protegeproject / webprotege Goto Github PK

View Code? Open in Web Editor NEW

602.0 65.0 248.0 68.16 MB

The webprotege code base

License: Other

Java 83.04% CSS 0.66% HTML 0.37% JavaScript 15.90% Dockerfile 0.01% Shell 0.03%

ontology ontology-engineering knowledge-graph webapp owl obo ontologies rdf semantics knowledge-management

webprotege's Introduction

WebProtégé

PLEASE NOTE

This repository is in the process of being superceded with a collection of other, more fine-grained, repositories. We are moving WebProtégé to a microservice architecture and each microservice and each common library now has its own repository. While this repository still serves as the repository for the current WebProtégé release, all active development is now taking place in these repositories. You can read more about this on the WebProtégé Next Gen Wiki.

What is WebProtégé?

WebProtégé is a free, open source collaborative ontology development environment.

It provides the following features:

Support for editing OWL 2 ontologies
A default simple editing interface, which provides access to commonly used OWL constructs
Full change tracking and revision history
Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
Customizable user interface
Support for editing OBO ontologies
Multiple file formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)

WebProtégé runs as a Web application. End users access it through their Web browsers. They do not need to download or install any software. We encourage end-users to use

https://webprotege.stanford.edu

If you have downloaded the webprotege war file from GitHub, and would like to deploy it on your own server, please follow the instructions at:

https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation

Building

To build WebProtégé from source

Clone the github repository

git clone https://github.com/protegeproject/webprotege.git

Open a terminal in the directory where you clone the repository to
Use maven to package WebProtégé
```
mvn clean package
```
The WebProtege .war file will be built into the webprotege-server directory

Running from Maven

To run WebProtégé in SuperDev Mode using maven

Start the GWT code server in one terminal window
```
mvn gwt:codeserver
```
In a different terminal window start the tomcat server
```
mvn -Denv=dev tomcat7:run
```
Browse to WebProtégé in a Web browser by navigating to http://localhost:8080

Running from Docker

To run WebProtégé using Docker containers:

Enter this following command in the Terminal to start the docker container in the background
```
docker-compose up -d
```
Create the admin user (follow the questions prompted to provider username, email and password)
```
docker exec -it webprotege java -jar /webprotege-cli.jar create-admin-account
```
Browse to WebProtégé Settings page in a Web browser by navigating to http://localhost:5000/#application/settings
1. Define the System notification email address and application host URL
2. Enable User creation, Project creation and Project import

To stop WebProtégé and MongoDB:

docker-compose down

Sharing the volumes used by the WebProtégé app and MongoDB allow to keep persistent data, even when the containers stop. Default shared data storage:

WebProtégé will store its data in the source code folder at ./.protegedata/protege where you run docker-compose
MongoDB will store its data in the source code folder at ./.protegedata/mongodb where you run docker-compose

Path to the shared volumes can be changed in the docker-compose.yml file.

webprotege's People

Contributors

Stargazers

Watchers

Forkers

netconstructor spclops irirnelnistor mever aidandelaney kublaj ivolazy kennisnet yuhaozhang imclab jabenitez88 sesuncedu benangmerah sparker360 chiralbehaviors pianyu prakharg14 shendrix cereynaud coderiot marcosmro zzhgit hammar jellevdster intrixius g-vidal grantpax boazavellar ecolife fx1061076658 shuanzi frictionlesscoin marcyborg visualdataweb daxid xsls yuriymilov yayan23fs zhou5852 mariamichou solo-code metaphorcode 0607060123 michaeljcompton brunifrancesco ch93 tribemedia mikeaddison93 chengxiaoxian jimsow digosisinfo lz930303 semanticnavigator denggeng maastroclinic rpietzsch netsquire indirabh pitcons furyphoenix sinodang hemed nkscorpion wendelas veneranda ismaelrh acidburn0zzz pass-o-guava sumpacle ndcroosthesis haochenluo confidentmachine sdiraimondo huobao36 rebrn titsuki fenggao86 mosence rogervaas jefwillems zzgulu epeter- light-city marlitosdev hggit igxactly zl520878 cjhurst luckyangle mdheller matthieus scismycat liangxiaojian910 imrankhan1984 zhangziliang04 chazu louisroehrs nikhitajatain drsnowbird nyamiou

webprotege's Issues

Hard coded links to the webprotege server are used in various places

Some places contain hard coded links to the webprotege server. This appears in some end user facing places (e.g. in comments).

Notes that have empty bodies are not saved

Add a new note to an entity with a blank subject line. The note does not get saved.

