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Cytoscope inside the GUI integration #377

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puria opened this issue Feb 8, 2023 · 5 comments
Open

Cytoscope inside the GUI integration #377

puria opened this issue Feb 8, 2023 · 5 comments
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@puria @denizenging @phoebus-84

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@puria
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puria commented Feb 8, 2023 •
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At some point we need to integrate the DPP viz made by @sbocconi ask for details of the version of the library and find a react or just plain js to be included.
@sbocconi
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sbocconi commented Feb 23, 2023 •
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In the repository https://github.com/interfacerproject/Interfacer_DPP-visualisations the file id_to_cytp.py provides an example for a service that given an id writes the data file for cytoscape.

Since the server-side trace is much faster than the client-side trace, the former should be used. This requires the back-end algorithm (traceDpp) to be updated by @albertolerda (or possibly @srfsh), taking as example the *_before functions in if_dpp.py in https://github.com/interfacerproject/Interfacer-notebook

denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 4, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
350159d 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 4, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
cbf859e 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 4, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
4c60102 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 8, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
e9a3140 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 8, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
fedce42 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
denizenging added a commit to interfacerproject/zenflows that referenced this issue Mar 9, 2023
@denizenging
vf/{economic_{event,resource},process}: re-implement trace_dpp
4518dac 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
@denizenging denizenging self-assigned this Mar 9, 2023
@sbocconi
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sbocconi commented Mar 9, 2023

Update: @srfsh has implemented the trace functionality in the back-end, but in order to be completed, we need a final list of attributes that need to be visualised in the DPP.
In the meantime @srfsh can proceed to implement the service based on id_to_cyto.py.

@sbocconi
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sbocconi commented Mar 9, 2023

This issue partially depends on interfacerproject/Interfacer_DPP-visualisations#4

@jaromil
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jaromil commented Mar 30, 2023

TODO: Specify what relations need to be fetched in the backend @srfsh with a bare minimum set of information to be shown on nodes.

@puria
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puria commented Mar 30, 2023 •
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sbocconi pushed a commit to interfacerproject/zenflows that referenced this issue Apr 27, 2023
@denizenging @sbocconi
vf/{economic_{event,resource},process}: re-implement trace_dpp
c856b85 
As requested by Stefano here:
interfacerproject/interfacer-gui#377 (comment)

Implements the algorithms listed here:
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L145
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L220
https://github.com/interfacerproject/Interfacer-notebook/blob/326750b1cae445ce5faa0fafb057e50538077910/if_dpp.py#L311
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