Add src package

src/main.py

@@ -0,0 +1,200 @@
+from flask import Flask
+from flask_restful import Api
+
+from src.resources.entities.dataset_type_endpoints import *
+from src.resources.entities.applications_endpoints import *
+from src.resources.entities.datacollection_datafiles_endpoints import *
+from src.resources.entities.datacollection_datasets_endpoints import *
+from src.resources.entities.datacollection_parameters_endpoints import *
+from src.resources.entities.datacollections_endpoints import *
+from src.resources.entities.datafile_formats_endpoints import *
+from src.resources.entities.datafile_parameters_endpoints import *
+from src.resources.entities.datafiles_endpoints import *
+from src.resources.entities.datasets_endpoints import *
+from src.resources.entities.facilities_endpoints import *
+from src.resources.entities.facility_cycles_endpoints import *
+from src.resources.entities.groupings_endpoints import *
+from src.resources.entities.instrument_scientists_endpoints import *
+from src.resources.entities.instruments_endpoints import *
+from src.resources.entities.investigation_groups_endpoints import *
+from src.resources.entities.investigation_instruments_endpoints import *
+from src.resources.entities.investigation_parameters_endpoints import *
+from src.resources.entities.investigation_types_endpoints import *
+from src.resources.entities.investigation_users_endpoints import *
+from src.resources.entities.investigations_endpoints import *
+from src.resources.entities.jobs_endpoints import *
+from src.resources.entities.keywords_endpoints import *
+from src.resources.entities.parameter_types_endpoints import *
+from src.resources.entities.permissible_string_values_endpoints import *
+from src.resources.entities.public_steps_endpoints import *
+from src.resources.entities.publications_endpoints import *
+from src.resources.entities.related_datafiles_endpoints import *
+from src.resources.entities.rules_endpoints import *
+from src.resources.entities.sample_parameters_endpoints import *
+from src.resources.entities.sample_types_endpoints import *
+from src.resources.entities.samples_endpoints import *
+from src.resources.non_entities.sessions_endpoints import *
+from src.resources.entities.shifts_endpoints import *
+from src.resources.entities.studies_endpoints import *
+from src.resources.entities.study_investigations_endpoints import *
+from src.resources.entities.user_groups_endpoints import *
+from src.resources.entities.users_endpoints import *
+
+
+app = Flask(__name__)
+api = Api(app)
+
+
+api.add_resource(Applications, "/applications")
+api.add_resource(ApplicationsWithID, "/applications/<string:id>")
+api.add_resource(ApplicationsCount, "/applications/count")
+api.add_resource(ApplicationsFindOne, "/applications/findOne")
+api.add_resource(DataCollections, "/datacollections")
+api.add_resource(DataCollectionsWithID, "/datacollections/<string:id>")
+api.add_resource(DataCollectionsCount, "/datacollections/count")
+api.add_resource(DataCollectionsFindOne, "/datacollections/findOne")
+api.add_resource(DataCollectionDatafiles, "/datacollectiondatafiles")
+api.add_resource(DataCollectionDatafilesWithID, "/datacollectiondatafiles/<string:id>")
+api.add_resource(DataCollectionDatafilesCount, "/datacollectiondatafiles/count")
+api.add_resource(DataCollectionDatafilesFindOne, "/datacollectiondatafiles/findOne")
+api.add_resource(DataCollectionDatasets, "/datacollectiondatasets")
+api.add_resource(DataCollectionDatasetsWithID, "/datacollectiondatasets/<string:id>")
+api.add_resource(DataCollectionDatasetsCount, "/datacollectiondatasets/count")
+api.add_resource(DataCollectionDatasetsFindOne, "/datacollectiondatasets/findOne")
+api.add_resource(DataCollectionParameters, "/datacollectionparameters")
+api.add_resource(DataCollectionParametersWithID, "/datacollectionparameters/<string:id>")
+api.add_resource(DataCollectionParametersCount, "/datacollectionparameters/count")
+api.add_resource(DataCollectionParametersFindOne, "/datacollectionparameters/findOne")
