core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2024-02-22T10:11:25+01:00https://git-r3lab.uni.lu/minerva/core/-/issues/1635Feature request: automated user registration2024-02-22T10:11:25+01:00Marek OstaszewskiFeature request: automated user registrationPlease introduce a functionality allowing users to register and automate the process of registration.
Suggested way this could work:
1. The user click on the "Request an account" button
2. A form pops up prompting the user for an email ...Please introduce a functionality allowing users to register and automate the process of registration.
Suggested way this could work:
1. The user click on the "Request an account" button
2. A form pops up prompting the user for an email and password
3. The user appears in the system as "requesting", with login == email
4. An email with an activation link is sent to the user
5. After the activation link is clicked the user gets an on-screen notification that his request will be reviewed
6. the status of the user changes to "pending"
7. A notification is sent to the admins (contact email) to review the user and assign a role
8. When a role is assigned, the user gets a notification that his account is set up
@piotr.gawron what do you think? We discussed this for a bit with @ewa.smula .
We could consider skipping steps 4-6 (activation link), but then there will be no control if the email is valid.17.0.0-beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1624sbgn-ml support2022-02-14T14:45:38+01:00Piotr Gawronsbgn-ml supportCurrent implementation skip some glyphs/arc that can be used when importing model from SBGN. We should improve ETL to support those types. Here is the list:
https://docs.google.com/document/d/1UG7EGNAV1UKGmpCTZC9SBDGt7rbIJDWeu4KRWZ0hqKY/...Current implementation skip some glyphs/arc that can be used when importing model from SBGN. We should improve ETL to support those types. Here is the list:
https://docs.google.com/document/d/1UG7EGNAV1UKGmpCTZC9SBDGt7rbIJDWeu4KRWZ0hqKY/edit?usp=sharingv16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1621"Input file is invalid" response should provide more details whenever it's po...2022-02-01T10:20:22+01:00Piotr Gawron"Input file is invalid" response should provide more details whenever it's possiblev16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1616Add support for kinetics MathML functions2021-12-16T11:12:17+01:00Piotr GawronAdd support for kinetics MathML functionsFull list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, fact...Full list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, factorial, quotient, max, min, rem
* trigonometric operators: sin, cos, tan, sec, csc, cot, sinh, cosh, tanh, sech, csch, coth, arcsin, arccos, arctan, arcsec, arccsc, arccot, arcsinh, arccosh, arctanh, arcsech, arccsch, arccothhttps://git-r3lab.uni.lu/minerva/core/-/issues/1615file format name in converion should be case-insensitive2022-03-23T11:44:36+01:00Piotr Gawronfile format name in converion should be case-insensitivefor example you should be able to convert to `SVG` or to `svg`for example you should be able to convert to `SVG` or to `svg`v16.1.0~beta.2https://git-r3lab.uni.lu/minerva/core/-/issues/1612invalid SBML unit type throws 5002022-01-31T08:35:30+01:00Piotr Gawroninvalid SBML unit type throws 500```
2021-12-14 08:43:00,061 ERROR [http-nio-8080-exec-5] (BaseController.java:64) - lcsb.mapviewer.common.exception.InvalidArgumentException: Unknown sbml unit type: AVOGADRO
lcsb.mapviewer.common.exception.InvalidArgumentException: Unkn...```
2021-12-14 08:43:00,061 ERROR [http-nio-8080-exec-5] (BaseController.java:64) - lcsb.mapviewer.common.exception.InvalidArgumentException: Unknown sbml unit type: AVOGADRO
lcsb.mapviewer.common.exception.InvalidArgumentException: Unknown sbml unit type: AVOGADRO
at lcsb.mapviewer.converter.model.sbml.units.UnitMapping.kindToUnitType(UnitMapping.java:96) ~[converter-sbml-16.0.4.jar:?]
at lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser.parse(SbmlUnitsParser.java:25) ~[converter-sbml-16.0.4.jar:?]
at lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser.parseList(SbmlUnitsParser.java:39) ~[converter-sbml-16.0.4.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlParser.createModel(SbmlParser.java:80) ~[converter-sbml-16.0.4.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl.convert(ConvertRestImpl.java:58) ~[rest-api-16.0.4.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl$$FastClassBySpringCGLIB$$c6591b50.invoke(<generated>) ~[rest-api-16.0.4.jar:?]
