python2.7/site-packages/SPARQLWrapper/Wrapper.py", line 541, in _query raise QueryBadFormed(e.read()) QueryBadFormed: QueryBadFormed: a bad request has been sent to the endpoint, probably the sparql query is bad formed. Response: SPARQL-QUERY: queryStr=PREFIX doid: <http://purl.obolibrary.org/obo/DOID_> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX subt: <https://www.github.com/superphy/typing#> PREFIX dc: <http://purl.org/dc/elements/1.1/> PREFIX ge: <http://purl.obolibrary.org/obo/GENEPIO_> PREFIX g: <http://www.biointerchange.org/gfvo#> PREFIX ncbi: <http://purl.obolibrary.org/obo/NCBI_Taxon_> PREFIX obi: <http://purl.obolibrary.org/obo/OBI_> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX envo: <http://purl.obolibrary.org/obo/ENVO_> PREFIX so: <http://purl.obolibrary.org/obo/SO_> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX : <https://www.github.com/superphy#> PREFIX typon: <http://purl.phyloviz.net/ontology/typon#> SELECT DISTINCT ?Genome ?submitted ?otype ?htype ?recordid ?vf ?amr WHERE { ?uriContig a g:Contig ; g:Identifier ?recordid . VALUES ?recordid { CP027599.1 } ?uriContig :isFoundIn ?GenomeObject . ?GenomeObject a g:Genome ; dc:description ?Genome; dc:date ?submitted . ?GenomeObject :isFoundIn ?spfyIdObject . ?spfyIdObject a :spfyId . OPTIONAL { ?spfyIdObject ge:0001076 ?otype . ?spfyIdObject ge:0001077 ?htype . ?uriContig :hasPart ?vf. ?vf a :VirulenceFactor. ?uriContig :hasPart ?amr. ?amr a :AntimicrobialResistanceGene. } } java.util.concurrent.ExecutionException: org.openrdf.query.MalformedQueryException: Lexical error at line 4, column 38. Encountered: " " (32), after : "CP027599.1" at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at com.bigdata.rdf.sail.webapp.BigdataServlet.submitApiTask(BigdataServlet.java:281) at com.bigdata.rdf.sail.webapp.QueryServlet.doSparqlQuery(QueryServlet.java:653) at com.bigdata.rdf.sail.webapp.QueryServlet.doGet(QueryServlet.java:288) at com.bigdata.rdf.sail.webapp.RESTServlet.doGet(RESTServlet.java:240) at javax.servlet.http.HttpServlet.service(HttpServlet.java:687) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:841) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634) at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:206) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1621) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:541) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1592) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1239) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:481) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1561) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1141) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213) at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:118) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:564) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:320) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:110) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:672) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:590) at java.lang.Thread.run(Thread.java:745) Caused by: org.openrdf.query.MalformedQueryException: Lexical error at line 4, column 38. Encountered: " " (32), after : "CP027599.1" at com.bigdata.rdf.sail.sparql.Bigdata2ASTSPARQLParser.parseQuery2(Bigdata2ASTSPARQLParser.java:404) at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlQueryTask.call(QueryServlet.java:716) at com.bigdata.rdf.sail.webapp.QueryServlet$SparqlQueryTask.call(QueryServlet.java:670) at com.bigdata.rdf.task.ApiTaskForIndexManager.call(ApiTaskForIndexManager.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ... 1 more Caused by: com.bigdata.rdf.sail.sparql.ast.TokenMgrError: Lexical error at line 4, column 38. Encountered: " " (32), after : "CP027599.1" at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilderTokenManager.getNextToken(SyntaxTreeBuilderTokenManager.java:3994) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.jj_ntk(SyntaxTreeBuilder.java:9633) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.InlineDataOneVar(SyntaxTreeBuilder.java:1150) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.DataBlock(SyntaxTreeBuilder.java:1132) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.InlineData(SyntaxTreeBuilder.java:1106) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.GraphPatternNotTriples(SyntaxTreeBuilder.java:2369) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.GraphPattern(SyntaxTreeBuilder.java:2043) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.GroupGraphPattern(SyntaxTreeBuilder.java:1965) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.WhereClause(SyntaxTreeBuilder.java:1009) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.SelectQuery(SyntaxTreeBuilder.java:373) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.Query(SyntaxTreeBuilder.java:324) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.QueryContainer(SyntaxTreeBuilder.java:212) at com.bigdata.rdf.sail.sparql.ast.SyntaxTreeBuilder.parseQuery(SyntaxTreeBuilder.java:32) at com.bigdata.rdf.sail.sparql.Bigdata2ASTSPARQLParser.parseQuery2(Bigdata2ASTSPARQLParser.java:336) ... 7 more
kevinkle commented 6 years ago 
PREFIX doid: <http://purl.obolibrary.org/obo/DOID_> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX subt: <https://www.github.com/superphy/typing#> PREFIX dc: <http://purl.org/dc/elements/1.1/> PREFIX ge: <http://purl.obolibrary.org/obo/GENEPIO_> PREFIX g: <http://www.biointerchange.org/gfvo#> PREFIX ncbi: <http://purl.obolibrary.org/obo/NCBI_Taxon_> PREFIX obi: <http://purl.obolibrary.org/obo/OBI_> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX envo: <http://purl.obolibrary.org/obo/ENVO_> PREFIX so: <http://purl.obolibrary.org/obo/SO_> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX : <https://www.github.com/superphy#> PREFIX typon: <http://purl.phyloviz.net/ontology/typon#> SELECT DISTINCT ?Genome ?submitted ?otype ?htype ?recordid ?vf ?amr WHERE { ?uriContig a g:Contig ; g:Identifier ?recordid . VALUES ?recordid { CP027599.1 } ?uriContig :isFoundIn ?GenomeObject . ?GenomeObject a g:Genome ; dc:description ?Genome; dc:date ?submitted . ?GenomeObject :isFoundIn ?spfyIdObject . ?spfyIdObject a :spfyId . OPTIONAL { ?spfyIdObject ge:0001076 ?otype . ?spfyIdObject ge:0001077 ?htype . ?uriContig :hasPart ?vf. ?vf a :VirulenceFactor. ?uriContig :hasPart ?amr. ?amr a :AntimicrobialResistanceGene. } }
kevinkle commented 6 years ago

