pySPECCHIO is a Python interface and command line utility to upload raw data such as spectra and metadata into the SPECCHIO spectral information system. It uses the JPype Python-Java bridge package to communicate with the SPECCHIO API (written in Java by the SPECCHIO developers).
pySPECCHIO is currently configured to work with a specific field campaign at the University of Edinburgh, but you are welcome to fork and modify it for your own use.
- You must have the SPECCHIO java interface installed. You can either use the Virtual Machine supplied from the SPECCHIO website, or download the java interface (client) from the website and install it following the instructions on the site.
(The installation procedure does not require root/admin access rights - you can install it to your home directory following the instructions in the pdf/SPECCHIO website.)
http://specchio.ch/app_download.php
The SPECCHIO_ReleaseNotes.pdf document contains instruction on how to set up, create a user account, and test the connection.
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You must have made an initial connection to the database using the java client in step 1, and created a user account.
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Setting the environment variable to the directory path:
pySPECCHIO now requires you to set an environment variable, telling it where to find the specchio-client.jar file, installed above. You can set this as follows from the linux command line/terminal:
export SPECCHIO_JAVA_CLIENT=[FULL PATH TO INSTALLATION OF .JAR FILE]
e.g.:
export SPECCHIO_JAVA_CLIENT=/home/dvalters/specchio2019_test/SPECCHIO_java/specchio-client.jar
The python program depends on this environment variable being set. To avoid having to redo this step each time you open a new terminal window or session. you can add the above line to your ~/.bashrc file.
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Adding the database columns/headings. (TO FOLLOW)
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Having configured the above, you can now proceed to use the pySPECCHIO python program. To do this, download or clone this git repository and follow the Documentation