+api.add_resource(Datafiles,"/datafiles")
+api.add_resource(DatafilesWithID, "/datafiles/<string:id>")
+api.add_resource(DatafilesFindOne, "/datafiles/findOne")
+api.add_resource(DatafilesCount, "/datafiles/count")
+api.add_resource(DatafileFormats, "/datafileformats")
+api.add_resource(DatafileFormatsWithID, "/datafileformats/<string:id>")
+api.add_resource(DatafileFormatsCount, "/datafileformats/count")
+api.add_resource(DatafileFormatsFindOne, "/datafileformats/findOne")
+api.add_resource(DatafileParameters, "/datafileparameters")
+api.add_resource(DatafileParametersWithID, "/datafileparameters/<string:id>")
+api.add_resource(DatafileParametersCount, "/datafileparameters/count")
+api.add_resource(DatafileParametersFindOne, "/datafileparameters/findOne")
+api.add_resource(Datasets, "/datasets")
+api.add_resource(DatasetsWithID, "/datasets/<string:id>")
+api.add_resource(DatasetsCount, "/datasets/count")
+api.add_resource(DatasetsFindOne, "/datasets/findOne")
+api.add_resource(DatasetTypes, "/datasettypes")
+api.add_resource(DatasetTypesWithID, "/datasettypes/<string:id>")
+api.add_resource(DatasetTypesCount, "/datasettypes/count")
+api.add_resource(DatasetTypesFindOne, "/datasettypes/findOne")
+api.add_resource(Facilities, "/facilities")
+api.add_resource(FacilitiesWithID, "/facilities/<string:id>")
+api.add_resource(FacilitiesCount, "/facilities/count")
+api.add_resource(FacilitiesFindOne, "/facilities/findOne")
+api.add_resource(FacilityCycles, "/facilitycycles")
+api.add_resource(FacilityCyclesWithID, "/facilitycycles/<string:id>")
+api.add_resource(FacilityCyclesCount, "/facilitycycles/count")
+api.add_resource(FacilityCyclesFindOne, "/facilitycycles/findOne")
+api.add_resource(Groupings, "/groupings")
+api.add_resource(GroupingsWithID, "/groupings/<string:id>")
+api.add_resource(GroupingsCount, "/groupings/count")
+api.add_resource(GroupingsFindOne, "/groupings/findOne")
+api.add_resource(Instruments, "/instruments")
+api.add_resource(InstrumentsWithID, "/instruments/<string:id>")
+api.add_resource(InstrumentsCount, "/instruments/count")
+api.add_resource(InstrumentsFindOne, "/instruments/findOne")
+api.add_resource(InstrumentScientists, "/instrumentscientists")
+api.add_resource(InstrumentScientistsWithID, "/instrumentscientists/<string:id>")
+api.add_resource(InstrumentScientistsCount, "/instrumentscientists/count")
+api.add_resource(InstrumentScientistsFindOne, "/instrumentscientists/findOne")
+api.add_resource(Investigations, "/investigations")
+api.add_resource(InvestigationsWithID, "/investigations/<string:id>")
+api.add_resource(InvestigationsCount, "/investigations/count")
+api.add_resource(InvestigationsFindOne, "/investigations/findOne")
+api.add_resource(InvestigationGroups, "/investigationgroups")
+api.add_resource(InvestigationGroupsWithID, "/investigationgroups/<string:id>")
+api.add_resource(InvestigationGroupsCount, "/investigationgroups/count")
+api.add_resource(InvestigationGroupsFindOne, "/investigationgroups/findOne")
+api.add_resource(InvestigationInstruments, "/investigationinstruments")
+api.add_resource(InvestigationInstrumentsWithID, "/investigationinstruments/<string:id>")
+api.add_resource(InvestigationInstrumentsCount, "/investigationinstruments/count")
+api.add_resource(InvestigationInstrumentsFindOne, "/investigationinstruments/findOne")
+api.add_resource(InvestigationParameters, "/investigationparameters")
+api.add_resource(InvestigationParametersWithID, "/investigationparameters/<string:id>")
+api.add_resource(InvestigationParametersCount, "/investigationparameters/count")
+api.add_resource(InvestigationParametersFindOne, "/investigationparameters/findOne")
+api.add_resource(InvestigationTypes, "/investigationtypes")
+api.add_resource(InvestigationTypesWithID, "/investigationtypes/<string:id>")
+api.add_resource(InvestigationTypesCount, "/investigationtypes/count")
+api.add_resource(InvestigationTypesFindOne, "/investigationtypes/findOne")
+api.add_resource(InvestigationUsers, "/investigationusers")
