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admin/log no reply from SBH3 #445

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anjalakaturi opened this issue Jun 3, 2023 · 0 comments · May be fixed by #441
Open

admin/log no reply from SBH3 #445

anjalakaturi opened this issue Jun 3, 2023 · 0 comments · May be fixed by #441
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@danielfang97
Labels
admin backend backend test failure
Milestone
SBH 3.0.0

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@anjalakaturi
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[synbiohub test] test_admin_log starting
http://localhost:7777/admin/log
SBH1

[{"level":"error","line":" SynBioHub server is restarting"},{"level":"info","line":" config: set revision => "358d068c""},{"level":"info","line":" [Java] Starting main loop"},{"level":"info","line":" [Java] Received job type org.synbiohub.InitializeJob"},{"level":"info","line":" [Java] Sending result for job ID 1"},{"level":"info","line":" Java initialized; JVM 1.8.0_275"},{"level":"info","line":" Resuming 0 job(s)"},{"level":"warn","line":" Browserslist: caniuse-lite is outdated. Please run:
 npx browserslist@latest --update-db
 Why you should do it regularly: https://github.com/browserslist/browserslist#browsers-data-updating"},{"level":"info","line":" redirecting"},{"level":"info","line":" config: set instanceName => "Test Synbiohub""},{"level":"info","line":" config: set sessionSecret => "379e24b0-27e6-4646-b495-c236c889798f""},{"level":"info","line":" config: set shareLinkSalt => "97f42169-7333-41c6-a40c-071576ca77aa""},{"level":"info","line":" config: set passwordSalt => "5cded249-eecd-43e6-b309-5a6aac832cbf""},{"level":"info","line":" config: set instanceUrl => "http://localhost:7777/""},{"level":"info","line":" config: set webOfRegistries => {"https://synbiohub.org":"http://localhost:7777"}"},{"level":"info","line":" config: set databasePrefix => "http://localhost:7777/""},{"level":"info","line":" config: set themeParameters => {"default":{"baseColor":"#D25627"}}"},{"level":"info","line":" config: set frontPageText => "text""},{"level":"info","line":" config: set allowPublicSignup => true"},{"level":"info","line":" config: set databasePrefix => "https://synbiohub.org/""},{"level":"info","line":" config: set triplestore => {"sparqlEndpoint":"http://virtuoso:8890/sparql","graphStoreEndpoint":"http://virtuoso:8890/sparql-graph-crud-auth/","defaultGraph":"https://synbiohub.org/public","graphPrefix":"https://synbiohub.org/","username":"dba","password":"dba","virtuosoINI":"/etc/virtuoso-opensource-7/virtuoso.ini","virtuosoDB":"/var/lib/virtuoso-opensource-7/db","isql":"isql-vt"}"},{"level":"info","line":" config: set externalAuth => {"enabled":false,"provider":null,"google":{}}"},{"level":"info","line":" config: set firstLaunch => false"},{"level":"info","line":" config: set webOfRegistries => {"https://synbiohub.org":"http://localhost:7777","https://synbiohub.programmingbiology.org":"https://synbiohub.programmingbiology.org","http://sevahub.es":"http://sevahub.es"}"},{"level":"info","line":" config: set instances => [{"id":1,"uriPrefix":"https://synbiohub.org","instanceUrl":"https://synbiohub.org","description":"<a href=\"/About\">SynBioHub</a> is a <i>design repository</i> for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources. ","name":"SynBioHub","approved":true,"administratorEmail":"[email protected]","updateWorking":true},{"id":3,"uriPrefix":"https://synbiohub.programmingbiology.org","instanceUrl":"https://synbiohub.programmingbiology.org","description":"<a href=\"/About\">SynBioHub</a> is a <i>design repository</i> for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources.","name":"LCP SynBioHub","approved":true,"administratorEmail":"[email protected]","updateWorking":true},{"id":11,"uriPrefix":"http://sevahub.es","instanceUrl":"http://sevahub.es","description":"The <a href=\"http://seva.cnb.csic.es\">SEVA database (SEVA-DB)</a> is a resource for implementation of a standard for physical assembly of vector plasmids and for their non-ambiguous nomenclature as well as the index for a repository of functional sequences and actual constructs available to the community. This resource, SEVAhub, is an instance of the <a href=\"http://wiki.synbiohub.org/\">SynBioHub</a> design repository providing access to SEVA-DB converted to the Synthetic Biology Open Language (SBOL). ","name":"SEVAhub","approved":true,"administratorEmail":"[email protected]","updateWorking":true}]"},{"level":"info","line":" "},{"level":"info","line":" "},{"level":"info","line":" query:BBa_B00"},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 select (sum(?tempcount) as ?count) WHERE {
 {
 SELECT (count(distinct ?subject) as ?tempcount)
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('BBa_B00'))||CONTAINS(lcase(?name), lcase('BBa_B00'))||CONTAINS(lcase(?description), lcase('BBa_B00'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject .
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }\t\t
 OPTIONAL { ?subject dcterms:description ?description . }\t
 }
 }
 }
 "},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT
 ?subject
 ?displayId
 ?version
 ?name
 ?description
 ?type
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('BBa_B00'))||CONTAINS(lcase(?name), lcase('BBa_B00'))||CONTAINS(lcase(?description), lcase('BBa_B00'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }
 OPTIONAL { ?subject dcterms:description ?description . }
 }
 
