mir-mu / mathmlcaneval Goto Github PK

View Code? Open in Web Editor NEW

2.0 2.0 3.0 2.57 MB

Provides a web application for the evaluation of the MathML Canonicalizer

Home Page: https://mir.fi.muni.cz/mathml-normalization/#mathml-canonicalizer-evaluation

License: Apache License 2.0

Java 90.47% CSS 5.63% JavaScript 3.90%

mathmlcaneval's People

Contributors

Stargazers

Watchers

Forkers

empt-ak xlalik

mathmlcaneval's Issues

Canonicalization output – Find similar: exception

Find similar function on the canonicalization output page throws exception:

exception

org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.hibernate.search.SearchException: Search parameter on field similarForm could not be converted. Are the parameter and the field of the same type?Alternatively, apply the ignoreFieldBridge() option to pass String parameters
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:973)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

root cause

org.hibernate.search.SearchException: Search parameter on field similarForm could not be converted. Are the parameter and the field of the same type?Alternatively, apply the ignoreFieldBridge() option to pass String parameters
    org.hibernate.search.query.dsl.impl.Helper.getAllTermsFromText(Helper.java:86)
    org.hibernate.search.query.dsl.impl.ConnectedMultiFieldsTermQueryBuilder.getAllTermsFromText(ConnectedMultiFieldsTermQueryBuilder.java:181)
    org.hibernate.search.query.dsl.impl.ConnectedMultiFieldsTermQueryBuilder.createQuery(ConnectedMultiFieldsTermQueryBuilder.java:106)
    org.hibernate.search.query.dsl.impl.ConnectedMultiFieldsTermQueryBuilder.createQuery(ConnectedMultiFieldsTermQueryBuilder.java:81)
    cz.muni.fi.mir.db.dao.impl.CanonicOutputDAOImpl.getSimilarCanonicOutputs(CanonicOutputDAOImpl.java:142)
    cz.muni.fi.mir.db.service.impl.CanonicOutputServiceImpl.getSimilarCanonicOutputs(CanonicOutputServiceImpl.java:92)
    cz.muni.fi.mir.db.service.impl.CanonicOutputServiceImpl$$FastClassBySpringCGLIB$$87f59a5f.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:711)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    cz.muni.fi.mir.db.service.impl.CanonicOutputServiceImpl$$EnhancerBySpringCGLIB$$109b2d94.getSimilarCanonicOutputs(<generated>)
    cz.muni.fi.mir.controllers.CanonicOutputController.searchResults(CanonicOutputController.java:125)
    cz.muni.fi.mir.controllers.CanonicOutputController$$FastClassBySpringCGLIB$$972c2c20.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:640)
    cz.muni.fi.mir.controllers.CanonicOutputController$$EnhancerBySpringCGLIB$$ad25ec68.searchResults(<generated>)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:690)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:876)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

Database change

When new version of application is put to production please update the database schema using command ALTER TABLE annotation RENAME COLUMN note TO annotationContent; due to commit 0fbbeb6. Also make sure to have a backup of database, in case something breaks.

Canonicalizer configuration should be read-only

Maybe configuration should be bound to a particular canonicalizer revision as in case of adding new configuration options, those will be undefined when using an old configuration file.
Currently it is possible to edit existing configurations, which may cause problems. E. g. after editing configuration file, you can never tell what actual configuration was used for canonicalizer runs performed in the past.

improve configuration system

separate index config from test and jdbc config file
find out how to build application if index folder is missing or cannot by created

Implement input formula meaning(less) indication

Some formulae in the input database can be meaningless (e.g. regular text presented as a formula consisting from the text letters as sequence of multiplied variables) as results of OCR processing that has been used to get them.

The system should allow users to mark input formulae as
*meaningful,

meaningless, or
remove this evaluation.

These categories should be integrated with the statistical reports (#14).

Index changes

Sort of more proper index setup based on Hibernate Searched which runs upon Lucene.
Extraction of outputs that are supposed to be similar form out of canonic form into Separate Index entity.
Redesign install procedure with possibility of restarting entire database if setup was already run.

ApplicationRuns

Create interface that would allow users to:

create application run regardless of input formula (e.g pick random 50, pick by some filter etc.)
browse previous application runs

Separate footer

Separate footer for each page, so all the javascript code is not executed on all the pages .

Element Count method (must,should)

Implement functionality of must and should method profile. Currently values are tokenized and when query is requested token are bind together with should (or). For must there is a need to create i think BooleanJunction via .bool() method.

