How to test upload images with your own sandbox » History » Version 7
Amber Herold, 10/01/2010 03:27 PM
| 1 | 1 | Amber Herold | h1. How to test upload images with your own sandbox |
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| 4 | Just had to do this so taking some notes: |
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| 6 | 6 | Amber Herold | h2. +the objective+ |
| 7 | 1 | Amber Herold | |
| 8 | 4 | Amber Herold | I have images that I want to upload located in my home directory. |
| 9 | 1 | Amber Herold | I want to use my sandbox on the web side of appion. |
| 10 | 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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| 11 | I want to upload the images to my own private database that is located on the fly server. |
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| 12 | When the images are uploaded, I want them stored in my home directory rather than on /ami/data00. |
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| 15 | 6 | Amber Herold | h2. +setup+ |
| 16 | 1 | Amber Herold | |
| 17 | h3. sinedon.cfg in home directory |
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| 19 | Make sure sinedon.cfg is in your home directory and the host, user and password correspond to your database. |
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| 20 | Make sure the projectdata and leginondata settings are set to the name of your db. |
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| 22 | h3. leginon.cfg in home directory |
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| 24 | 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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| 26 | 5 | Amber Herold | h3. config.php located in your sandbox under myamiweb |
| 27 | 1 | Amber Herold | |
| 28 | 5 | Amber Herold | Make sure the database information matches what is found in sinedon.cfg. |
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| 30 | 6 | Amber Herold | h2. +create the command+ |
| 31 | 5 | Amber Herold | |
| 32 | 1 | Amber Herold | * open myamiweb |
| 33 | 7 | Amber Herold | Go to fly/~your_username/myamiweb which has been set up per the instructions found under _Use Cronus3 or Fly to view your web app_ in the [[AMI_ |
| 34 | 1 | Amber Herold | |
| 35 | * Go to or create a project for your images to be uploaded into. |
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| 36 | * make sure there is a database set for the project (ex. ap123) |
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| 37 | * click on [upload images to new session] |
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| 38 | * 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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| 39 | * Select _just show command_ |
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| 41 | 6 | Amber Herold | h2. +execute the command+ |
| 42 | 2 | Amber Herold | |
| 43 | Fly does not have the python parts installed. |
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| 44 | 3 | Amber Herold | Guppy does not have access to your home directory to get the images. |
| 45 | 2 | Amber Herold | |
| 46 | # ssh into amibox02 or amibox03 to run uploadimage.py |
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| 47 | # Copy and past the command that was provided by the web page into the terminal |
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| 48 | # 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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| 49 | This is probably /opt/myamisnap/bin/appion and it should be pre-pended to the command. |
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| 51 | example: |
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| 52 | <pre> |
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| 53 | /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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| 54 | </pre> |