+api.add_resource(InvestigationUsersWithID, "/investigationusers/<string:id>")
+api.add_resource(InvestigationUsersCount, "/investigationusers/count")
+api.add_resource(InvestigationUsersFindOne, "/investigationusers/findOne")
+api.add_resource(Jobs, "/jobs")
+api.add_resource(JobsWithID, "/jobs/<string:id>")
+api.add_resource(JobsCount, "/jobs/count")
+api.add_resource(JobsFindOne, "/jobs/findOne")
+api.add_resource(Keywords, "/keywords")
+api.add_resource(KeywordsWithID, "/keywords/<string:id>")
+api.add_resource(KeywordsCount, "/keywords/count")
+api.add_resource(KeywordsFindOne, "/keywords/findOne")
+api.add_resource(ParameterTypes, "/parametertypes")
+api.add_resource(ParameterTypesWithID, "/parametertypes/<string:id>")
+api.add_resource(ParameterTypesCount, "/parametertypes/count")
+api.add_resource(ParameterTypesFindOne, "/parametertypes/findOne")
+api.add_resource(PermissibleStringValues, "/permissiblestringvalues")
+api.add_resource(PermissibleStringValuesWithID, "/permissiblestringvalues/<string:id>")
+api.add_resource(PermissibleStringValuesCount, "/permissiblestringvalues/count")
+api.add_resource(PermissibleStringValuesFindOne, "/permissiblestringvalues/findOne")
+api.add_resource(Publications, "/publications")
+api.add_resource(PublicationsWithID, "/publications/<string:id>")
+api.add_resource(PublicationsCount, "/publications/count")
+api.add_resource(PublicationsFindOne, "/publications/findOne")
+api.add_resource(PublicSteps, "/publicsteps")
+api.add_resource(PublicStepsWithID, "/publicsteps/<string:id>")
+api.add_resource(PublicStepsCount, "/publicsteps/count")
+api.add_resource(PublicStepsFindOne, "/publicsteps/findOne")
+api.add_resource(RelatedDatafiles, "/relateddatafiles")
+api.add_resource(RelatedDatafilesWithID, "/relateddatafiles/<string:id>")
+api.add_resource(RelatedDatafilesCount, "/relateddatafiles/count")
+api.add_resource(RelatedDatafilesFindOne, "/relateddatafiles/findOne")
+api.add_resource(Rules, "/rules")
+api.add_resource(RulesWithID, "/rules/<string:id>")
+api.add_resource(RulesCount, "/rules/count")
+api.add_resource(RulesFindOne, "/rules/findOne")
+api.add_resource(Samples, "/samples")
+api.add_resource(SamplesWithID, "/samples/<string:id>")
+api.add_resource(SamplesCount, "/samples/count")
+api.add_resource(SamplesFindOne, "/samples/findOne")
+api.add_resource(SampleParameters, "/sampleparameters")
+api.add_resource(SampleParametersWithID, "/sampleparameters/<string:id>")
+api.add_resource(SampleParametersCount, "/sampleparameters/count")
+api.add_resource(SampleParametersFindOne, "/sampleparameters/findOne")
+api.add_resource(SampleTypes, "/sampletypes")
+api.add_resource(SampleTypesWithID, "/sampletypes/<string:id>")
+api.add_resource(SampleTypesCount, "/sampletypes/count")
+api.add_resource(SampleTypesFindOne, "/sampletypes/findOne")
+api.add_resource(Sessions, "/sessions")
+api.add_resource(Shifts, "/shifts")
+api.add_resource(ShiftsWithID, "/shifts/<string:id>")
+api.add_resource(ShiftsCount, "/shifts/count")
+api.add_resource(ShiftsFindOne, "/shifts/findOne")
+api.add_resource(Studies, "/studies")
+api.add_resource(StudiesWithID, "/studies/<string:id>")
+api.add_resource(StudiesCount, "/studies/count")
+api.add_resource(StudiesFindOne, "/studies/findOne")
+api.add_resource(StudyInvestigations, "/studyinvestigations")
+api.add_resource(StudyInvestigationsWithID, "/studyinvestigations/<string:id>")
+api.add_resource(StudyInvestigationsCount, "/studyinvestigations/count")
+api.add_resource(StudyInvestigationsFindOne, "/studyinvestigations/findOne")
+api.add_resource(Users, "/users")
+api.add_resource(UsersWithID, "/users/<string:id>")
+api.add_resource(UsersCount, "/users/count")
+api.add_resource(UsersFindOne, "/users/findOne")
+api.add_resource(UserGroups, "/usergroups")
+api.add_resource(UserGroupsWithID, "/usergroups/<string:id>")
+api.add_resource(UserGroupsCount, "/usergroups/count")
+api.add_resource(UserGroupsFindOne, "/usergroups/findOne")
+
+
+if __name__ == "__main__":
+    app.run(debug=True)