Wider view for formulae

View for MathML code is too narrow for comfortable reviewing of larger formulae, I would prefer page-wide area with code under rendered formula and without scrollbars.

Canonicalization result – diff view headings

Add headers identifying original/canonical half of the diff view. From the current interface it is not clear whether the original code is on the right side of the diff and the canonicalized code is on the left or vice versa.

Fix exception errors

Fix exception error when trying to delete object that is associated with other entity. For example if we try to remove Source document assigned to formula we get nasty stack trace instead of obtaining proper error message.

Undefined hashtag annotation tooltip

Shows "Marks result with following annotation: undefined"

Formula browser – scrollbar improvement

Current implementation of formula browser a the scrollbar is suboptimal.

The page should show more than 20 formulae at one page.
- Use number of formulae appropriate to the current page size?
The scrollbar allows infinite scrolling over empty pages.
The scrollbar is showing all the used pages.
The new version of scrollbar could be as follows:

<< < [ current page number ] (Go button) / [number of pages] > >>

<< / >> – go to the first/last page
< / > – go to the previous/next page
[current page number] (Go button) – editable input form allowing to directly enter new page number and go to the page when the Go button is pushed
[number of pages] – read only number showing number of pages

"Application Runs" link shows PersistenceException

https://mir.fi.muni.cz/apps/MathCalEval/appruns/
#16

Implement interface to browse formulae according to annotations

Implement interface to brows formulae according to their annotations, i.e. show all formulae marked as uncertain etc.

Implementation of web system log

Implement web interface showing system log:

errors of the application (e.g. ‘Too many opened files exception’)
errors of the canonicalization

Improved statistics

Implement enhanced version of statistics, that would allow to capture state of database from better view against configuration and revision. It would be also better if these values were generated automatically out of values from AnnotationValue class.

Mass delete Exception

In mass delete mode clicking on permanently delete selected formulas without selecting any formulas raises an exception

Implementation of system status dashboard

Implement web interface showing current state of the system, especially view of action currently running in the system such as

running mass import
- from what directory
- number of processed files, number of files to be processed
background canonicalization
- number of files to be processed
time of action start/end
...

Mass deletion of input formulae

Allow mass deletion of formulae from the input database.

Formula view – no timestamp shown for performed canonicalizations

The formula view page do not shows timestamps for preformed canonicalizations. Other data (id, hash, configuration, running time) are correctly shown.

Canonicalization does not work for me

I have added new revision and configuration. When I click the canonicalize button, it shows bubble 'canonicalization started' but formula is not canonicalized and no task is added to dashboard nor error produced.

Remove search form from entity/configuration/... pages

Remove search form from entity/configuration/... pages as there no need for server site search.

Implement missing functionality on the controllers.

Creating, editing & removing of all entities.

Show canonicalizer revision on canonicalized formula page

It would be useful to have some info about the canonicalizer run (canonicalizer revision, configuration) displayed directly on the canonicalized formula page.

Canonicalization after mass import do not work

Automatic canonicalization after mass import fails due to database constraints violation:

WARN 2014-07-29 14:21:58,364 taskExecutor-1 org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 0, SQLState: 23503
ERROR 2014-07-29 14:21:58,369 taskExecutor-1 org.hibernate.engine.jdbc.spi.SqlExceptionHelper - ERROR: insert or update on table "canonicoutput" violates foreign key constraint "fk_dldcek83hqa4xkwukis9ebs7a"
  Detail: Key (applicationrun_id)=(4) is not present in table "applicationrun".
INFO 2014-07-29 14:21:58,370 taskExecutor-1 org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl - HHH000010: On release of batch it still contained JDBC statements

Description of annotations

Annotation tool tips should describe annotation purposes:

Formula annotations:

#formulaRemove – Formula should be removed from the database as the formula markup is invalid (i.e. the formula MathML is not valid XML).
#formulaMeaningless – Formula is valid MathML but is meaningless, for example some text improperly encoded as string of math variables.

Canonicalization results:

#isValid – Canonicalization result is correct according to current implementation of the canonicalization functions, i.e. all the canonicalization methods were applied correctly and the result is valid MathML with the same meaning of the input formula.
#isInvalid – Implemented canonicalization methods were not applied correctly according their specification, or the result is not valid MathML, or the result formula has different meaning as the input one.
#uncertain – The annotator is not able to decide the canonicalization was applied correctly.
#removeResult – The result should be removed for any reason.

