Add cites api #3726
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Add cites api #3726
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dimasciput
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May 29, 2024
* Preparing for multi tenant (#3639) * Upgrade django, and remove wagtail * Add flower for celery monitoring * Add django-taggit * Fix missing libraries * Show theme based on site * Update summary api * Use site setting based on domain (#3640) * Use site setting based on domain * Update site_setting.py * Add source_site to records, update search, fix tests (#3642) * Add source_site to records, update search, fix tests * Improve search and tests * Taxa management improvement (#3643) * Improve the layout of taxa management page * Show taxa management page to normal user, add permissions handler, update tests * Fix broken tests (#3645) * Feature/update bio filter owner embargo (#3651) * Bump django from 4.1.10 to 4.1.13 in /deployment/production (#3569) Bumps [django](https://github.com/django/django) from 4.1.10 to 4.1.13. - [Commits](django/django@4.1.10...4.1.13) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump gitpython from 3.1.35 to 3.1.37 in /deployment/docker (#3520) Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.35 to 3.1.37. - [Release notes](https://github.com/gitpython-developers/GitPython/releases) - [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES) - [Commits](gitpython-developers/GitPython@3.1.35...3.1.37) --- updated-dependencies: - dependency-name: gitpython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix search wetland sites by site code, fix db restore (#3646) * Fix wetland site codes incorrect when uploaded as csv (#3647) * Fix delete site visit (#3648) * Feature delete records by source reference id (#3649) * Add button * Feature to delete records by source reference id * Develop functionality to show occurrence data per month (#3650) * Add chart data by month for site dashboard * Implement switch dashboard frequency in frontend * Update bio query to include owner check with embargo date --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Taxa hierarchical user management (#3652) * Automatically create taxonomic groups based on the expert level * Add experts selection in taxon group edit * Update JSONFIELD * Fix search by site * Fix add collection and search process * Fix site visit list * Update admin to show associated site * Fix taxon management * Initial implementation of tagging taxa (#3654) * Initial implementation of tagging taxa * Filter taxa by tags * Add embargo date to sass form (#3655) * Add cites api wrapper (#3661) * Add gbif util to fetch species by area (#3678) * Add view to harvest gbif species (#3679) * Add view to harvest gbif species * Improve find_species_by_area * Add site to location context group (#3683) * Build and push multi tenant tag * Implement a user interface to allow species to be designated as the parent point for retrieving species data from GBIF. (#3684) * Show map in harvest species (#3685) * Feature to show non-biodiversity layers on different sites (#3692) * Expert should be able to add taxon (#3693) * Show taxon sub groups (#3694) * Show taxon sub groups * Improve the ux * Add validation status, endemism, and origin to TaxonGroupTaxonomies table (#3695) * API Endpoint and Model for Taxonomy Update Proposals (#3697) * Backend API and model for reviewing taxon update proposals (#3700) * Api to approve taxon update proposal * Temp * Add reviewer * Improve taxon update review process * Add reject test * Additional observation sites for collection record (#3701) * Additional observation sites for collection record * Update search * Update import gbif to update existing record to add current site id * Update models for multi-tenant (#3703) * Handle source site in occurrences upload (#3707) * Update DATABASE setting for prod * Refactor taxa management (#3710) * UI for Managing Submodule in Taxon Management Page (#3711) * Add devops build automation (#3712) * Update landing page icons for FBIS (#3699) * Add devops build automation --------- Co-authored-by: Dimas Ciputra <dimas.ciputra@gmail.com> * Reload page after adding new taxon (#3715) * Update UI for taxon approval workflow (#3716) * Update UI for taxon approval workflow * Update reject workflow * Add feature to upload geojson boundary file (#3705) * Add feature to upload geojson boundary file * Logged in only * Improve UI * Fix migrations * Excel download (#3722) * Download excel (#3718) * Update landing page icons for FBIS (#3699) * add download excel * remove csv file --------- Co-authored-by: Dimas Ciputra <dimas.ciputra@gmail.com> * Improve excel download workflow (#3723) * Fix migrations * Add xls resource type to download request --------- Co-authored-by: Faneva Andriamiadantsoa <fanevanjanahary@gmail.com> * Fix custom theme cache not invalidated (#3725) * Add confidence score to bims tables (#3724) * Add SASS migration (#3728) * Fix layer upload, improve gbif species harvester (#3729) * Fix unvalidated species returned in taxa list (#3730) * Improve find_species_by_area (#3731) * Update max limit in find_species_by_area * Add additional sites field in non_biodiversity_layer (#3733) * Import common names in gbif species harvester (#3736) * Used defaultWMSSiteParameters for emptySite (#3734) * Collect parent species in the harvester (#3737) * Upload images in flat pages (#3738) * Use FBIS Site legend (#3739) * Improve harvest gbif species (#3740) * Fix get_feature_info (#3741) * Harvest species per feature (#3742) * Fix get_feature_info * Harvest gbif species per feature * Fix taxon approval (#3743) * Taxa management fixes and improvements (#3745) * Harvest species by facet (#3747) * Multi tenant