kousu
commented
3 years ago After looking at this for a couple hours, the biggest stumbling block to this is that the XML file gets format converted to a DataFrame:
and all other processing is done in that format:
This makes working backwards tricky, because you can't directly look at the relevant publication in the XML when you find a mistake. In fact the XML object has been thrown away by that point.
In https://github.com/jcohenadad/bibeasy/pull/11/commits/f261436463334efc02644c977a952098c7575a2e I make the DataFrame retain the IDs used in the XML, so at least there's a chance of going from one to the other.
As a note to seld, some avenues that could be explored:
- Maybe I can call
find_matching_ref()but then feed its results into a new function that re-parses the XML file a second time and fixes - Move the XML parsing from
xml_to_dfintofind_matching_ref; pandas is being used as a query language there currently but it should be equally easy to use XPath there. Maybe even clearer? XPath is not super clear but it's one less abstraction to work with. And from there maybefind_matching_refcan be given an extra flag, or maybe split into subroutines, so that one path does XML editing and the other - ?
jcohenadad
alexfoias
namgo
Currently, when there is a mismatch, fields are manually updated on the CCV website.
Example of output
```console julien-macbook:~/Desktop $ bibeasy -x CCV-98720.xml -c publications_article.csv -t article Reading input file: 'publications_article.csv'... Publication type: 'article' GSHEET J1 CCV J153 Activation detection in diffuse optical imaging by means of the general linear model Mismatched fields: Journal/Conference GSHEET J2 CCV J150 Development of clinical diffusion tensor MRI of the spinal cord in a context of spinal cord injury GSHEET J3 CCV J151 In vivo DTI of the healthy and injured cat spinal cord at high spatial and angular resolution Mismatched fields: Authors, Journal/Conference GSHEET J4 CCV J152 Detection of multiple pathways in the spinal cord using q-ball imaging Mismatched fields: Authors, Journal/Conference GSHEET J5 CCV J148 Investigations on spinal cord fMRI of cats under ketamine Mismatched fields: Authors, Journal/Conference GSHEET J6 CCV J149 Characterization of cardiac-related noise in fMRI of the cervical spinal cord Mismatched fields: Authors GSHEET J7 CCV J145 BOLD signal responses to controlled hypercapnia in human spinal cord Mismatched fields: Authors, Journal/Conference ```What would be useful is if bibeasy could update the XML, so that I would then import the XML into CCV to update the publication records.