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Feat/individuals #259

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mvergez
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@mvergez mvergez commented Nov 24, 2023

Depends on PnX-SI/GeoNature#2740
Closes #213

@mvergez mvergez force-pushed the feat/individuals branch 2 times, most recently from b02c532 to c971619 Compare December 21, 2023 11:13
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mvergez commented Jan 9, 2024

Pour ceux que ça intéresse, j'ai créé ce petit sous module qui permet de créer un protocole de suivi d'individus monospécifique. Cela permet de confirmer que la PR fonctionne bien

test_individuals_module.tar.gz

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mvergez commented Jan 9, 2024 •
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Et un protocole de suivi d'individus multi espèces :
test_individuals_module_multi.tar.gz

@mvergez mvergez marked this pull request as ready for review January 9, 2024 11:15
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codecov bot commented Mar 1, 2024 •
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Codecov Report

Attention: Patch coverage is 0% with 27 lines in your changes are missing coverage. Please review.

Project coverage is 0.14%. Comparing base (579d972) to head (f955ed3).
Report is 2 commits behind head on develop.

❗ Current head f955ed3 differs from pull request most recent head dba9cdf

Please upload reports for the commit dba9cdf to get more accurate results.

Files Patch % Lines
backend/gn_module_monitoring/monitoring/objects.py 0.00% 10 Missing ⚠️
...kend/gn_module_monitoring/monitoring/serializer.py 0.00% 7 Missing ⚠️
backend/gn_module_monitoring/monitoring/models.py 0.00% 5 Missing ⚠️
...end/gn_module_monitoring/monitoring/definitions.py 0.00% 2 Missing ⚠️
...nd/gn_module_monitoring/monitoring/repositories.py 0.00% 2 Missing ⚠️
backend/gn_module_monitoring/routes/data_utils.py 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           develop    #259      +/-   ##
==========================================
- Coverage     0.14%   0.14%   -0.01%     
==========================================
  Files           23      23              
  Lines         1345    1368      +23     
==========================================
  Hits             2       2              
- Misses        1343    1366      +23
Flag Coverage Δ
pytest 0.14% <0.00%> (-0.01%) ⬇️

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Maxime Vergez added 23 commits May 21, 2024 10:11
@andriacap
feat(db): add migration for individuals
f052df0
@andriacap
refactor(db): move base individuals tables to GN
14d29b8
@andriacap
feat(api): add orm models
aa4f048
@andriacap
feat(api): add definition, linking to orm models
93c4936
@andriacap
feat(api): add more attributes to orm models
a81b133
@andriacap
refactor(api): move everything to GeoNature
94be1be
@andriacap
feat(api): specific model dict for individuals
eaa2779
@andriacap
feat(config): add first individual json file
6367d8a
@andriacap
feat(api): more config to individuals.json
7870ffa
@andriacap
refactor: update config following changes in model
9fd2dd8
@andriacap
feat(api): add soft delete
9a8a294
@andriacap
style: apply black
ee8d5df
@andriacap
refactor(api): add marking as a individual child
a2145b1
@andriacap
refactor(config): mv marking props to marking.json
6ee2e0e 
From individual.json
@andriacap
feat(api): add nb_sites for individuals
8c4b11c
@andriacap
feat(api): add nb_individuals to site
cc6cce3
@andriacap
feat: add individuals to site.json
8b67e0f
@andriacap
feat(db): add id_individual col to observations
f93d0f9
@andriacap
feat(api): add id_individual column
7b42584
@andriacap
feat(api): add id_individual in observation.json
e7c2d8e 
Otherwise it goes into data
@andriacap
feat(api): add individual permissions
817249b
@andriacap
docs: add individual docs
e2680a9
@andriacap
docs: fix details and add more
01ac8bf
Maxime Vergez and others added 13 commits May 21, 2024 10:11
@andriacap
feat(api): add cd_nom parameter for the module
9009143 
Add a global variable __MODULE.CD_NOM, stored in the
t_module_complements table. It enables the user to provide the CD_NOM
several times in the json config files like __MODULE.ID_LIST_TAXONOMY
for instance...
@andriacap
docs: update docs following required id_module
fd04340 
And new cd_nom setting
@andriacap
feat(api): remove relationship
e902100 
Since it has been moved to GeoNature
@andriacap
chore(api): fix sqlalchemy warning
e90a8f0 
ViewOnly & scalar_subquery()
@andriacap
feat(config): hide cd_nom by default
f475a54
@andriacap
feat(api): really delete object no deactivation
27678c7
@andriacap
style(api): apply black
4ad23cc
@andriacap
docs: more doc for individiuals
d16bd25
@edelclaux @andriacap
fix: disable viewOnl=True to remove warning
fddadcc
@edelclaux @andriacap
fix: reorder revisions to make it ok for clean install
53ef966
@andriacap
fix: cd_nom missing on post observation
45a7ca4 
Reviewed-by: andriacap
@andriacap
fix: change revises migration to the good one
36ddd1f 
Reviewed-by: andriac
@andriacap
fix: replace revises by the good one and rm pass
66ae097 
Change revises to match with the one used
Remove useless "pass"

Reviewed-by: andriac
@andriacap
style(backend): apply backend
536fddb 
Reviewed-by: andriacap
@andriacap
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andriacap commented May 21, 2024 •
edited
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La PR PnX-SI/GeoNature#2740 ne doit plus être pris en compte .

C'est cette PR qui doit être prise en compte : PnX-SI/GeoNature#3056

Un protocole de test est disponible sur cette branche : https://github.com/naturalsolutions/protocoles_suivi/tree/protocole-test-suivi-individu

andriacap and others added 9 commits May 22, 2024 16:01
@andriacap
fix: nb_individus and nb_sites for Tindividuals
8c5048e 
problem with query to find number of site and individuals

Reviewed-by: andriacap
@andriacap
fix: add distinct on nb_individuals for site
5aeffc2 
Reviewed-by: andriacap
@andriacap
refactor: add nb_individuals outside models
b04db06 
Add nb_inidivuals property as before but write notes
to understand why it was needed ?

It seems to work without .. (tried)

Reviewed-by: andriacap
@andriacap
style(backend) apply black
dba9cdf 
Reviewed-by: andriacap
@andriacap
fix(back): change order alembic revision
93220d7 
- need to change alembic in order to be usable
for update of monitoring and for install monitoring
from scratch

Reviewed-by: andriacap
@andriacap
fix(backend): warning sqlalchemy
05fb478 
Reviewed-by: andriacap
@andriacap
fix(back): manage if no nomenclature value is empty
c69532a 
Reviewed-by: andriacap
@andriacap
style(back): apply black
8662d99 
Reviewed-by: andriacap
@amandine-sahl @andriacap
Fix/clean transfert permissions ALL TO MONTORING_XXX (PnX-SI#291)
5b0de36 
* Script sql de migration des permissions

* Changelog
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5 participants
@mvergez @andriacap @edelclaux @amandine-sahl @DonovanMaillard