From 9986080dbc318df589437cf7f4de3981d72602d6 Mon Sep 17 00:00:00 2001 From: SimonKonar Date: Wed, 30 Oct 2024 11:50:41 +0100 Subject: [PATCH] feat: move packages from src to root of the project --- README.md | 18 +++++------ .../NonExistentResourceException.py | 0 .../blaze_client => blaze_client}/__init__.py | 0 .../blaze_client.py | 24 +++++++-------- .../__init__.py | 0 .../biobank.py | 10 +++---- .../collection.py | 14 ++++----- .../collection_organization.py | 10 +++---- .../condition.py | 8 ++--- .../diagnosis_report.py | 8 ++--- .../MIABIS_on_FHIR => miabis_model}/gender.py | 0 .../incorrect_json_format.py | 0 .../network.py | 8 ++--- .../network_organization.py | 10 +++---- .../observation.py | 8 ++--- .../MIABIS_on_FHIR => miabis_model}/sample.py | 12 ++++---- .../sample_donor.py | 12 ++++---- .../storage_temperature.py | 0 .../util/__init__.py | 0 .../util/config.py | 0 .../util/constants.py | 0 .../util/parsing_util.py | 2 +- .../util/util.py | 0 pyproject.toml | 9 ++---- test/service/test_blaze_client.py | 30 +++++++++---------- test/unit/model/test_biobank.py | 2 +- test/unit/model/test_collection.py | 6 ++-- test/unit/model/test_collection_org.py | 2 +- test/unit/model/test_condition.py | 2 +- test/unit/model/test_diagnosis_report.py | 2 +- test/unit/model/test_network.py | 2 +- test/unit/model/test_network_org.py | 2 +- test/unit/model/test_observation.py | 2 +- test/unit/model/test_sample.py | 4 +-- test/unit/model/test_sample_donor.py | 4 +-- 35 files changed, 103 insertions(+), 108 deletions(-) rename {src/blaze_client => blaze_client}/NonExistentResourceException.py (100%) rename {src/blaze_client => blaze_client}/__init__.py (100%) rename {src/blaze_client => blaze_client}/blaze_client.py (99%) rename {src/MIABIS_on_FHIR => miabis_model}/__init__.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/biobank.py (97%) rename {src/MIABIS_on_FHIR => miabis_model}/collection.py (97%) rename {src/MIABIS_on_FHIR => miabis_model}/collection_organization.py (97%) rename {src/MIABIS_on_FHIR => miabis_model}/condition.py (96%) rename {src/MIABIS_on_FHIR => miabis_model}/diagnosis_report.py (97%) rename {src/MIABIS_on_FHIR => miabis_model}/gender.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/incorrect_json_format.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/network.py (96%) rename {src/MIABIS_on_FHIR => miabis_model}/network_organization.py (96%) rename {src/MIABIS_on_FHIR => miabis_model}/observation.py (96%) rename {src/MIABIS_on_FHIR => miabis_model}/sample.py (96%) rename {src/MIABIS_on_FHIR => miabis_model}/sample_donor.py (93%) rename {src/MIABIS_on_FHIR => miabis_model}/storage_temperature.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/util/__init__.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/util/config.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/util/constants.py (100%) rename {src/MIABIS_on_FHIR => miabis_model}/util/parsing_util.py (91%) rename {src/MIABIS_on_FHIR => miabis_model}/util/util.py (100%) diff --git a/README.md b/README.md index 343f20b..3fab096 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,8 @@ The MIABIS on FHIR profile full specification along with the guide is available ## Modules -### 1. `MIABIS_on_FHIR` -The `MIABIS_on_FHIR` module includes a set of classes to help developers: +### 1. `miabis_model` +The `miabis_model` module includes a set of classes to help developers: - **Create** MIABIS on FHIR resources. - **Read** and **validate** these resources. - **Convert** resources to and from JSON format. @@ -37,14 +37,14 @@ This package is ideal for developers looking to work with MIABIS on FHIR resourc ## Installation ```bash -pip install MIABIS_on_FHIR +pip install miabis_model ``` ## How to use Here is how you can create a MIABIS on FHIR sample resource: ```python -from MIABIS_on_FHIR import Sample -from MIABIS_on_FHIR import StorageTemperature +from miabis_model import Sample +from miabis_model import StorageTemperature sample = Sample("sampleId", "donorId", "Urine", storage_temperature=StorageTemperature.TEMPERATURE_ROOM, use_restrictions="No restrictions") @@ -58,12 +58,12 @@ Here is an example on how to communicate with blaze server via the BlazeClient: ```python import datetime -from MIABIS_on_FHIR import Gender +from miabis_model import Gender from blaze_client import BlazeClient -from MIABIS_on_FHIR import SampleDonor +from miabis_model import SampleDonor -client = BlazeClient("example_url","username","password") +client = BlazeClient("example_url", "username", "password") -donor = SampleDonor("donorId", Gender.MALE, birth_date=datetime.datetime(year=2000,month=12,day=12)) +donor = SampleDonor("donorId", Gender.MALE, birth_date=datetime.datetime(year=2000, month=12, day=12)) donor_fhir_id = client.upload_donor(donor) ``` diff --git a/src/blaze_client/NonExistentResourceException.py b/blaze_client/NonExistentResourceException.py similarity index 100% rename from src/blaze_client/NonExistentResourceException.py rename to blaze_client/NonExistentResourceException.py diff --git a/src/blaze_client/__init__.py b/blaze_client/__init__.py similarity index 100% rename from src/blaze_client/__init__.py rename to blaze_client/__init__.py diff --git a/src/blaze_client/blaze_client.py b/blaze_client/blaze_client.py similarity index 99% rename from src/blaze_client/blaze_client.py rename to blaze_client/blaze_client.py index 15b411d..2ec28ce 100644 --- a/src/blaze_client/blaze_client.py +++ b/blaze_client/blaze_client.py @@ -3,19 +3,19 @@ from requests import Response from requests.adapters import HTTPAdapter, Retry -from src.MIABIS_on_FHIR.biobank import Biobank -from src.MIABIS_on_FHIR.collection import Collection -from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization -from src.MIABIS_on_FHIR.condition import Condition -from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport -from src.MIABIS_on_FHIR.network import Network -from src.MIABIS_on_FHIR.network_organization import NetworkOrganization -from src.MIABIS_on_FHIR.observation import Observation -from src.MIABIS_on_FHIR.sample import Sample -from src.MIABIS_on_FHIR.sample_donor import SampleDonor -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id, \ +from miabis_model.biobank import Biobank +from miabis_model.collection import Collection +from miabis_model.collection_organization import CollectionOrganization +from miabis_model.condition import Condition +from miabis_model.diagnosis_report import DiagnosisReport +from miabis_model.network import Network +from miabis_model.network_organization import NetworkOrganization +from miabis_model.observation import Observation +from miabis_model.sample import Sample +from miabis_model.sample_donor import SampleDonor +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id, \ get_material_type_from_detailed_material_type -from src.blaze_client.NonExistentResourceException import NonExistentResourceException +from blaze_client.NonExistentResourceException import NonExistentResourceException class BlazeClient: diff --git a/src/MIABIS_on_FHIR/__init__.py b/miabis_model/__init__.py similarity index 100% rename from src/MIABIS_on_FHIR/__init__.py rename to miabis_model/__init__.py diff --git a/src/MIABIS_on_FHIR/biobank.py b/miabis_model/biobank.py similarity index 97% rename from src/MIABIS_on_FHIR/biobank.py rename to miabis_model/biobank.py index bb85eb4..55c39db 100644 --- a/src/MIABIS_on_FHIR/biobank.py +++ b/miabis_model/biobank.py @@ -3,13 +3,13 @@ from fhirclient.models.meta import Meta from fhirclient.models.organization import Organization -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import BIOBANK_BIOPROCESSING_AND_ANALYTICAL_CAPABILITIES, \ +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import BIOBANK_BIOPROCESSING_AND_ANALYTICAL_CAPABILITIES, \ BIOBANK_INFRASTRUCTURAL_CAPABILITIES, \ BIOBANK_ORGANISATIONAL_CAPABILITIES, DEFINITION_BASE_URL -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \ +from miabis_model.util.parsing_util import get_nested_value, parse_contact +from miabis_model.