It should be possible to specify a license for a project

Class hierarchy does not always refresh when deleting classes

It seems that if I delete a class by pressing the delete button, there are some UI issues. The node doesn't automatically disappear. If I press the refresh button (in the UI, not the browser), in at least some cases, ALL classes disappear from the UI, which is rather scary. Pressing refresh again seems to bring them back as expected.

NullPointer exception thrown in NotesManager

Caused by: java.lang.NullPointerException at edu.stanford.bmir.protege.web.server.notes.OWLAPINotesManagerNotesAPIImpl.setNoteStatus(OWLAPINotesManagerNotesAPIImpl.java:243) at edu.stanford.bmir.protege.web.server.notes.SetNoteStatusActionHandler.execute(SetNoteStatusActionHandler.java:28) at edu.stanford.bmir.protege.web.server.notes.SetNoteStatusActionHandler.execute(SetNoteStatusActionHandler.java:18) at edu.stanford.bmir.protege.web.server.dispatch.AbstractHasProjectActionHandler.execute(AbstractHasProjectActionHandler.java:47) at edu.stanford.bmir.protege.web.server.dispatch.impl.DefaultDispatchServiceExecutor.execute(DefaultDispatchServiceExecutor.java:34) at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceImpl.executeAction(DispatchServiceImpl.java:34) at sun.reflect.GeneratedMethodAccessor298.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:561) ... 22 more

Allow email addresses to be reused over multiple accounts

At the moment the relationship between account name and email address is one-to-one. It should be possible to specify the same email address for multiple accounts. Some consideration is needed, because there is some code which looks up user accounts by email address!

edu.stanford.bmir.protege.web.shared.user.UserEmailAlreadyExistsException: User email address already exists: [email protected] at edu.stanford.bmir.protege.web.server.LocalMetaProjectManager.registerUser(LocalMetaProjectManager.java:100) at edu.stanford.bmir.protege.web.server.AccessPolicyManager.createTemporaryAccountForInvitation(AccessPolicyManager.java:666) at edu.stanford.bmir.protege.web.server.SharingSettingsServiceImplP3Delegate.sendEmailInvitation(SharingSettingsServiceImplP3Delegate.java:206) at edu.stanford.bmir.protege.web.server.SharingSettingsServiceImplP3Delegate.createUsersBySharingSettingMap(SharingSettingsServiceImplP3Delegate.java:186) at edu.stanford.bmir.protege.web.server.SharingSettingsServiceImplP3Delegate.updateSharingSettings(SharingSettingsServiceImplP3Delegate.java:146) at edu.stanford.bmir.protege.web.server.SharingSettingsManager.updateSharingSettings(SharingSettingsManager.java:52) at edu.stanford.bmir.protege.web.server.SharingSettingsServiceImpl.updateSharingSettings(SharingSettingsServiceImpl.java:21)

Only project owners can change the status of notes

It should be possible for anyone with write access to change the status of notes

Pressing Enter on a Multi-line primitive data editor when the suggest box is showing causes a new line to be added rather than accepting the suggestion

Pressing Enter on a Multi-line primitive data editor when the suggest box is showing causes a new line to be added rather than accepting the suggestion.

Support custom IRI suffix generation

IRI generation cannot be configured via the UI. This needs to be supported.

MongoDB default port is wrong

The default port for mongodb, as specified in WebProtegePropertyName, is incorrect. It should be 27017.

Inverse properties cannot be edited in the UI

It's not possible to edit inverse properties in WebProtege.

Provide a mechanism for permanently deleting projects

At the moment projects cannot be deleted - they can only be moved to the trash. Some people have asked for the possibility to permanently delete projects. Moving things to the trash ensures that projects can be recovered - we need to decide if permanent delete is really necessary.

Clicking to autocomplete in primitive data editor can cause the field to go blank

If I'm creating a Property, and start typing in the Annotations Property Name box, then select an item (e.g., rdfs:comment) with the mouse, then the partial property name disappears and I seemingly create an annotation of name empty-string, which is not so good. I get a little yellow popup box saying "! is a new property name". I'd expect that the field should properly autocomplete here. Thanks.

Drag and Drop is not available in the property hierarchy

Hi. I mistakenly created a Property in the wrong place in the property hierarchy. It doesn't seem like the UI lets me move that property to the right place. It does look like I can move Classes elsewhere in that hierarchy, so I was a bit surprised to see this. As it is, I think the only thing I can do is to delete the property and recreate it in the right place. Would love to see drag-and-drop functionality work here.

Add option to prevent UI reconfiguration

One can disable closing a tab with the param:

closable
false

Portlets however do not expose this parameter.
It would be more consistent if this option is also enabled for indivual portlets, so one can truely disable (client side) interface modifications .