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) ~[spring-core-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:746) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:688) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at lcsb.mapviewer.api.convert.ConvertRestImpl$$EnhancerBySpringCGLIB$$c9bc8f88.convert(<generated>) ~[rest-api-16.0.4.jar:?]
at lcsb.mapviewer.api.convert.ConvertController.convertInput(ConvertController.java:47) ~[rest-api-16.0.4.jar:?]
at sun.reflect.GeneratedMethodAccessor173.invoke(Unknown Source) ~[?:?]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_292]
at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_292]
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:891) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:974) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:877) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:661) [tomcat8-servlet-api.jar:?]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:851) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) [tomcat8-servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:37) [classes/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat8-websocket-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.CORSFilter.doFilter(CORSFilter.java:43) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.CacheFilter.doFilter(CacheFilter.java:38) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:37) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:200) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:660) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:798) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat8-coyote-8.5.39.jar:8.5.39]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_292]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_292]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat8-util-8.5.39.jar:8.5.39]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_292]
```v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1610add support for this identifiers2022-02-16T15:58:58+01:00Piotr Gawronadd support for this identifiersFollowing miriam identifiers are missing in minerva. This list is composed from warnings in minerva-service:
* urn:miriam:mod:MOD:00048
* urn:miriam:obo.bto:BTO:0000007
* urn:miriam:obo.clo:CL:0000066
* urn:miriam:sbo:SBO:0000179
* http:...Following miriam identifiers are missing in minerva. This list is composed from warnings in minerva-service:
* urn:miriam:mod:MOD:00048
* urn:miriam:obo.bto:BTO:0000007
* urn:miriam:obo.clo:CL:0000066
* urn:miriam:sbo:SBO:0000179
* http://identifiers.org/mamo/MAMO_0000040
* http://identifiers.org/eco/ECO:0000212
* http://identifiers.org/omim/139150
* http://identifiers.org/atc/A10BB09
* http://identifiers.org/biocyc/META:10-FORMYL-THF
* http://identifiers.org/bto/0000782
* http://identifiers.org/bto/BTO:0000007
* http://identifiers.org/cco/CCO:13867
* http://identifiers.org/cl/CL:0000000
* http://identifiers.org/efo/0000305
* http://identifiers.org/efo/EFO:0000616
* http://identifiers.org/ensembl.gene/ENSG00000011485
* http://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
* http://identifiers.org/fma/FMA:20394
* http://identifiers.org/gdc/e1c8af06-9ea4-4062-9264-aa916e0025d1
* http://identifiers.org/go.ref/GO:0001906
* http://identifiers.org/hp/HP:0032322
* http://identifiers.org/inchi/InChI=1S/C10H10N2O/c1-8-7-10(13
* http://identifiers.org/inchi_key/AAAFZMYJJHWUPN-TXICZTDVSA-J
* http://identifiers.org/isbn/1555810845
* http://identifiers.org/kegg.genome/ppa
* http://identifiers.org/metanetx.chemical/MNXM1
* http://identifiers.org/metanetx.reaction/MNXR100018
* http://identifiers.org/narcis/oai:cwi.nl:4725
* http://identifiers.org/ncit/C104081
* http://identifiers.org/obo.bto/BTO:0004911
* http://identifiers.org/obo.psi-mod/MOD:00000
* http://identifiers.org/omit/0006811
* http://identifiers.org/pirsf/PIRSF005483
* http://identifiers.org/pr/PR:000001940
* http://identifiers.org/psimod/MOD:00000
* http://identifiers.org/pw/PW:0000015
* http://identifiers.org/reactome.compound/109275
* http://identifiers.org/reactome.reaction/R-ATH-110144
* http://identifiers.org/sabiork/100
* http://identifiers.org/sbo/0000117
* http://identifiers.org/sbo/degradation
* http://identifiers.org/sbo/SBO:0000169
* http://identifiers.org/seed.compound/cpd00001
* http://identifiers.org/seed.reaction/rxn00001
* http://identifiers.org/slm/000000297
* http://identifiers.org/t3db/T3D3477
* http://identifiers.org/tcdb/1.D.6.1.1
* http://identifiers.org/unipathway.reaction/Q9Z1E3
* http://identifiers.org/uniprot.genename/ADAM10
* https://identifiers.org/inchikey/ADVPTQAUNPRNPO-REOHCLBHSA-M
* https://identifiers.org/metabolights/MTBLC10782
* https://identifiers.org/umbbd.compound/c0023
Weird ones, should we handle them as special cases? Or provide as urls without type recognition?
