A short description of the app structure is provided here, following the alphabetically sorted subfolders of the repository. All code was transferred with effort minimalized, most refactoring is connected only to necessary changes (like db calls or Dependency Injection). I had a wish to split methods according to entities/domains, but struggle mostly on it - the priority is to get working copy now, refactor when deployed. E.g. Statistics or search of specimens represents a little bit more elaborated remake.
when walking through the code, I had sometimes comments - all are kept inline with //TODO notation; but they do not need any immediate action, just kept for evidence and future use.
.github setup GitHub Continues integrations, that is build&push of the image or obsolete dependency checks. Dockerfile this dockerfile is used for production image build
assets
JS and CSS(SASS) files are stored outside and compiled by Webpack. The app.js is central point of the build, so do not forget import new code there. When you work on UI use ./npm.sh run watch - on files change the assets are recompiled nearly immediately. Do you need a new external library? - add it to package.json, run ./npm.sh update && ./npm.sh run build.
bin An elegant way how to run shell-like scripts using the whole application code base.
config Configuration, the only thing that is really framework-specific
database Temporal storage used by Petr
public This folder is publicly visible in production - logos, assets build etc.
src PHP code of the application
templates TWIG templates of individual pages. The file structure is optional, but a link to specific template is always hardcoded in the related route
The remaining is clear, let's look deeper in src.
Command For console commands, not used at this moment, but in future the regular cron proceeded tasks will live here.
Controller Definition of routes, what should be done and what should be returned
Entity Doctrine ORM entities, that is mapping of database tables to data. Many database calls are kept in raw SQL approach. Benefits of Doctrine ORM are not fully utilized. The RW and RO database automatic switch is covered by Doctrine. If interested, read more here, in general executeQuery() runs on replica(s) and executeStatement() on writable.
Enum PHP enums
EventSubscriber Powerful but not relevant at this moment
Facade some are preliminary proposed and used, but many opportunities for refactoring
Repository Doctrine ORM repositories - that is "lookup and filter" operations. Not used as much one would like to see.
Service Application logic, but a lot of the code should be migrated into Repositories
Twig Extensions for templates, used for hacking the frontend - parts of legacy code that is used for displaying some values is stored here in to keep the templates clean.
Requires DATABASE_URL to be directed to writable database (like the one from docker-compose) with structure from /htdocs/database/demo.sql. (or use Migrations&Console, but the sql dump is easier).
- Generate a private/public key pair at the location defined in .env file, using the value of the OAUTH_PASSPHRASE as passphrase: https://oauth2.thephpleague.com/installation/#generating-public-and-private-keys
cd htdocs/config/jwt
openssl genrsa -aes128 -passout pass:jacq -out private.pem 2048
openssl rsa -in private.pem -passin pass:jacq -pubout -out public.pemand facultative "encryption key" via php -r 'echo base64_encode(random_bytes(32)), PHP_EOL;' + update al this info in .env file.
in jacq-services repository are more folders than "rest:"
https://github.com/jacq-system/jacq-services/tree/develop/commonNames/references/scientificName - is it used (and should be implemented in Symfony also), where can I find it online? https://github.com/jacq-system/jacq-services/tree/develop/monitor - dtto? https://github.com/jacq-system/jacq-services/tree/develop/oai - as Johannes is working on it, I skipped it for now To agree the Symfony version as equivalent to jacq-services (beside routing, see above), there are some things I please for a help (prefixed with the route, links and results see bellow, line specific comments provided by TODOs in code):
/services/rest/classification/download/{referenceType}/{referenceID} this service requires two configuration keys I do not know (and do not satisfy with my vision of the architecture) - $this->settings['apikey'] and $this->settings['classifications_license'] /services/rest/iiif/createManifest/{serverID}/{imageIdentifier} - can anybode please provide parameters those provide 200 response at JACQ.org? /services/rest/livingplants/derivatives - "Table 'herbarinput.tbl_organisation' doesn't exist" - should this route be implemented or deleted? /services/rest/objects/specimens/search - similar - delete or implement? /services/rest/JACQscinames/uuid/{taxonID} + /services/rest/JACQscinames/name/{taxonID} + /services/rest/JACQscinames/resolve/{uuid} - UUID topic - need the API key