Currently returning:

{
  "head": {
    "vars": [
      "Genome", 
      "submitted", 
      "otype", 
      "htype", 
      "recordid", 
      "vf", 
      "amr"
    ]
  }, 
  "results": {
    "bindings": [
      {
        "Genome": {
          "type": "literal", 
          "value": "1.fa"
        }, 
        "recordid": {
          "type": "literal", 
          "value": "gi|1370526529|gb|CP027599.1|"
        }, 
        "submitted": {
          "type": "literal", 
          "value": "2018-06-20"
        }
      }
    ]
  }
}
kevinkle commented 6 years ago 
[
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#stgC", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#tar/cheM", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#tir", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#upaG/ehaG", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtE", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtP", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtQ", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtS", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtU", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtX", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ycbS", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ygeH", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#yijP", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#Z2203", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ibeB", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ibeC", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#icmF", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#iha", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#irp1", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#irp2", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#iucA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#iucC", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#iucD", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#iutA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#malx", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#mchf", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#nadb", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#nleA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#nleL", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#stgC", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#tar/cheM", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#tir", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#upaG/ehaG", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "http://purl.phyloviz.net/ontology/typon#Locus", 
    "submitted": "2018-06-20"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#ybtE", 
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kevinkle commented 6 years ago

<https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1_1597_1599017_1602130_1_ID1_1597partial00start_typeATGrbs_motifGAGGrbs_spacer10bpgc>

kevinkle commented 6 years ago

<https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1>

kevinkle commented 6 years ago

Hotfix worked, this also means we'll have to recompute the latest set ;(

kevinkle commented 6 years ago

Starting a new run, the docker bug I was tracking turned out to be our react app grouch decided it wanted to run on 5000 instead of 3000 - super weird.

kevinkle commented 6 years ago 
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    "marker": "https://www.github.com/superphy#espX5", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#espX7", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
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    "marker": "https://www.github.com/superphy#fdeC", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#fepA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
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    "Genome": "1.fa", 
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    "marker": "https://www.github.com/superphy#fimD", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
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    "marker": "https://www.github.com/superphy#flgE", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#flgK", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#flhA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#fliF", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#fliI", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }, 
  {
    "Genome": "1.fa", 
    "htype": "H11", 
    "marker": "https://www.github.com/superphy#fyuA", 
    "otype": "O26", 
    "recordid": "gi|1370526529|gb|CP027599.1|", 
    "subclass": "https://www.github.com/superphy#VirulenceFactor", 
    "submitted": "2018-06-21", 
    "uriContig": "https://www.github.com/superphy#34fd3eac70aaa89059d748faf93dad0229914ec8/contigs/gi1370526529gbCP027599.1"
  }
]
kevinkle commented 6 years ago

Basic feature set done in https://github.com/superphy/spfy/pull/314. Closing.