JSPException including path '/templates/default/template.jsp'

Current version (edb7e3a) of the application is not working after Tomcat6 deployment.

org.apache.jasper.JasperException: org.apache.tiles.request.render.CannotRenderException: JSPException including path '/templates/default/template.jsp'.
    org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:502)
    org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:430)
    org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
    org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:209)
    org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:267)
    org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1221)
    org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:1005)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:952)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:870)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

Canonicalization Diff shows nothing

E.g. https://mir.fi.muni.cz/apps/MathCalEval/canonicoutput/view/4380

Autoregenerate statistics on regular basis

Implement automatic recalculation of statistics every night. (See #14.)

Statistics are calculated twice

Statistics are currently calculated twice at midnight.

Confirm submitting annotation

Confirm adding an annotation after clicking submit button, prevent submitting the same annotation twice

Mass import – fails with large number of input formulae

Mass import fails with large number (tested on 4972 input files) of input formulae with exception:

exception

org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.lang.IllegalArgumentException: Input buffer too short
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:973)
    org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:863)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

root cause

java.lang.IllegalArgumentException: Input buffer too short
    java.security.MessageDigest.update(MessageDigest.java:311)
    cz.muni.fi.mir.tools.Tools.SHA1(Tools.java:207)
    cz.muni.fi.mir.db.service.impl.FormulaServiceImpl.massFormulaImport(FormulaServiceImpl.java:173)
    cz.muni.fi.mir.db.service.impl.FormulaServiceImpl$$FastClassBySpringCGLIB$$1f6c9be3.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:711)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    cz.muni.fi.mir.db.service.impl.FormulaServiceImpl$$EnhancerBySpringCGLIB$$ef532298.massFormulaImport(<generated>)
    cz.muni.fi.mir.controllers.FormulaController.submitMassImport(FormulaController.java:266)
    cz.muni.fi.mir.controllers.FormulaController$$FastClassBySpringCGLIB$$7ec449c.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:640)
    cz.muni.fi.mir.controllers.FormulaController$$EnhancerBySpringCGLIB$$566bd164.submitMassImport(<generated>)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:690)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:876)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:863)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

With smaller number of formulae (test with 153) everything works as expected.

Proper meaning of 'isValid' tag

I think there are two approches to evaluating canonicalization validity:

Canonicalization is valid when I cannot imagine any better result (but this can change often and it could be tricky to evaluate canonicalization of invalid input formulae)
Canonicalization is valid when all canonicalization techniques implemented in current version are applied correctly and completely (e.g. number of mrow elements is minimal)

So which from these we actually use and shouldn't we add annotation tag for the other one?

update configuration

update configuration procedure creates new instance instead of updating the old one

Implement rating interface of canonicalization outputs

Implement user interface allowing users to mark canonicalization outputs as

valid canonicalization,
invalid canonicalization,
uncertain canonicalization, or
remove canonicalization result evaluation.

User activity tracking

It would be useful to track history of user actions ("Formula 123 annotated by user X" etc.)

Canonicalization timestamp

Start and stop time is not recorded when running canonicalizer on single formula.

Annotation removal

Allow users to remove annotations from a formula.

Implementation of statistics reports dashboard

Implement statistical reports showing

number of formulae in the system,
number of canonicalization results in the system
- number of successful/unsuccessful/unrated results (see #13).

Advanced formulae search / filtering

Browsing formulae in "explore" mode is inefficient (and it is going to be worse after importing more formulae), it would be useful to filter them by various criteria such as:

source document
conversion program used
number of canonicalization runs performed on them
annotation tags
containing MathML elements
search in formula content
search in notes and annotations
size of formula (number of elements or characters)

I consider this more important than searching similar formulae.

Language interface only in English

As we expect use of the application not only by Czech people I suggest to focus on the English user interface. Localization to other languages is not important (but should be possible).

Dynamic web page titles

HTML title of every web page should be constructed dynamically to describe content of the page (e.g. number of the show formula / conicalization result, list of formulae, etc.). It significantly helps with orientation in the web browser history, multitab browsing.

mass import

restore functionallity from previous commits that allows mass import.

Pagination for similarity & search results

Add functionality that would allow to paginate similarity results, because on huge results java runs out of heap memory.

Import – no values in menus

Import function provides users with empty list of values in ‘Source document’ and ‘Conversion program’ menus even though there these are defined.

The mass import function is not affected.