 LIMIT 50
 
 "},{"level":"info","line":" query:BBa_B00"},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 select (sum(?tempcount) as ?count) WHERE {
 {
 SELECT (count(distinct ?subject) as ?tempcount)
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('BBa_B00'))||CONTAINS(lcase(?name), lcase('BBa_B00'))||CONTAINS(lcase(?description), lcase('BBa_B00'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject .
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }\t\t
 OPTIONAL { ?subject dcterms:description ?description . }\t
 }
 }
 }
 "},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT
 ?subject
 ?displayId
 ?version
 ?name
 ?description
 ?type
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('BBa_B00'))||CONTAINS(lcase(?name), lcase('BBa_B00'))||CONTAINS(lcase(?description), lcase('BBa_B00'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }
 OPTIONAL { ?subject dcterms:description ?description . }
 }
 
 LIMIT 50
 
 "},{"level":"info","line":" query:abcdefg"},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 select (sum(?tempcount) as ?count) WHERE {
 {
 SELECT (count(distinct ?subject) as ?tempcount)
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('abcdefg'))||CONTAINS(lcase(?name), lcase('abcdefg'))||CONTAINS(lcase(?description), lcase('abcdefg'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject .
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }\t\t
 OPTIONAL { ?subject dcterms:description ?description . }\t
 }
 }
 }
 "},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT
 ?subject
 ?displayId
 ?version
 ?name
 ?description
 ?type
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 FILTER ((CONTAINS(lcase(?displayId), lcase('abcdefg'))||CONTAINS(lcase(?name), lcase('abcdefg'))||CONTAINS(lcase(?description), lcase('abcdefg'))))
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }
 OPTIONAL { ?subject dcterms:description ?description . }
 }
 
 LIMIT 50
 
 "},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 select (sum(?tempcount) as ?count) WHERE {
 {
 SELECT (count(distinct ?subject) as ?tempcount)
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 { ?subject ?p <https://synbiohub.org/public/igem/BBa_B0034/1> } UNION { ?subject ?p ?use . ?use ?useP <https://synbiohub.org/public/igem/BBa_B0034/1> } . FILTER(?useP != <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel>)# USES
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject .
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }\t\t
 OPTIONAL { ?subject dcterms:description ?description . }\t
 }
 }
 }
 "},{"level":"debug","line":" PREFIX sbol2: <http://sbols.org/v2#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX ncbi: <http://www.ncbi.nlm.nih.gov#>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX igem: <http://wiki.synbiohub.org/wiki/Terms/igem#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
 PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT
 ?subject
 ?displayId
 ?version
 ?name
 ?description
 ?type
 FROM <https://synbiohub.org/public> FROM <https://synbiohub.org/user/testuser1>
 WHERE {
 { ?subject ?p <https://synbiohub.org/public/igem/BBa_B0034/1> } UNION { ?subject ?p ?use . ?use ?useP <https://synbiohub.org/public/igem/BBa_B0034/1> } . FILTER(?useP != <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel>)# USES
 
 ?subject a ?type .
 ?subject sbh:topLevel ?subject
 OPTIONAL { ?subject sbol2:displayId ?displayId . }
 OPTIONAL { ?subject sbol2:version ?version . }
 OPTIONAL { ?subject dcterms:title ?name . }
 OPTIONAL { ?subject dcterms:description ?description . }
 }
 
 LIMIT 50
 
 
 "}]

http://localhost:6789/admin/log
SBH3

RESPONSE CODE TEST PASSED: Status Code: 200
@anjalakaturi anjalakaturi linked a pull request Jun 3, 2023 that will close this issue
Open
@cjmyers cjmyers added this to the SBH 3.0.0 milestone Oct 30, 2023
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admin/log SynBioHub/synbiohub3
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@cjmyers @danielfang97 @anjalakaturi