* https://reactome.org/content/detail/R-ALL-113518
* https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:00005
* https://www.ebi.ac.uk/QuickGO/term/GO:0000139
* https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=10172
* https://www.rhea-db.org/rhea/11261
* http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377
* http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000008405
* http://www.ensembl.org/Homo_sapiens/transview?transcript=ENST00000317276;db=core
* http://www.geneontology.org/GO:0006006
* http://www.ncbi.nlm.nih.gov/pubmed/10203854
* http://arxiv.org/pdf/1305.6449v1.pdf
* http://hdl.handle.net/1903/11919v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1595register of maps on minerva.net2022-01-25T14:04:49+01:00Piotr Gawronregister of maps on minerva.netThere should be possibility to register map in the publicly available resource (https://minerva-net.lcsb.uni.lu/) that would contain information about publicly available maps. Following information should be available in the registry:
* ...There should be possibility to register map in the publicly available resource (https://minerva-net.lcsb.uni.lu/) that would contain information about publicly available maps. Following information should be available in the registry:
* url
* map name, version
* disease
* organism
* creator + timestamp
* contact email address
@marek.ostaszewski anything else?v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1594rewrite API2024-02-29T14:52:38+01:00Piotr Gawronrewrite APICurrent API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization shou...Current API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization should be done automatically using Jackson
* patch/post/delete requests should handle properly simultaneous modifications of the objects (https://www.mscharhag.com/api-design/rest-concurrent-updates)
* when accessing collections use Pageable interface
* use JPA validation for input parametershttps://git-r3lab.uni.lu/minerva/core/-/issues/1545provide map files for resoureces2021-09-08T13:45:47+02:00Piotr Gawronprovide map files for resoureces
```
2021-09-03 14:10:54,606 WARN [http-nio-8080-exec-7] (DispatcherServlet.java:1205) - No mapping found for HTTP request with URI [/minerva/javax.faces.resource/minerva.js.map] in DispatcherServlet with name 'dispatcher'
2021-09-03 14...
```
2021-09-03 14:10:54,606 WARN [http-nio-8080-exec-7] (DispatcherServlet.java:1205) - No mapping found for HTTP request with URI [/minerva/javax.faces.resource/minerva.js.map] in DispatcherServlet with name 'dispatcher'
2021-09-03 14:10:54,606 WARN [http-nio-8080-exec-3] (DispatcherServlet.java:1205) - No mapping found for HTTP request with URI [/minerva/javax.faces.resource/BrowserCheck.js.map] in DispatcherServlet with name 'dispatcher'
2021-09-03 14:10:55,632 WARN [http-nio-8080-exec-7] (DispatcherServlet.java:1205) - No mapping found for HTTP request with URI [/minerva/javax.faces.resource/BrowserCheck.js.map] in DispatcherServlet with name 'dispatcher'
2021-09-03 14:10:56,334 WARN [http-nio-8080-exec-3] (DispatcherServlet.java:1205) - No mapping found for HTTP request with URI [/minerva/javax.faces.resource/minerva.js.map] in DispatcherServlet with name 'dispatcher'
```v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1542after changing details of user refresh USERS page automatically (nice to have)2024-02-13T13:27:18+01:00Ewa Smulaafter changing details of user refresh USERS page automatically (nice to have)Now user has to click REFRESH button. For example in PROJECTS page the project's details are refreshed automatically after changing its details in EDIT.Now user has to click REFRESH button. For example in PROJECTS page the project's details are refreshed automatically after changing its details in EDIT.v17.0.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1491Change active tab when choosing a "Show all" element from pin popup2021-06-22T10:29:07+02:00Ewa SmulaChange active tab when choosing a "Show all" element from pin popuprelated to issue #1365 - fixed.
