caleydo / neo4j-kshortestpaths-plugin Goto Github PK

Eclipse plugin calculates the k-shortest paths in a graph using Neo4j

Java 100.00%

neo4j-kshortestpaths-plugin's Introduction

Caleydo - Visualization for Molecular Biology

Caleydo is a visualization framework for molecular biology data. It is targeted at analyzing multiple heterogeneous but related tabular datasets (e.g., mRNA expression, copy number status and clinical variables), stratifications or clusters in these datasets and their relationships to biological pathways.

For user documentation please refer to the Caleydo Help. For general information and downloads based on binaries please use the Caleydo Website. This guide assumes that you want to install Caleydo from source.

Installation

Caleydo uses Java, OpenGL and the Eclipse Rich Client Platform (RCP). Things you need to install before being able to run Caleydo:

Eclipse Kepler for RCP and RAP Developers, which you can get from the eclipse download page. Other Eclipse versions won't work.
Install EGit in Eclipse using software updates.
Java SDK >= 1.7

To install Caleydo use EGit within Eclipse and clone the repository. Each directory in the caleydo-dev folder corresponds to an Eclipse project. Here is a good tutorial on how to import Eclipse projects from git.

If you want to use ssh (instead of https) for communicating with github out of eclipse follow these instructions. You will have to generate a new RSA key and save it to you ~/.ssh folder. Remeber to set a passphrase for you key. This will result in a file ida_rsa and ida_rsa.pub turning up in your ssh folder. Save your public rsa key with your eclipse account folder.

When cloning the repository follow the above tutorial. Don't change the username "git" to your username!

Team

Caleydo is an academic project currently developed by members of

Institute for Computer Graphics and Vision at Graz University of Technology, Austria
Institute of Computer Graphics at Johannes Kepler University Linz, Austria
Pfister Lab at the School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
Park Lab at Harvard Medical School, Boston, USA

Acknowledgements

Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

Bubble Sets - A Java implementation of the visualization technique.
CDK - The Chemistry Development Kit.
JGrahT - A graph library.
Jogl - Java bindings for OpenGL.
PathVisio - loading and parsing WikiPathways.
WordHoard - statistical utilities.

Bioinformatics Resources

David Bioinformatics Resources - Gene ID mapping.
KEGG - Pathways.
WikiPathways - Pathways.

Datasets

CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
TCGA - The Cancer Genome Atlas.

Resources

GitHub - Hosting our source code.
WebStorm - Free developer licenses for our web projects from JetBrains.

neo4j-kshortestpaths-plugin's People

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neo4j-kshortestpaths-plugin's Issues

problem in accessing the kshortestpath service

Hi after following the steps for building the project and storing jar file in neo4j plugin directory and then clicking http://localhost:7474/db/data/ext/KShortestPaths/graphdb/kShortestPaths

I get the following error:

No such ServerPlugin: "KShortestPaths"
PluginLookupException
	At org.neo4j.server.plugins.PluginManager.extension (PluginManager.java:114)
	At org.neo4j.server.plugins.PluginManager.describe (PluginManager.java:123)
	At org.neo4j.server.rest.web.ExtensionService.describeGraphDatabaseExtension (ExtensionService.java:318)
	At org.neo4j.server.rest.web.ExtensionService.getGraphDatabaseExtensionDescription (ExtensionService.java:169)
	At java.lang.reflect.Method.invoke (Method.java:497)
	At org.neo4j.server.rest.transactional.TransactionalRequestDispatcher.dispatch (TransactionalRequestDispatcher.java:147)
	At org.neo4j.server.rest.dbms.AuthorizationEnabledFilter.doFilter (AuthorizationEnabledFilter.java:122)
	At org.neo4j.server.rest.web.CollectUserAgentFilter.doFilter (CollectUserAgentFilter.java:69)
	At java.lang.Thread.run (Thread.java:745)

what should I do?

Rest API call [POST] giving BadInputException

As given in README file, I queried the API endpoint

[GET] http://localhost:7474/db/data/ext/KShortestPaths/graphdb/kShortestPaths

provided output:

{'extends': 'graphdb', 'name': 'kShortestPaths', 'parameters': [{'type': 'node', 'optional': False, 'name': 'source', 'description': 'Source node of the path'}, {'type': 'node', 'optional': False, 'name': 'target', 'description': 'Target node of the path'}, {'type': 'integer', 'optional': False, 'name': 'k', 'description': 'The max number of paths to retrieve'}, {'type': 'string', 'optional': True, 'name': 'costFunction', 'description': 'Javascript cost function to determine the cost of an edge'}, {'type': 'string', 'optional': True, 'name': 'constraints', 'description': 'constraints'}], 'description': 'get the k shortest paths from source to target'}

Expected Parameters are : Source (Node) , Target(Node) , K(integer) as mandatory parameters

My problem is how do I ,using REST API, provide Node type object as input? It should be NodeID or it should accept a standard JSON Object as returned by Neo4j GetNode REST API Call.

This makes the plugin unusable outside Java environment. I am using Neo4j with Python and hence cannot use this plugin

cannot build package using maven

Apache Maven 3.0.5
Maven home: /usr/share/maven
Java version: 1.8.0_111, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-8-oracle/jre
Default locale: en_IN, platform encoding: UTF-8
OS name: "linux", version: "4.4.0-45-generic", arch: "amd64", family: "unix"

Tested for neo4j-community-2.3.2 and neo4j-enterprise-3.1.0 separately
NEO4J_HOME is set to neo4j install directory
PATH and CLASSPATH have the path to the lib folder of the neo4j database

====ERROR===
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /home/priyank/workspace/crowdLogistics/neo4j-kshortestpaths-plugin/src/main/java/org/caleydo/neo4j/plugins/kshortestpaths/constraints/RegionRelation.java:[7,25] package org.neo4j.graphdb does not exist
[ERROR] /home/priyank/workspace/crowdLogistics/neo4j-kshortestpaths-plugin/src/main/java/org/caleydo/neo4j/plugins/kshortestpaths/constraints/IPathConstraint.java:[6,25] package org.neo4j.graphdb does not exist
[ERROR] /home/priyank/workspace/crowdLogistics/neo4j-kshortestpaths-plugin/src/main/java/org/caleydo/neo4j/plugins/kshortestpaths/constraints/IPathConstraint.java:[9,52] cannot find symbol
symbol: class Path

==========
Full log in attached file
log.txt

Any documentation for costFunction or constraints?

Hi guys,

I was wondering if you had any documentation(or examples) on how to use the costFunction and constraints field. Specially for the constraints field.

Thanks!