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How to test upload images with your own sandbox » History » Version 5

Amber Herold, 10/01/2010 03:22 PM

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h1. How to test upload images with your own sandbox
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Just had to do this so taking some notes:
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h2. *the objective*
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I have images that I want to upload located in my home directory.
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I want to use my sandbox on the web side of appion.
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I want to use the wrapper/appion snapshot/beta appion for the python parts. However you want to call it, I just need a recent version.
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I want to upload the images to my own private database that is located on the fly server.
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When the images are uploaded, I want them stored in my home directory rather than on /ami/data00.
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h2. *setup*
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h3. sinedon.cfg in home directory
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Make sure sinedon.cfg is in your home directory and the host, user and password correspond to your database.
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Make sure the projectdata and leginondata settings are set to the name of your db. 
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h3. leginon.cfg in home directory
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Make sure leginon.cfg is in your home directory and the images path is set to a folder in your home directory.
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h3. config.php located in your sandbox under myamiweb
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Make sure the database information matches what is found in sinedon.cfg.
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h2. *create the command*
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* open myamiweb
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 Go to fly/~your_username/myamiweb which has been set up per the following instructions...
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* Go to or create a project for your images to be uploaded into.
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* make sure there is a database set for the project (ex. ap123)
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* click on [upload images to new session]
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* Under the _directory containing images_ field copy the path to the images on your home directory ex. /home/your_username/dir1/dir2
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* Select _just show command_
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h2. *execute the command*
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Fly does not have the python parts installed.
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Guppy does not have access to your home directory to get the images.
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# ssh into amibox02 or amibox03 to run uploadimage.py
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# Copy and past the command that was provided by the web page into the terminal
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# Add the path to the wrapper installation to make sure you are executing the most recent version of the python code. 
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 This is probably /opt/myamisnap/bin/appion and it should be pre-pended to the command. 
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example:
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<pre>
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/opt/myamisnap/bin/appion uploadImages.py --projectid=268 --image-dir=/home/amber/uploadedimages/pairedimages --mpix=1E-09 --type=defocalseries --images-per-series=2 --defocus-list=-1E-10,-2E-10 --mag=50000 --kv=120 --description="defocal test" --jobtype=uploadimage
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</pre>