HDF Server is a Python-based web service that can be used to send and receive HDF5 data using an HTTP-based REST interface.
Python packages required: NumPy 1.10.4 or later h5py 2.5 or later tornado 4.0.2 or later watchdog 0.8.3 or later * requests 2.3 or later (for client tests)
a.) Install Anaconda
conda create -n h5serv python=2.7 h5py tornado requests pytz activate h5serv pip install watchdog
b.) Clone the hdf5-json project:
git clone https://github.com/HDFGroup/hdf5-json.git cd hdf5-json/ python setup.py install
c.) Clone the h5serv project:
git clone https://github.com/HDFGroup/h5serv.git cd h5serv/server/ python app.py
The server would start running. This would be indicated by the output - Starting event loop on port: 5000
a.) Launch an AWS Instance
b.) Perform the above mentioned steps to install the HDF server in the instance.
c.) Run the server
cd h5serv/server python app.py
The server would start running. This would be indicated by the output - Starting event loop on port: 5000
To verify that the h5serv was installed correctly:
Open a new terminal[for local installation] / Launch the AWS instance again [for installation on AWS instance]
Run Anaconda command prompt
source activate h5serv cd h5serv/test python testall.py
This would run a number of tests to verify the installation.
Currently, the HDF server has been installed and is running on : AWS Public AMI id: ami-4e77ac58
a.)With this AMI, launch an AWS instance. ( ssh -i /path/to/keyfile.pem ec2-user@publicipoftheinstance )
source activate h5serv cd hdf5-json/h5serv/server/ python app.py
b.)Launch the instance again in a separate terminal.
cd scripts python tall_test.py
For example, if we want to get the assays.h5 file (for geuFPKM data) from our local machine onto the server running on an instance:
scp -i/path/keyfile.pem /path/assays.h5 ec2-user@publicipoftheinstance:/hdf5-json/h5serv/data/
The file placed in the /data folder gets picked up by the server and it generates a domain name. e.g: for the assays.h5 file, domain name : assays.hdfgroup.org.
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