fix and improvements (#3748) * Update harvest gbif to use boundary model instead * Update location context script to get correct geocontext keys * Filter out extinct species * Improve GBIF species harvester (#3749) * Update parent if the parent is different from gbif (#3750) * Only import occurrences with basisRecord HUMAN_OBSERVATION (#3751) * Improve gbif occurrence harvester (#3753) * Resume harvest functionality (#3758) * Update landing page icons for FBIS (#3699) * Fix print map not working (#3754) * Update overview table in pesticide dashboard (#3727) * update overview table in pesticide dashboard * Update pesticide/templates/pesticide_dashboard.html --------- Co-authored-by: Dimas Ciputra <dimas@kartoza.com> * Fix form update not submitted (#3755) * Remove module info (#3757) * Add function to resume harvest --------- Co-authored-by: Faneva Andriamiadantsoa <fanevanjanahary@gmail.com> * Improve module summary * Improve module summary query * Add database routing * Notification for specific site * Update source collection * Fix site legend (#3769) * Improve taxa management (#3770) * Update location_context_group command to fetch specific site (#3771) * Implement role-based access control for biologicalcollectionrecord (#3773) * Harvest occurrences by boundaries (#3774) * Set uwsgi processes to 4 * Update uwsgi.ini * Update get_location_context_data to fetch by site * Update psycopg2 lib * [feat] Add feature to upload polygon * Add edit taxon form feature * Fix tests * Handle other fields * Fix missing parent when updating taxon * Create an api to download taxa list as pdf * Ensure all taxonomy changes are times tamped and logged * Improve taxa list download (#3833) * Show download request modal * Add ui to download pdf * Source references by site (#3834) * Show source references based on current site id * Ensure source references are assigned to correct site * Add auth background field in custom theme (#3836) * Add settings to change site name and hide site visit (#3837) * Fix add source reference not updating active sites * Fix and improve gbif harvester (#3839) * Update script to fix duplicate site visits (#3843) * Fix module list and source reference list (#3845) * Implement schema per tenant, add script to migrate data (#3848) * Implement schema per tenant, add script to migrate data * Fix source reference api * Fix spatial scale filter * Update module_summary * Update prod multi-tenant database setting (#3851) * Update scripts * Fix location site view on multi-tenant (#3852) * Fix bug where incorrect sites appear when searching with ecosystem (#3850) (#3853) * Improve multi-tenant and fix tests (#3855) * Improve multi-tenant and fix tests * Fix broken tests * Improve embargo implementation (#3856) * Fix incorrect embargo date (#3859) * Handle synonym and multiple common names in uploader (#3861) * Add variety and forma to taxa upload logic (#3862) * Add resend email backend (#3863) Signed-off-by: Dimas <dimas.ciputra@gmail.com> * Fix custom theme in multi-tenant (#3864) * Add the ability to include a subcategory within a subcategory in a taxon group (#3865) * Update db replica implementation (#3866) * Fix gbif species harvester (#3867) * Fix db replica for multi tenant (#3868) * Fix database config startup (#3869) * Fix email sent from wrong tenant (#3870) * Add FADA Taxa Templates 0.1 (#3885) * Add FADA Taxa Templates 0.1 * Update FADA_template_0.1.csv * Improve taxa validation workflow (#3871) * Improve taxa validation workflow * Update taxon validation workflow * Fix taxa management js * Fix data source filter (#3897) * Fix site code generator (#3898) * Remove abiotic form and fix download request page (#3899) * Remove abiotic form and fix download request page * Update SASS form * Remove Life and Cultivar group from taxon ranks (#3900) * Add cites api (#3726) * add cites api * Update cites.py --------- Co-authored-by: Dimas Ciputra <dimas@kartoza.com> Co-authored-by: Dimas Ciputra <dimas.ciputra@gmail.com> * Implement cites api and dashboard (#3901) * Add species plus link to cites dashboard (#3902) * Clear search results when adding or removing occurrence/SASS (#3903) * feat: Add RedirectHomePageMiddleware with SiteSetting-based redirection (#3914) * feat: Add CustomLogo and Title in login modal (#3915) * feat: Add CustomLogo and Title in login modal * Add templates * feat: Add celery beat to check and resume harvester sessions (#3917) * Add celery beat to check and resume harvester sessions * Add RotatingFileHandler * feat: Make auto-resume feature multi-tenant aware (#3918) * feat: Make auto-resume feature multi-tenant aware * Improve query * fix: Improve Visibility of Tooltips in Overview Table (#3919) * feat: Add x to close the filter panel (#3923) * feat: Enable Taxon Editing for Users Beyond the Creator (#3920) * feat: Add flag to indicate if system need to update filters (#3928) * fix: Change site name to park name for sanparks (#3929) * Fix tests (#3930) * feat: GeoContext harvester from admin page, with the log view (#3931) * Add button to harvest geocontext in admin page * Initiate geocontext harvester from admin, save the log to file * Add api to show the logs * fix: Error in set tenant scheme (#3932) * fix: KeyError schema name (#3933) * feat: Add Author When Adding New Taxon (#3934) * fix: Missing overview in pesticide dashboard (#3935) * patch: update from main (#3936) * Remove django-nose * Update db in docker-compose.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Dimas <dimas.ciputra@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Leon <106655586+lgkgh@users.noreply.github.com> Co-authored-by: Faneva Andriamiadantsoa <fanevanjanahary@gmail.com>
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fixes #3613