src/resources/entities/applications_endpoints.py

@@ -0,0 +1,60 @@
+from common.models.db_models import APPLICATION
+from flask import request
+from flask_restful import Resource
+
+from common.database_helpers import get_row_by_id, delete_row_by_id, update_row_from_id, get_rows_by_filter, \
+    get_filtered_row_count, get_first_filtered_row, create_row_from_json
+from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
+
+
+class Applications(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        return get_rows_by_filter(APPLICATION, request.json), 200
+
+    @requires_session_id
+    @queries_records
+    def post(self):
+        create_row_from_json(APPLICATION, request.json)
+        return get_row_by_id(APPLICATION, request.json["id"].to_dict()), 200
+
+    @requires_session_id
+    @queries_records
+    def patch(self):
+        pass
+
+
+class ApplicationsWithID(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self, id):
+        return get_row_by_id(APPLICATION, id).to_dict(), 200
+
+    @requires_session_id
+    @queries_records
+    def delete(self, id):
+        delete_row_by_id(APPLICATION, id)
+        return "", 204
+
+    @requires_session_id
+    @queries_records
+    def patch(self, id):
+        update_row_from_id(APPLICATION, id, str(request.json))
+        return get_row_by_id(APPLICATION, id).to_dict(), 200
+
+
+class ApplicationsCount(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_filtered_row_count(APPLICATION, filters), 200
+
+
+class ApplicationsFindOne(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_first_filtered_row(APPLICATION, filters), 200

src/resources/entities/datacollection_datafiles_endpoints.py

@@ -0,0 +1,60 @@
+from flask import request
+from flask_restful import Resource
+
+from common.database_helpers import get_row_by_id, delete_row_by_id, update_row_from_id, get_rows_by_filter, \
+    get_filtered_row_count, get_first_filtered_row, create_row_from_json
+from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
+from common.models.db_models import DATACOLLECTIONDATAFILE
+
+
+class DataCollectionDatafiles(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        return get_rows_by_filter(DATACOLLECTIONDATAFILE, request.json), 200
+
+    @requires_session_id
+    @queries_records
+    def post(self):
+        create_row_from_json(DATACOLLECTIONDATAFILE, request.json)
+        return get_row_by_id(DATACOLLECTIONDATAFILE, request.json["id"].to_dict()), 200
+
+    @requires_session_id
+    @queries_records
+    def patch(self):
+        pass
+
+
+class DataCollectionDatafilesWithID(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self, id):
+        return get_row_by_id(DATACOLLECTIONDATAFILE, id).to_dict(), 200
+
+    @requires_session_id
+    @queries_records
+    def delete(self, id):
+        delete_row_by_id(DATACOLLECTIONDATAFILE, id)
+        return "", 204
+
+    @requires_session_id
+    @queries_records
+    def patch(self, id):
+        update_row_from_id(DATACOLLECTIONDATAFILE, id, str(request.json))
+        return get_row_by_id(DATACOLLECTIONDATAFILE, id).to_dict(), 200
+
+
+class DataCollectionDatafilesCount(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_filtered_row_count(DATACOLLECTIONDATAFILE, filters), 200
+
+
+class DataCollectionDatafilesFindOne(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_first_filtered_row(DATACOLLECTIONDATAFILE, filters), 200

src/resources/entities/datacollection_datasets_endpoints.py

@@ -0,0 +1,60 @@
+from flask import request
+from flask_restful import Resource
+
+from common.database_helpers import get_row_by_id, delete_row_by_id, update_row_from_id, get_rows_by_filter, \
+    get_filtered_row_count, get_first_filtered_row, create_row_from_json
+from common.helpers import requires_session_id, queries_records, get_filters_from_query_string
+from common.models.db_models import DATACOLLECTIONDATASET
+
+
+class DataCollectionDatasets(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        return get_rows_by_filter(DATACOLLECTIONDATASET, request.json), 200
+
+    @requires_session_id
+    @queries_records
+    def post(self):
+        create_row_from_json(DATACOLLECTIONDATASET, request.json)
+        return get_row_by_id(DATACOLLECTIONDATASET, request.json["id"].to_dict()), 200
+
+    @requires_session_id
+    @queries_records
+    def patch(self):
+        pass
+
+
+class DataCollectionDatasetsWithID(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self, id):
+        return get_row_by_id(DATACOLLECTIONDATASET, id).to_dict(), 200
+
+    @requires_session_id
+    @queries_records
+    def delete(self, id):
+        delete_row_by_id(DATACOLLECTIONDATASET, id)
+        return "", 204
+
+    @requires_session_id
+    @queries_records
+    def patch(self, id):
+        update_row_from_id(DATACOLLECTIONDATASET, id, str(request.json))
+        return get_row_by_id(DATACOLLECTIONDATASET, id).to_dict(), 200
+
+
+class DataCollectionDatasetsCount(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_filtered_row_count(DATACOLLECTIONDATASET, filters), 200
+
+
+class DataCollectionDatasetsFindOne(Resource):
+    @requires_session_id
+    @queries_records
+    def get(self):
+        filters = get_filters_from_query_string()
+        return get_first_filtered_row(DATACOLLECTIONDATASET, filters), 200