Script param

[evenhuis]

Replacing hard-coded variables in scripts

Issue

• storing username and passwords in the script or in credentials. txt are real security risk:

  • many OMERO servers use LDAP so the name username/password is single-sign for whole institution
  • storing passwords in plain text is poor practice
  • high risk of committing a file with username +password to a GitHub repo

• Less reuse of script of each script needs to be altered for user, imageID etc

Fix

Use the #@parameter script function in ImageJ:

• very easy way to add a dialog box
• Sensible defaults with value=
• style='password' keeps the password secure
• previous inputs replace the default (this saves a lot of typing)

If this is good solution I'll change the rest of the scripts in the examples.

Cheers,

Chris

[jburel]

Thanks @evenhuis. This option will work. We only use the name and password in the script solely for convenience during the training session, and we did not recommend to use that approach for general usage
The diff of
1d97e50
does not look right.

If you want to change the other scripts that will be great.

[evenhuis]

Hi @jburel,

Thanks, I’ll have a go at changing the rest of the scripts when I get a chance.

Let me know if there’s any examples handling password better. Except for some python/jupyter codes using get pass, I couldn’t find anything.

The diff you mention is new file. In the script editor I have it doesn’t recognize the ‘.jy’ so the scripts appear as plain text and can’t be executed. Setting the language to python changes the extension to ‘.py’.

I think if would be easier to change the extensions to ‘.py’.

Thanks,

Chris

[jburel]

sorry I missed the extension. Which version of Fiji are you using? I never had that problem with the script editor

[pwalczysko]

This issue was raised during Oxford workshop again by the attendees.