Please add one more thing: if user is in different tab than SEARCH, and click on a (drug/chem/mirna) target in pin popup, redirect the left panel to corresponding SEARCH > drugs/chemical/mirna.related to issue #1365 - fixed.
Please add one more thing: if user is in different tab than SEARCH, and click on a (drug/chem/mirna) target in pin popup, redirect the left panel to corresponding SEARCH > drugs/chemical/mirna.v16.0.0~beta.1Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1481Comment Notification2022-02-03T08:01:16+01:00Matti Hochmatti.hoch@uni-rostock.deComment NotificationIs there a possibility to get an Email notification each time someone leaves a comment on the map?Is there a possibility to get an Email notification each time someone leaves a comment on the map?v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1480User Groups2021-06-09T11:22:02+02:00Matti Hochmatti.hoch@uni-rostock.deUser GroupsPossibility to put users into customized groups to facilitate assignment of access to projects, etc.Possibility to put users into customized groups to facilitate assignment of access to projects, etc.https://git-r3lab.uni.lu/minerva/core/-/issues/1478proper complex-child relation in sbml2022-02-02T13:53:46+01:00Piotr Gawronproper complex-child relation in sbmlcreated from discussion with Robert Phair
```
@Robert Phair
You identified one of the problems that I had with multi package. In theory there is possibility to define complex formation in multi but I just could not figure out how to do i...created from discussion with Robert Phair
```
@Robert Phair
You identified one of the problems that I had with multi package. In theory there is possibility to define complex formation in multi but I just could not figure out how to do it properly. I would happily add it but I need to know how. Are you or your developers familiar with the package and could help here? I just need a proof of concept and I will implement it by myself.
The only thing that could do to discover the complex formation is to check the coordinates in layout extension. But I know it's far from perfect (for instance nested complexes are a bit tricky to handle)
Robert Phair 2 months ago
@piotr I had a conversation with Fengkai Zhang on the sbml-discuss Google group. He is one of the principal developers of multi, and is the developer of SIMMUNE, a tool for modeling and simulation of the immune system. He's in Ron Germain's group at the US NIH. He was eager to help. I asked him how he would code the SMAD1/5/8 complex in SBML multi. and this was his response: "Hi Robert,
Thank you for working to support the multi package! Thank you for the question. I include this reply to the multi list. I think we could also continue to discuss here as multi is part of sbml.
Specific to your question, you could first define mult:speciesTypes in the following way:
<multi:listOfSpeciesTypes>
<multi:speciesType multi:id="st_SMAD1" multi:name=" SMAD1" …/>
<multi:speciesType multi:id="st_SMAD5" multi:name=" SMAD5" …/>
<multi:speciesType multi:id="st_SMAD8" multi:name=" SMAD8" …/>
<multi:speciesType multi:id="st_SMAD1_5_8" multi:name=" SMAD1_5_8" …>
<multi:listOfSpecieTypeInstances>
<multi:speciesTypeInstance multi:id="sti_SMAD1" multi:speciesType="st_SMAD1" … />
<multi:speciesTypeInstance multi:id="sti_SMAD5" multi:speciesType="st_SMAD5" … />
<multi:speciesTypeInstance multi:id="sti_SMAD8" multi:speciesType="st_SMAD8" … />
</ multi:listOfSpecieTypeInstances >
</multi:speciesType >
…
</multi:listOfSpeciesTypes >
And in speces to reference the speciesTypes, you may have:
<listOfSpeces>
<species id="species_SMAD1_5_8" multi:speciesType="st_SMAD1_5_8"… />
<species id="species_SMAD1" multi:speciesType="st_SMAD1"… />
<species id="species_SMAD5" multi:speciesType="st_SMAD5"… />
<species id="species_SMAD8" multi:speciesType="st_SMAD8"… />
…
</listOfSpeces>
Depending the purpose, annotation can be added to species, speciesType, and/or speciesTypeInstance. I consider species should be a good place to be annotated with a uniprot id."