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \ create_codeable_concept_extension, create_string_extension diff --git a/src/MIABIS_on_FHIR/collection.py b/miabis_model/collection.py similarity index 97% rename from src/MIABIS_on_FHIR/collection.py rename to miabis_model/collection.py index c674ed7..dbc2be8 100644 --- a/src/MIABIS_on_FHIR/collection.py +++ b/miabis_model/collection.py @@ -9,13 +9,13 @@ from fhirclient.models.quantity import Quantity from fhirclient.models.range import Range -from src.MIABIS_on_FHIR.gender import Gender -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import COLLECTION_INCLUSION_CRITERIA, COLLECTION_MATERIAL_TYPE_CODES -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_integer_extension, \ +from miabis_model.gender import Gender +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.storage_temperature import StorageTemperature +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import COLLECTION_INCLUSION_CRITERIA, COLLECTION_MATERIAL_TYPE_CODES +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier, create_integer_extension, \ create_codeable_concept_extension, \ create_codeable_concept diff --git a/src/MIABIS_on_FHIR/collection_organization.py b/miabis_model/collection_organization.py similarity index 97% rename from src/MIABIS_on_FHIR/collection_organization.py rename to miabis_model/collection_organization.py index df7df5d..29bf3fa 100644 --- a/src/MIABIS_on_FHIR/collection_organization.py +++ b/miabis_model/collection_organization.py @@ -6,12 +6,12 @@ from fhirclient.models.meta import Meta from fhirclient.models.organization import Organization -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import COLLECTION_DESIGN, COLLECTION_SAMPLE_COLLECTION_SETTING, \ +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import COLLECTION_DESIGN, COLLECTION_SAMPLE_COLLECTION_SETTING, \ COLLECTION_SAMPLE_SOURCE, COLLECTION_DATASET_TYPE, COLLECTION_USE_AND_ACCESS_CONDITIONS -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_country_of_residence, create_contact, create_codeable_concept_extension, \ +from miabis_model.util.parsing_util import get_nested_value, parse_contact, parse_reference_id +from miabis_model.util.util import create_country_of_residence, create_contact, create_codeable_concept_extension, \ create_string_extension, create_fhir_identifier diff --git a/src/MIABIS_on_FHIR/condition.py b/miabis_model/condition.py similarity index 96% rename from src/MIABIS_on_FHIR/condition.py rename to miabis_model/condition.py index 45b2917..2700cae 100644 --- a/src/MIABIS_on_FHIR/condition.py +++ b/miabis_model/condition.py @@ -7,10 +7,10 @@ from fhirclient.models.fhirreference import FHIRReference from fhirclient.models.meta import Meta -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier class Condition: diff --git a/src/MIABIS_on_FHIR/diagnosis_report.py b/miabis_model/diagnosis_report.py similarity index 97% rename from src/MIABIS_on_FHIR/diagnosis_report.py rename to miabis_model/diagnosis_report.py index 1729879..ce8b990 100644 --- a/src/MIABIS_on_FHIR/diagnosis_report.py +++ b/miabis_model/diagnosis_report.py @@ -6,10 +6,10 @@ from fhirclient.models.fhirreference import FHIRReference from fhirclient.models.meta import Meta -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier class DiagnosisReport: diff --git a/src/MIABIS_on_FHIR/gender.py b/miabis_model/gender.py similarity index 100% rename from src/MIABIS_on_FHIR/gender.py rename to miabis_model/gender.py diff --git a/src/MIABIS_on_FHIR/incorrect_json_format.py b/miabis_model/incorrect_json_format.py similarity index 100% rename from src/MIABIS_on_FHIR/incorrect_json_format.py rename to miabis_model/incorrect_json_format.py diff --git a/src/MIABIS_on_FHIR/network.py b/miabis_model/network.py similarity index 96% rename from src/MIABIS_on_FHIR/network.py rename to miabis_model/network.py index 8ebf950..faaf609 100644 --- a/src/MIABIS_on_FHIR/network.py +++ b/miabis_model/network.py @@ -5,10 +5,10 @@ from fhirclient.models.group import Group from fhirclient.models.meta import Meta -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier class Network: diff --git a/src/MIABIS_on_FHIR/network_organization.py b/miabis_model/network_organization.py similarity index 96% rename from src/MIABIS_on_FHIR/network_organization.py rename to miabis_model/network_organization.py index cda8f3e..5f613ee 100644 --- a/src/MIABIS_on_FHIR/network_organization.py +++ b/miabis_model/network_organization.py @@ -4,11 +4,11 @@ from fhirclient.models.meta import Meta from fhirclient.models.organization import Organization -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import NETWORK_COMMON_COLLAB_TOPICS -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_contact, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \ +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import NETWORK_COMMON_COLLAB_TOPICS +from miabis_model.util.parsing_util import get_nested_value, parse_contact, parse_reference_id +from miabis_model.util.util import create_fhir_identifier, create_contact, create_country_of_residence, \ create_codeable_concept_extension, create_string_extension diff --git a/src/MIABIS_on_FHIR/observation.py b/miabis_model/observation.py similarity index 96% rename from src/MIABIS_on_FHIR/observation.py rename to miabis_model/observation.py index 91ca094..b181247 100644 --- a/src/MIABIS_on_FHIR/observation.py +++ b/miabis_model/observation.py @@ -11,10 +11,10 @@ from fhirclient.models.fhirreference import FHIRReference from fhirclient.models.meta import Meta -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier class Observation: diff --git a/src/MIABIS_on_FHIR/sample.py b/miabis_model/sample.py similarity index 96% rename from src/MIABIS_on_FHIR/sample.py rename to miabis_model/sample.py index 4d0d588..d7724ac 100644 --- a/src/MIABIS_on_FHIR/sample.py +++ b/miabis_model/sample.py @@ -9,12 +9,12 @@ from fhirclient.models.meta import Meta from fhirclient.models.specimen import Specimen, SpecimenCollection, SpecimenProcessing -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import DETAILED_MATERIAL_TYPE_CODES -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value, parse_reference_id -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_codeable_concept, \ +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.storage_temperature import StorageTemperature +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import DETAILED_MATERIAL_TYPE_CODES +from miabis_model.util.parsing_util import get_nested_value, parse_reference_id +from miabis_model.util.util import create_fhir_identifier, create_codeable_concept, \ create_codeable_concept_extension diff --git a/src/MIABIS_on_FHIR/sample_donor.py b/miabis_model/sample_donor.py similarity index 93% rename from src/MIABIS_on_FHIR/sample_donor.py rename to miabis_model/sample_donor.py index eb1d10c..e33c691 100644 --- a/src/MIABIS_on_FHIR/sample_donor.py +++ b/miabis_model/sample_donor.py @@ -6,12 +6,12 @@ from fhirclient.models.meta import Meta from fhirclient.models.patient import Patient -from src.MIABIS_on_FHIR.gender import Gender -from src.MIABIS_on_FHIR.incorrect_json_format import IncorrectJsonFormatException -from src.MIABIS_on_FHIR.util.config import FHIRConfig -from src.MIABIS_on_FHIR.util.constants import DONOR_DATASET_TYPE -from src.MIABIS_on_FHIR.util.parsing_util import get_nested_value -from src.MIABIS_on_FHIR.util.util import create_fhir_identifier, create_codeable_concept_extension +from miabis_model.gender import Gender +from miabis_model.incorrect_json_format import IncorrectJsonFormatException +from miabis_model.util.config import FHIRConfig +from miabis_model.util.constants import DONOR_DATASET_TYPE +from miabis_model.util.parsing_util import get_nested_value +from miabis_model.util.util import create_fhir_identifier, create_codeable_concept_extension class SampleDonor: diff --git a/src/MIABIS_on_FHIR/storage_temperature.py b/miabis_model/storage_temperature.py