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MOLGENIS is an collaborative open source project on a mission to generate great software infrastructure for life science research.
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Merge pull request #2699 from dennishendriksen/feature/restwritable

REST entity meta: add writable property
latest commit fdd21a11c5
@tommydeboer tommydeboer authored
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molgenis-annotators Fix annotators for the new Data-API + add username to logging and pro…
molgenis-app change the xcategorialmrefnillable_value column name to
molgenis-catalogue Bump MOLGENIS v1.4.0-SNAPSHOT to v1.5.0
molgenis-charts Merge branch 'master' of https://github.com/molgenis/molgenis into fe…
molgenis-core-ui Fix #2695 Attribute with auto=true broken for DATE and DATE_TIME data…
molgenis-core Merge pull request #2668 from dennishendriksen/feature/categoricalmref
molgenis-das Bump MOLGENIS v1.4.0-SNAPSHOT to v1.5.0
molgenis-data-annotators Eclipse formatting + use the new utility class
molgenis-data-csv Added method hasRepository
molgenis-data-elasticsearch add/update test cases
molgenis-data-examples Added method hasRepository
molgenis-data-excel Fix #2602
molgenis-data-googlespreadsheet Fix #2602
molgenis-data-import Add String type to list
molgenis-data-jpa Merge branch 'master' of https://github.com/molgenis/molgenis into fe…
molgenis-data-mapper Fix #2674 Eclipse overwrites filtered resources with incorrectly filt…
molgenis-data-merge Fix for github issue #2621
molgenis-data-mysql Fixes after comments
molgenis-data-rest-client src/test/resources -> src/test/java for the demo code
molgenis-data-rest update doc
molgenis-data-semanticsearch typo
molgenis-data-system Implement molgenis autoid for JPA so we can upload JPA entities
molgenis-data-vcf Fixed: #2660 No WRITE permission on entity when importing VCF as norm…
molgenis-data Fix #2695 Attribute with auto=true broken for DATE and DATE_TIME data…
molgenis-dataexplorer Fix Landing on a datae-explorer plugin after login results in errors
molgenis-disease-matcher Bump MOLGENIS v1.4.0-SNAPSHOT to v1.5.0
molgenis-js Fix Date conversion from and to JS + unittest.
molgenis-model-registry Merge branch 'master' of https://github.com/molgenis/molgenis into fe…
molgenis-ontology-core Merge pull request #2649 from tommydeboer/fix/2602
molgenis-ontology Fix ontology and ontology-core unit tests on windows
molgenis-pathways Fix #2674 Eclipse overwrites filtered resources with incorrectly filt…
molgenis-python Bump MOLGENIS v1.4.0-SNAPSHOT to v1.5.0
molgenis-r Merge branch 'master' of github.com:molgenis/molgenis
molgenis-scripts Merge branch 'master' of https://github.com/molgenis/molgenis into fe…
molgenis-security-core added none to Permissions enum
molgenis-security Add RunnableAsSystem class.
.gitignore Add factory path to git ignore file
LICENSE add license
README.md Add instructions to configure eclipse's annotation processing to sync…
eclipse-java-molgenis-style.xml eclipse molgenis java code formatter: insert new line after annotatio…
eclipse-javascript-molgenis-style.xml tweak settings: less padding and line breaks
pom.xml Add generated resources to jar/war

README.md

Build Status

Welcome to MOLGENIS

MOLGENIS is a collaborative open source project on a mission to generate great software infrastructure for life science research.

The procedure below tells you how to checkout the molgenis project and build one of the example apps.

1. Install software needed

install java8 JDK (not JRE) from http://www.oracle.com/technetwork/java/javase/downloads/index.html

install eclipse (we used Luna) from https://www.eclipse.org/downloads/

install mysql from (we used 5.6.23 DMG) http://dev.mysql.com/downloads/mysql/

install git from http://git-scm.com/download/

2. Configure mysql

open terminal and start mysql client (command differs in Windows, Linux, Mac):

/usr/local/mysql/bin/mysql -u root

in mysql client create database and permissions via command:

create database omx;
grant all privileges on omx.* to molgenis@localhost identified by 'molgenis';
flush privileges;

3. Configure Eclipse

start Eclipse from the commandline (via Dock will not work!)

when asked, create fresh workspace folder (not same folder as git!)

go to 'Help' -> 'Eclipse market place'

find and install plugins:

  • 'JBoss Tools', during install only select Freemarker IDE
  • 'TestNG for Eclipse'
  • 'm2e-apt'

go to 'Eclipse' -> 'Preferences' -> 'installed JREs' and select 'java 8' go to 'Eclipse' -> 'Preferences' -> 'Maven' -> 'Annotation Processing' and select 'Automatically Configure JDT APT'

4. Get the code

create acount on github.com

'fork' on http://github.com/molgenis/molgenis

copy the cloneURL

open terminal (mkdir if needed) and type

cd ~/git 
git clone http://github.com/[YOURACCOUNT]/molgenis

Optionally select stable molgenis version:

git fetch --tags origin
git checkout -b <tag name: see https://github.com/molgenis/molgenis/releases>

More information about forking can be found here: https://help.github.com/articles/fork-a-repo

5. Configure the default admin password

Create the directory ~/.molgenis/omx and create a file called molgenis-server.properties in this folder (~ is your home folder)

Add user and database properties to this file, such as this example:

db_user=molgenis
db_password=molgenis
db_uri=jdbc:mysql://localhost/omx
admin.password=admin
user.password=admin

If these properties are not present, the MolgenisDatabasePopulator will fail (RuntimeException). This properties-file should be in your home folder, if the file is not there yet, just create it.

6. Import, build and run MOLGENIS in Eclipse

In eclpise, if still open, close the 'Welcome' screen.

Choose 'File' -> 'Import' -> 'Import existing Maven projects'

Browse to your /git/molgenis directory

Select (and wait to install all kinds of maven connectors)

Right mouse 'molgenis' -> Run as -> Maven install.

Right mouse 'molgenis-app' -> Run as -> Maven build ... -> in goals type 'jetty:run' and push run button

Open your browser at http://localhost:8080/

You should see the application. Login as 'admin', 'admin' to be able to upload and view data, create users, etc etc.

7. Keep your code up to date

Add the original molgenis repository as a remote location.

cd ~/git/molgenis
git remote add blessed https://github.com/molgenis/molgenis.git

Perform regular updates so the latest changes are merged with your local clone.

git pull blessed master

And push back any merges or commits of your own to your online fork.

git push origin master

8. Troubleshooting

When I build I get maven build error 'env not available'.

Solution: start Eclipse from commandline.

When I try to start an application, the console tells me 'Address already in use'!

Run the Maven target 'jetty:stop'. If that does not help, use your opering systems process manager to kill anything running on port 8080. For example:

kill -9 `lsof -i :8080 -t`
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