I, too, have problems with the multi-spec, largely because it does not explicitly define how to handle any particular biological scenario. In other words, I think the spec is more like a framework. The trouble with a framework is that different developers can handle the same task in different ways. To me, this is antithetical to to the SBML goal of interoperability - model exchange among software tools. This was probably caused by the SBML competing priority to satisfy multiple development groups. I was not there. I am not an expert. So I have no grounds for complaint. But I think Fengkai is more than willing to help. (edited)
Robert Phair 2 months ago
@piotr I think your method for encoding complexes is logical, but maybe Fengkai's method has something to teach us. Our lead developer, @Jason Zwolak, has a long history working with SBML, but he has not worked with multi. He has, however, read the multi spec, and might want to join in this conversation because we want to be able to import MINERVA models into ProcessDB.
piotr 2 months ago
@Robert Phair In theory it should be doable, the only issue that I can see (that might become a problem) is that we have to create separate multi type for every single species on the map. We also need to somehow identify the BioEntity type of the multi type at the same level (if it's a small moleculer/protein/phenotype/etc). In theory the distinction should be doable using SBO term, but I remember there was an issue with that don't remember what it was though.
Another issue is that we would need to duplicate definitions of modification residue types and structural type information in every multi type defined. And this might result in a very messy SBML.
Nevertheless I can give it a try when I find some time.
```v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1457generate process rectangles for SBML render layout2021-03-19T09:48:55+01:00Piotr Gawrongenerate process rectangles for SBML render layoutv16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1456SBML layout/render should contain information about modification states2021-03-19T08:48:25+01:00Piotr GawronSBML layout/render should contain information about modification statesv16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1451Group search results by diagram2021-04-26T15:00:52+02:00Marek OstaszewskiGroup search results by diagramWith the submaps becoming more and more used, search functionality can be improved not to overload the left panel, and help to browse the results.
In the left panel, if a project has submaps, search results can be grouped by submap, w...With the submaps becoming more and more used, search functionality can be improved not to overload the left panel, and help to browse the results.
In the left panel, if a project has submaps, search results can be grouped by submap, with an overall number of hits per a collapsed "group item". The "group item" should be expandable. The link to a submap should be available only in the "group item", in both collapsed and expanded form.
@piotr.gawron @ewa.smula your comments?v16.0.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1450Handle MIRIAM PMC2021-02-09T09:13:55+01:00Marek OstaszewskiHandle MIRIAM PMCCurrently MINERVA throws
Invalid miriam uri: urn:miriam:pmc:___Currently MINERVA throws
Invalid miriam uri: urn:miriam:pmc:___v16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1427remove Default checkboxes in project Edit - > Overlays2021-08-12T12:55:45+02:00Ewa Smularemove Default checkboxes in project Edit - > OverlaysPlease remove 'Default' column in project Edit - > Overlays cause I think it is depreciated. It is not working currently :)
![Screen_Shot_2020-11-24_at_14.58.47](/uploads/e9a45aa81c048dd74807d00f72980273/Screen_Shot_2020-11-24_at_14.58...Please remove 'Default' column in project Edit - > Overlays cause I think it is depreciated. It is not working currently :)
![Screen_Shot_2020-11-24_at_14.58.47](/uploads/e9a45aa81c048dd74807d00f72980273/Screen_Shot_2020-11-24_at_14.58.47.png)v16.1.0~beta.0Piotr GawronPiotr Gawron