Add support for preconfigured properties on the entity edit form

Users should be able to specify a set of properties (e.g., rdfs:label, comment, skos:label, etc.) that should always show up on an entity edit form (classes, properties and individuals).

@symbols in literals are parsed into language tags

See the OWLDataFactory docs for the reason why. This shouldn't happen in the WebProtege UI though.

Unloadable Imports prevent project upload

When creating a project by uploading an ontology, if an import cannot be loaded the UnloadableImportException gets thrown and halts loading. It might be best to have silent missing import handling turned on.

Focus lost after entering a property value

Currently, tabbing out of the Annotations Name field properly goes to the Description text box, but tabbing out of the Description text box fails to go to the language text box. It appears as if control is getting captured by some code -- perhaps the Project Feed?

Searching within a portlet actually searches the whole ontology

The search box within a portlet (e.g. individuals portlet) exposes all possible results within the ontology.

Logical behaviour would be to expose only results displayed within the portlet.

Download project downloads an empty zip file

download project (from new created project) results in empty zip-file.
download from uploaded project works fine.

(running: local webprotege build 105, debian wheezy, tomcat 6, firefox 23.0.1)

Side bar postit notes are not configurable

It should be possible to add/edit/delete side bar postit notes.

The default layout is to large for lower screen resolutions

The total portlet height by default needs to be about 570 for common lower screen resolutions.

It should be possible to hide the "Create project" and "Upload project" buttons.

These only get shown at sign in. Perhaps related to permissions.

Support the configuration of multiple classes for the Individuals List portlet through the showOnlyClass property

Changed the label to enhancement based on detailed comment.

Currently, showOnlyClass works only for a particular class: the instance list portlet will display only the instances of that particular class.

The request is to support the display of instances of multiple classes, meaning that showOnlyClass should be able to take a list of classes as a value (it should be probably renamed to showOnlyClasses). The portlet would then show the union of the instances of all classes, which are values of the showOnlyClass property.

Download project fails

Hello,

I have installed webprotege_2013.07.24-105 in windows 7. I am not able to download projects. When I click the download icon I got the following error message.

type Exception report

message

description The server encountered an internal error () that prevented it from fulfilling this request.

exception

java.lang.NullPointerException
edu.stanford.bmir.protege.web.server.owlapi.change.OWLOntologyChangeRecordList.iterator(OWLOntologyChangeRecordList.java:95)
edu.stanford.bmir.protege.web.server.owlapi.change.Revision.iterator(Revision.java:216)
edu.stanford.bmir.protege.web.server.owlapi.change.OWLAPIChangeManager.getOntologyManagerForRevision(OWLAPIChangeManager.java:403)
edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.getOntologyManagerForRevision(OWLAPIProjectDocumentStore.java:452)
edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProjectRevision(OWLAPIProjectDocumentStore.java:178)
edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.createDownloadCacheIfNecessary(OWLAPIProjectDocumentStore.java:431)
edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProject(OWLAPIProjectDocumentStore.java:154)
edu.stanford.bmir.protege.web.server.filedownload.OWLAPIProjectDownloader.writeProject(OWLAPIProjectDownloader.java:51)
edu.stanford.bmir.protege.web.server.filedownload.FileDownloadServlet.doGet(FileDownloadServlet.java:34)
javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:65)

I appreciate your help.

Individuals List does not cause selection changes to be broadcast on key press

Pressing the up or down arrow keys in the Individuals List causes the selection in the list to change, but it does not cause the selection to be broadcast. Clicking with the mouse, however, does cause the selection to be changed and to be broadcast.

Updating the language tag for a property duplicates property

When editing a language attribute for a property, the property gets duplicated (one without language attribute, one with new value). Correct behaviour would be only one property with new entered language value.

(running: local webprotege build 105, debian wheezy, tomcat 6, firefox 23.0.1)

Editing an existing name in the primitive data editor causes the field to go blank

e.g. type a name hasPhoneNumber and then try to edit this to hasPhone.

NullPointer exception when retrieving "related property values"

The exception below appeared in the logs.

Caused by: java.lang.NullPointerException at edu.stanford.bmir.protege.web.server.owlapi.GetRelatedPropertiesStrategy.execute(GetRelatedPropertiesStrategy.java:36) at edu.stanford.bmir.protege.web.server.owlapi.OntologyServiceOWLAPIImpl.getRelatedProperties(OntologyServiceOWLAPIImpl.java:771) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:561) ... 22 more

It should be possible to hide the "Create account" and "Login" links

Requested by a user who wants a read only mode.

