met4j merge requestshttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests2023-01-06T17:35:38+01:00https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/26Fix handling of weighted metabolic graph as undirected2023-01-06T17:35:38+01:00Clement FrainayFix handling of weighted metabolic graph as undirectedThe "AsUndirected" processing of BioGraph simply add reverse edges for all existing edges. However, in the case of weighted graphs, edges' weight wasn't passed to the newly created ones. This raised other concerns, such as the use of nod...The "AsUndirected" processing of BioGraph simply add reverse edges for all existing edges. However, in the case of weighted graphs, edges' weight wasn't passed to the newly created ones. This raised other concerns, such as the use of node weighting transferred to edges (such as degree weighting used in distance matrices), where reversed and original edges sharing the same weight might not be suited despite ensuring the symmetry property of the metric space.
There is also special cases that might be of interest for some apps, such as avoiding doubling of reversible reaction edges in compound graphs.
This merge request aims at ensuring appropriate behaviour of "undirecting" BioGraphs and expand test casesClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/2[io] handle indentifiers.org urls with https2021-11-26T13:50:19+01:00Clement Frainay[io] handle indentifiers.org urls with httpsXref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in ...Xref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in met4J too, so change has been made to the unit tests.
However, please note that a sbml with http://identifiers.org uris will have them converted to https after exportLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/1handle indentifiers.org urls with https2021-11-09T10:55:41+01:00Clement Frainayhandle indentifiers.org urls with httpsMet4J IO parse xref only if it has a valid identifiers.org uri.
Since identifiers.org changed to https, the validity check now accept both http and https uri.
The default base uri is also switched to https in met4J
However, this means t...Met4J IO parse xref only if it has a valid identifiers.org uri.
Since identifiers.org changed to https, the validity check now accept both http and https uri.
The default base uri is also switched to https in met4J
However, this means that a sbml with http://identifiers.org/ xref will be converted to https:// after export from bionetworkLudovic CottretLudovic Cottret