Leginon

Hi Cheri,
Your error message indicates that there is not a scope or camera set up for Appion. This should be set up for you automatically during installation for Appion 2.0 or later, so I assume you are using an older version.
You will need to add some values for these fields. It is not important what you enter as it will not affect your upload, but they do need to exist.

To set them:
1. Go to browse to myamiweb/ to view the Appion and Leginon Tools home page.
2. Select the Administration tool
3. Select Instruments
4. Add new instruments AppionTEM and AppionCamera as shown in the attached screenshots
5. Set the Host, Instrument Host,Scope and Camera as shown in the screenshots.

Then try your upload again. When you upload images you can specify the absolute path such as /home/amber/images/imagesToUpload, but the processing server (where the appion python scripts are installed) does need to have access to the path that you specify. In other words, if you are logged into the processing server, you need to be able to change directories to the images you wish to upload.

If you are still having trouble after that please let me know!

Well, I was able to add AppionCamera and AppionTEM to the list on the left, but could not set host, instrument, camera across the top. I get an object not found error 404 medssage.

OK, you should be fine without those since they are used for Leginon rather than Appion. Try the upload again and when you see the command the important thing is that --scopeid and --cameraid parameters are set to the scope and camera that you added. I've attached a screenshot showing the command with these values set. If the command is not working you can check your database to make sure the id's in the command are the correct ones (let me know if you need instruction for this). If the ids are missing or incorrect, we will need to troubleshoot your installation.

Hello,

I have a similar problem. I am getting the following error message after attempting to upload images:

ERROR: Database does not contain instruments for appion image upload

I've tried to import instruments by going to Home > Administration > Instruments. I am able to add, but not remove, instruments (the "Remove" button does not work for me). I therefore have several copies of "AppionCamera" and "AppionTEM" in the left-hand column. How do I remove the duplicates?

Pressing the "Import" button gives me the following 404 error message:

Not Found

The requested URL /myamiweb/';echo $_SERVER['PHP_SELF']; was not found on this server.

Thanks for your help,
--Jason

Hi Jason, can you tell me a little more about your installation. Is it older, did you recently update to a newer version, or did you recently install for the first time? Do you know what version you have installed? It looks like your installation did not go quite right.

Also, please check the troubleshooting page to see if it reports any problems.

1. Go to the home page at myamiweb/
2. Click on the [test Dataset] link in the upper left region of the screen
3. You should see an image view with 2 images available and viewable - if not, there is a problem
4. Click on the [Troubleshoot] link in the upper left
5. There are several automated checks that occur.
6. Look for any bright red text. These indicate something that may need your attention, or may cause a problem. Toward the bottom of the page you should see 2 images displayed.

Let me know if the troubleshooter finds any problems.

Also, the Remove button for the instruments may have been disabled intentionally by us. I do not believe it will cause a problem to have duplicates, but I can look into it further if everything else checks out ok.

Thanks,
Amber

Hi Jason,
It looks like perhaps the database initialization code was not run during installation.

Please try running the initialization.
1. browse to YOURHOST/myamiweb/setup
2. Enter your database username and password - if you do not know it, it is listed in the myamiweb/config.php file. You will need access to the web directory to view the file. They are listed under DB_USER and DB_PASS.
3. Just click the next buttons through the wizard. Stop when you get to step 6 "Review Your Setup"
4. Press the "DB Initialization" button located at the top of the page. I have attached an image indicating its location.

If you recieve a message saying the initialization is only required for new Installations and you do not need to do anything, we may need to add the instrument information to your database manually.
Otherwise, try the upload again.

If you have installed PHPMyAdmin, or you are savvy with MySQL, you can check the database directly to ensure the instuments have been added correctly. Here is the data that you should see if the installation is correct (in xml format):
<sqltable name="InstrumentData" >
<field name="name" >AppionTEM</field>
<field name="hostname" >appion</field>
<field name="type" >TEM</field>
</sqltable>
<sqltable name="InstrumentData" >
<field name="name" >AppionCamera</field>
<field name="hostname" >appion</field>
<field name="type" >CCDCamera</field>
</sqltable>

Let me know if you need help adding these values manually if the automatic initialization does not work.

Thanks,
Amber