Disjoint classes axioms cannot be edited

There is no functionality for editing disjoint classes axioms. We need to consider nary disjoint classes axioms.

Add form widget for editing plain literals

Is currently not possible to edit the language tags in the property field widgets

Restrictions portlet should be called "Conditions Portlet"

The "Restrictions" name in the portlet menu does not match the name of the portlet "Conditions". (Restrictions are also a specific kind of class expression, and this portlet supports editing arbitrary class expressions).

Entity IRIs should not encode the entity type in the IRI prefix

WebProtege generates entity IRIs that encode the entity type in the IRI prefix. For example, http://webprotege.stanford.edu/classes/X. This isn't necessarily desirable and should probably be turned off by default.

CTRL+ENTER accelerator on Create Entity dialog is not intuitive

The create entity dialog accepts multiple lines, with one line for each entity that is being created. This requires the accelerator key to be CTRL+ENTER, which isn't exactly intuitive.

Make OAI and ORE builtin vocabularies

Currently dublin core (dc) and simple knowledge organisation system (skos) are default supported. Similar extension for oai ore would be great. (or in case this is not opportune provide possibility to integrate)

There is no link to the WebProtege privacy policy on the home screen.

Trying to download an empty, unopened project causes an error

Related to issue #33

Steps to reproduce:

Create an empty project. Do not open it.
Try to download the project. Observer that the download fails.

An exception is thrown on the server:

java.lang.NullPointerException: revisionRootOntology must not be null at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:208) at edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.applyRevisionMetadataAnnotationsToOntology(OWLAPIProjectDocumentStore.java:449) at edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProjectRevision(OWLAPIProjectDocumentStore.java:188) at edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.createDownloadCacheIfNecessary(OWLAPIProjectDocumentStore.java:437) at edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProject(OWLAPIProjectDocumentStore.java:160) at edu.stanford.bmir.protege.web.server.filedownload.OWLAPIProjectDownloader.writeProject(OWLAPIProjectDownloader.java:51) at edu.stanford.bmir.protege.web.server.filedownload.FileDownloadServlet.doGet(FileDownloadServlet.java:34) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:487) at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1097) at edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:65) at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1088) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:360) at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:181) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:729) at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:405) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) at org.mortbay.jetty.handler.RequestLogHandler.handle(RequestLogHandler.java:49) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) at org.mortbay.jetty.Server.handle(Server.java:324) at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:505) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:829) at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:513) at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:211) at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:380) at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:395) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:488)

It is not possible to customise the IRI prefix used for entity IRIs

It should be possible to configure the prefix used in entity IRIs. At the moment it is essentially hard coded (as far as the end user is concerned) to http://webprotege.stanford.edu/entities.

Usage portlet height is too small by default

The Usage portlet height is very small. The default height should be more.

Support revision reversion

It should be possible to revert to a previous revision.

WebProtege sometimes generates IRIs that require custom prefix generation when saving to RDF/XML

Consider the following IRI as a property IRI

http://webprotege.stanford.edu/8gQAvsFVAjAj7tQR77pJGi
�
If this IRI is used in a property assertion then an RDF/XML serializer has to generate a QName from it (so it's possible to have an XML element name that gets expanded to the IRI on parsing). Because this IRI contains a number directly after the last forward slash a render will have to generate something like http://webprotege.stanford.edu/8 as a prefix (say with the prefix wp) and gQAvsFVAjAj7tQR77pJGi as a non-colonized name so that wp:gQAvsFVAjAj7tQR77pJGi can be generated as a QName. This can get quite yucky and should probably be fixed.

Some buttons look strange on webkit based browsers

The WebProtege L&F CSS needs adjusting as some of the buttons aren't rendered correctly on webkit based browsers (e.g. Safari).

Should be like this

The problem is with the linear-gradient background. Webkit browsers need a -webkit- prefix.

Accessors for DB port and host are missing on WebProtegeProperties

Search results aren't ordered (alphabetically or otherwise)

Search results should at least be ordered alphabetically

There should be an option for showing frames that are from asserted superclasses of the selected class

The simple UI shows the frame for the selected class. It should also show the frames for the asserted superclasses.

There is no link to the WebProtege terms of use on the home screen

Allow display language tag to be specified

(Was: Allow 'Display name' contents to display non-english terms)

Value from rdfs:label is used for display name. This is automatically the attribute with 'en' language attribute.
It would be an improvement if can choose a different language for defaulting the display name to. In our case this could easily be a server configuration setting (rather than a project configuration setting).

Multi-ontology upload is not supported

It isn't possible to upload multiple ontologies into a project.