Just a note that the CSRF token must be acquired in a separate login step in order to allow POST actions on the catmaid server. If you are happy to use the R catmaid package, you can do:
id name type skid
1 19496665 Zwart et al. 2016 annotation NA
2 19711421 Berck, Khandelwal et al. 2016 annotation NA
3 19711583 Eichler, Li, Litwin-Kumar et al. 2017 annotation NA
4 19711972 Larderet, Fritsch et al. 2017 annotation NA
5 19712046 Ohyama, Schneider-Mizell et al. 2015 annotation NA
6 19712156 Jovanic, Schneider-Mizell et al. 2016 annotation NA
7 19712202 Schlegel et al. 2016 annotation NA
8 19712396 Fushiki et al. 2016 annotation NA
9 19716589 Takagi et al. 2017 annotation NA
10 19756504 Heckscher et al. 2015 annotation NA
11 19756692 Gerhard et al. 2017 annotation NA
12 19862922 Burgos et al 2018 annotation NA
13 20282757 Miroschnikow et al. 2018 annotation NA
14 20284758 "Carreira-Rosario, Arzan Zarin, Clark et al. 2018" annotation NA
Thanks Greg. @Robbie1977 - how are you doing this now? Would prefer to keep this all in Python in order to fit with the rest of our tool chain. At some point later this year I plan to work on Python code that pulls from this API and writes RDF to our new triple-store integration layer, so will need to have some basic stuff like this sorted first. @jefferis - do you know if anyone has written a Python wrapper for the CATMAID API?
@dosumis commented on Wed May 08 2019
AIM: Generate reports of new annotations when CATMAID is updated.
Sketch of how this could work via API:
https://l1em.catmaid.virtualflybrain.org/apis project_id: 1
Get a list of skeleton IDs: https://l1em.catmaid.virtualflybrain.org/1/skeletons/
Use Skeleton IDs to get annotations from
https://l1em.catmaid.virtualflybrain.org/1/annotations/forskeletons
Using post and passing skeleton_ids as list
->
skeleton_id=9813188 annotations include
Do we need to use RegEx to find anything that looks like a paper?
@Robbie1977 - is this on the right track? Do you have some example code from how you've been doing this up to now?
@mmc46 commented on Wed May 08 2019
There is a 'papers' meta-annotation that will list all paper citations (which in turn are annotations to skeletons).
@dosumis commented on Wed May 15 2019
@mmc46 @Robbie1977 - do you know how to get this via the API?
@Robbie1977 - do you have any existing code to share?
@mmc46 commented on Wed May 15 2019
/{project_id}/annotations/query-targets http://l1em.catmaid.virtualflybrain.org/apis/#!/annotations/annotations_query_targets_create
Try
to get
and you'll see the output.
@jefferis commented on Wed May 15 2019
Just a note that the CSRF token must be acquired in a separate login step in order to allow POST actions on the catmaid server. If you are happy to use the R catmaid package, you can do:
and get
@dosumis commented on Thu May 16 2019
Thanks Greg. @Robbie1977 - how are you doing this now? Would prefer to keep this all in Python in order to fit with the rest of our tool chain. At some point later this year I plan to work on Python code that pulls from this API and writes RDF to our new triple-store integration layer, so will need to have some basic stuff like this sorted first. @jefferis - do you know if anyone has written a Python wrapper for the CATMAID API?
@mmc46 commented on Thu May 16 2019
https://github.com/schlegelp/pyMaid
@Robbie1977 commented on Fri May 17 2019
@dosumis an example script - loads SWC files manually which is no longer used. (change project ID to 1 and password - can give privately)
@Robbie1977 commented on Thu Jun 06 2019
shtqPxJ742Rz6NsTARtRPkQ2p2WemshcPBCMK25u63bI0Jev4xVBePtAdtO5dpJe
@jefferis commented on Thu Jun 06 2019
Don't forget that @schlegelp has https://github.com/schlegelp/pyMaid/