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**Ocean Observatories Initiative Cyberinfrastructure**
**Integrated Observatory Network (ION)**
eoi-services - Classes and services for acquiring and publishing data from external sources
(C) UC Regents, 2010-2012
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This project contains modules, utilities, and services for acquisition of data from external sources within the OOICI-ION infrastructure. The repository is first and foremost a framework, designed to be extended with concrete implementations that facilitate data acquisition from specific data sources. However, it also contains concrete External Data Handler implementations for the services listed below:
- DAP
- WaterOneFlow (not yet, but very soon!)
Additional concrete implementations may be added to this repository over time. The repository can also be used as a library to allow implementation of concrete External Data Handlers by other projects.
References
EOI Development Page
EOI Architecture Page
#Prerequisites
This assumes basic development environment setup (git, directory structure). Please follow the "New Developers Tutorial" for basic steps.
Pyon: The main dependency of this repository is the pyon Capability Container. Follow the listed steps to install the minimal needed dependencies to run pyon on a Mac. For more details and Linux install instructions, check out the pyon README
Install the following if not yet present:
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git 1.7.7: Download the Mac or Linux installer and run it
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OS Packages and package management: For Mac, use homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.github.com/gist/323731)"
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python 2.7 see below for installation
- couchdb 1.1.0 (optional if memory mockdb is used) see below for installation
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rabbitmq 2.6.1 or later (recommended, but can use rabbitmq on amoeba) Download generic Linux version and unpack into a suitable directory. Note: May need erl (Erlang) and some dependencies installed before
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Install libevent, libyaml, zeromq, couchdb, python, and rabbitmq with Homebrew
brew install libevent libyaml zeromq couchdb python rabbitmq
You can even reinstall git using brew to clean up your /usr/local directory Be sure to read the pyon README for platform specific guidance to installing dependent libraries and packages. Linux: Note that many installs have much older versions installed by default. You will need to upgrade couchdb to at least 1.1.0.
Python packages and environment management:
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pip
easy_install pip
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virtualenv and virtualenvwrapper modules for your python 2.7 installation
easy_install --upgrade virtualenv easy_install --upgrade virtualenvwrapper Note: This may require Mac's XCode (use XCode 3.3 free version)
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Setup a virtualenv to run COI-services (use any name you like):
mkvirtualenv --no-site-packages --python=python2.7 eoi Note: Do not use the pyon virtualenv if you are a pyon developer
###Compiled Library Dependencies hdf5 library
brew install hdf5
netcdf
brew install netcdf
###Other OOI-CI Project Dependencies
This project requires that both the pyon and coi-services projects are installed in the same directory as the pydap-handlers-ion project (typically the "Dev/code" directory if the OOI-CI development directory structure is used). These projects can be obtained using the following commands:
git clone git@github.com:ooici/coi-services.git
git clone git@github.com:ooici/pyon.git
#Source
Obtain the eoi-agents project by running:
git clone git@github.com:ooici-eoi/eoi-services.git
cd eoi-services
#Buildout
Build the project using buildout (don't miss the -d flag on the first command):
python bootstrap.py -d
bin/buildout
#Generate Interfaces and Submodules
Before unit tests will pass, the following commands must be run (See below for further information about submodules):
git submodule update
bin/generate-interfaces
#Unit and Integration Tests The unit and integration tests for this project can be run as follows. Note that the -v flag can be used to get verbose output (prints the name and result of each test that is run). The --with-coverage flag can also be added to view a test coverage report.
##Running the Unit Tests
The unit tests for this project only require that a rabbitmq broker be running:
bin/nosetests -a UNIT,group=eoi
##Running the Integration Tests
Currently, the integration tests are only "psuedo" integration tests - they do not rely on any other ION services at this point, but they do reach out to external data servers for data:
bin/nosetests -a INT,group=eoi
#Development
You can develop services locally in this repository. Use this repository until subsystem specific repositories are available.
Please follow the following steps as long as you are new:
Get the latest code before you start editing, or anytime you want:
git pull
git submodule update # Do NOT forget. This does not happen automatically
See below for an automated approach to git-submodules.
Once in a while, service interfaces change. Generate interfaces frequently (especially in case of error):
bin/generate-interfaces
Before defining objects, services in ./obj, or defining app and deploy files in ./res, checkout the master branch:
cd extern/ion-definitions
git status # Just to see what's going on
git checkout master # To track the master branch (enables update and later push)
git pull origin master # To get latest from the server
Note: The res/ and obj/ dirs are symlinks to a subdirectory in a git submodule. Beware of the pitfalls of git submodule. You need to treat it as a separate GIT module. In case of changes, both GIT modules must be pushed, submodule first:
cd extern/ion-definitions
git status # Just to see what's going on
git commit -am "Something smart"
git push origin master
cd ../.. # To the root of coi-services
git commit -am "Something smarter"
git push
Put your services in ion/services//... (subdirectories are allowed).
#Git Submodule Hooks
A git hook is a script that executes during various points of using git. Some simple hooks have been written to help automate dealing with submodules for most people. See the steps here: http://blog.chaitanyagupta.com/2009/08/couple-of-hooks-to-make-life-easy-with.html
They do require an initial setup. Simple instructions:
Clone this repository:
cd /some/tmp/directory
git clone https://github.com/chaitanyagupta/gitutils.git
Use the provided install script:
sh gitutils/submodule-hooks/install.sh /path/to/your/pyon/or/coi-services/dir
The install script does the following (you can also do it manually):
cd /your/pyon/.git/hooks
cp /your/tmp/gitutils/submodule-hooks/pre-commit pre-commit
cp /your/tmp/gitutils/submodule-hooks/post-merge-commit post-merge
ln -s post-merge post-checkout
chmod +x post-merge post-checkout pre-commit
Now, when checking out a branch, pulling, merging etc, git will prompt you to automatically update if it notices a change to the commit that your supermodule points to.
The pre-commit script is so you don't forget to push changes to the submodule BEFORE you push changes to the supermodule.