Cross similarity

If we select formula A and formulas a,b,c are found as match implement algorithm that would set for

a values A,b,c as similar
b values A,a,c as similar
c values A,a,b as similar

it would be good if there would be some kind of checkbox in modal window allowing to override this behaviour (make it one way only).

Application runs exception

Application runs exception ends up with exception:

exception

org.springframework.web.util.NestedServletException: Request processing failed; nested exception is javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: could not extract ResultSet
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:973)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

root cause

javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: could not extract ResultSet
    org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1763)
    org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1677)
    org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:458)
    cz.muni.fi.mir.db.dao.impl.ApplicationRunDAOImpl.getAllApplicationRuns(ApplicationRunDAOImpl.java:84)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl.getAllApplicationRuns(ApplicationRunServiceImpl.java:62)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$FastClassBySpringCGLIB$$9ea9ff26.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:711)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$EnhancerBySpringCGLIB$$608c187b.getAllApplicationRuns(<generated>)
    cz.muni.fi.mir.controllers.ApplicationRunController.list(ApplicationRunController.java:33)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:690)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:876)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

root cause

org.hibernate.exception.SQLGrammarException: could not extract ResultSet
    org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:123)
    org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
    org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
    org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
    org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:89)
    org.hibernate.loader.Loader.getResultSet(Loader.java:2065)
    org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1862)
    org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1838)
    org.hibernate.loader.Loader.doQuery(Loader.java:909)
    org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:354)
    org.hibernate.loader.Loader.doList(Loader.java:2553)
    org.hibernate.loader.Loader.doList(Loader.java:2539)
    org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2369)
    org.hibernate.loader.Loader.list(Loader.java:2364)
    org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:496)
    org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:387)
    org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:231)
    org.hibernate.internal.SessionImpl.list(SessionImpl.java:1264)
    org.hibernate.internal.QueryImpl.list(QueryImpl.java:103)
    org.hibernate.jpa.internal.QueryImpl.list(QueryImpl.java:573)
    org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:449)
    cz.muni.fi.mir.db.dao.impl.ApplicationRunDAOImpl.getAllApplicationRuns(ApplicationRunDAOImpl.java:84)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl.getAllApplicationRuns(ApplicationRunServiceImpl.java:62)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$FastClassBySpringCGLIB$$9ea9ff26.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:711)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$EnhancerBySpringCGLIB$$608c187b.getAllApplicationRuns(<generated>)
    cz.muni.fi.mir.controllers.ApplicationRunController.list(ApplicationRunController.java:33)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:690)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:876)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

root cause

org.postgresql.util.PSQLException: ERROR: column "applicatio0_.configuration_id" must appear in the GROUP BY clause or be used in an aggregate function
  Position: 100
    org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2103)
    org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1836)
    org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
    org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:512)
    org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:388)
    org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:273)
    com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:144)
    org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:80)
    org.hibernate.loader.Loader.getResultSet(Loader.java:2065)
    org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1862)
    org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1838)
    org.hibernate.loader.Loader.doQuery(Loader.java:909)
    org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:354)
    org.hibernate.loader.Loader.doList(Loader.java:2553)
    org.hibernate.loader.Loader.doList(Loader.java:2539)
    org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2369)
    org.hibernate.loader.Loader.list(Loader.java:2364)
    org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:496)
    org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:387)
    org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:231)
    org.hibernate.internal.SessionImpl.list(SessionImpl.java:1264)
    org.hibernate.internal.QueryImpl.list(QueryImpl.java:103)
    org.hibernate.jpa.internal.QueryImpl.list(QueryImpl.java:573)
    org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:449)
    cz.muni.fi.mir.db.dao.impl.ApplicationRunDAOImpl.getAllApplicationRuns(ApplicationRunDAOImpl.java:84)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl.getAllApplicationRuns(ApplicationRunServiceImpl.java:62)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$FastClassBySpringCGLIB$$9ea9ff26.invoke(<generated>)
    org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:711)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    cz.muni.fi.mir.db.service.impl.ApplicationRunServiceImpl$$EnhancerBySpringCGLIB$$608c187b.getAllApplicationRuns(<generated>)
    cz.muni.fi.mir.controllers.ApplicationRunController.list(ApplicationRunController.java:33)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:690)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:876)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:108)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)

The behaviour is the same no matter the formulae database is empty or not.

Analysis and Querying

Improve analysis and query algorithm, because now it works somehow random. Distance method is totally weird, so based on logs, tutorials or book see how to improve this method.