I'm considering building in a mechanism for automatically fetching scripts from PyMOLWiki. The goal is to allow users to say
fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5
The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.).
Running untrusted code is trouble. Some ideas
- MediaWiki allows us to protect pages so that only administrators can edit them. We could protect all approved scripts.
- Alternately, we could have a protected page that links to the approved scripts.
- I lean towards using both of those options. Just requiring the page to be protected could cause trouble if there's an unrelated page that happens to both be protected and have a security leak due to the fact that it was never intended to be a fetchable script.
- Maybe a hybrid system where scripts have a development version and a release version? I don't want to make too much overhead, though. Current idea: setting secure=0 means you get the development version.
- We should print a warning each time a new script is fetched anyway
- Can fetched scripts persist across saved sessions? It's easy enough to save them in fetch_path.
- Plugins? This is probably more worth considering for a future version, but it would be nice to be able to load plugins as well. Since plugins are (now) installed permanently, we have to think carefully about the implications.
The main benefit is to make things as convenient and easy as possible, especially for new users.
- Local cache. This would make reloading scripts with each new session easier and faster. You could then stick a bunch of "fetch" lines in your pymolrc. fetch_path.
- A command to list all available scripts?
- How will users know that their script is doing the correct thing
- Perhaps we should have two classes of scripts: approved and validated
My guess is that we'll require fetchable scripts to follow a certain format on the wiki pages. That should include some metadata like
- Version number. This makes debugging easier and it makes smart caching possible
- Citation. Script authors should be able to provide a preferred citation, DOI, etc. One of the benefits is to get script authors more credit.
- Documentation. Or should this be handled in the doc string?
I think all of these things should be function attributes
def myScript(a,b,c): """ Documentation for myScript goes here """ myScript.citation = "I. Coder, A Journal, 2011, Vol. 2, Issue 1, pages 64-66" myScript.version = 1.2 blah blah cmd.extend('myScript',myScript)
- This will obviously be written in Python.
- We'll probably make use of some screen scraping library. I don't know the state of the art here, but I've seen at least the following, and would love some comments:
- Generic interfaces
- Specific interfaces
To download and update github scripts
Make a text file "github.sh" and make it executable
chmod u+x github.sh
Put this in the file, modify the first 2 lines
#!/bin/bash -e pymolscripts=/home/tlinnet/Software/pymol/Pymol-script-repo pymoldir=/home/tlinnet/Software/pymol if [ -d $pymolscripts ]; then echo "### Script library exist, updating it ###" cd $pymolscripts git pull fi if [ ! -d $pymolscripts ]; then echo "### Script library does not exist, downloading it ###" sudo apt-get install git git clone https://github.com/tlinnet/Pymol-script-repo.git $pymolscripts t="'" if grep -Fxq "import sys" ~/.pymolrc then echo "# 'import sys' already exist in ~/.pymolrc #" else echo "# Adding 'import sys' to ~/.pymolrc #" echo "import sys" >> ~/.pymolrc fi if grep -Fxq "sys.path.append($t$pymolscripts$t)" ~/.pymolrc then echo "# sys.path.append($t$pymolscripts$t) already exist in ~/.pymolrc #" else echo "# adding sys.path.append($t$pymolscripts$t) to ~/.pymolrc #" echo "sys.path.append($t$pymolscripts$t)" >> ~/.pymolrc fi fi
Changes to Github repository
You can do it online, https://github.com/tlinnet/Pymol-script-repo
Make yourself a user on https://github.com/
Locate token at: Account settings -> Account admin -> API Token Configure git
git config --global user.name "Your Name" git config --global user.email firstname.lastname@example.org git config --global github.token 0123456789yourf0123456789token cat ~/.gitconfig git remote show origin git remote set-url origin https://GITUSERNAME@github.com/GITUSERNAME/Pymol-script-repo.git git remote show origin
And see cheat sheet here http://help.github.com/git-cheat-sheets/
Scheduling the editing or addition of all files to the next commit
git add .
Checking the status of your repository
git commit -m "First import"
Push the changes to remote repository
Read more here
Test to fetch script from github
ERROR in secure-include.php: URL https://github.com/tlinnet/Pymol-script-repo/blob/master/README not in allowed list.