similarity index 100% rename from src/MIABIS_on_FHIR/storage_temperature.py rename to miabis_model/storage_temperature.py diff --git a/src/MIABIS_on_FHIR/util/__init__.py b/miabis_model/util/__init__.py similarity index 100% rename from src/MIABIS_on_FHIR/util/__init__.py rename to miabis_model/util/__init__.py diff --git a/src/MIABIS_on_FHIR/util/config.py b/miabis_model/util/config.py similarity index 100% rename from src/MIABIS_on_FHIR/util/config.py rename to miabis_model/util/config.py diff --git a/src/MIABIS_on_FHIR/util/constants.py b/miabis_model/util/constants.py similarity index 100% rename from src/MIABIS_on_FHIR/util/constants.py rename to miabis_model/util/constants.py diff --git a/src/MIABIS_on_FHIR/util/parsing_util.py b/miabis_model/util/parsing_util.py similarity index 91% rename from src/MIABIS_on_FHIR/util/parsing_util.py rename to miabis_model/util/parsing_util.py index e5adb9f..7a82a38 100644 --- a/src/MIABIS_on_FHIR/util/parsing_util.py +++ b/miabis_model/util/parsing_util.py @@ -1,7 +1,7 @@ from dateutil import parser as date_parser from datetime import date -from src.MIABIS_on_FHIR.util.constants import DETAILED_MATERIAL_TYPE_TO_COLLECTION_MATERIAL_TYPE_MAP +from miabis_model.util.constants import DETAILED_MATERIAL_TYPE_TO_COLLECTION_MATERIAL_TYPE_MAP def get_nested_value(data: dict, keys: list): diff --git a/src/MIABIS_on_FHIR/util/util.py b/miabis_model/util/util.py similarity index 100% rename from src/MIABIS_on_FHIR/util/util.py rename to miabis_model/util/util.py diff --git a/pyproject.toml b/pyproject.toml index 1c72335..b9bb4be 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta" [project] name = "MIABIS_on_FHIR" -version = "1.0.0" -description = "Library containing classes for easier handling of data according to the MIABIS on FHIR profile" +version = "1.1.0" +description = "Library containing classes for easier handling of data according to the MIABIS on FHIR profile, as well as client for communication with sample blaze server" readme = "README.md" authors = [{"name" = "Simon Konar", "email" = "simon.konar@gmail.com"}] license = { file = "LICENSE" } @@ -26,11 +26,8 @@ requires-python = ">=3.11" [project.optional-dependencies] test=["pytest >= 8.3.0"] -[tool.setuptools] -package-dir = { "" = "src" } [tool.setuptools.packages.find] -where = ["src"] -include = ["MIABIS_on_FHIR*", "blaze_client*"] +include = ["miabis_model*", "blaze_client*"] exclude =["test*"] \ No newline at end of file diff --git a/test/service/test_blaze_client.py b/test/service/test_blaze_client.py index 80aad04..a653a9a 100644 --- a/test/service/test_blaze_client.py +++ b/test/service/test_blaze_client.py @@ -3,24 +3,22 @@ import pytest as pytest import requests.exceptions -from fhirclient.models.bundle import Bundle, BundleEntry, BundleEntryRequest -from fhirclient.models.patient import Patient from requests.exceptions import HTTPError -from src.MIABIS_on_FHIR.biobank import Biobank -from src.MIABIS_on_FHIR.collection import Collection -from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization -from src.MIABIS_on_FHIR.condition import Condition -from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport -from src.MIABIS_on_FHIR.gender import Gender -from src.MIABIS_on_FHIR.network import Network -from src.MIABIS_on_FHIR.network_organization import NetworkOrganization -from src.MIABIS_on_FHIR.observation import Observation -from src.MIABIS_on_FHIR.sample import Sample -from src.MIABIS_on_FHIR.sample_donor import SampleDonor -from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature -from src.blaze_client.NonExistentResourceException import NonExistentResourceException -from src.blaze_client.blaze_client import BlazeClient +from miabis_model import Biobank +from miabis_model import Collection +from miabis_model.collection_organization import CollectionOrganization +from miabis_model import Condition +from miabis_model import DiagnosisReport +from miabis_model import Gender +from miabis_model import Network +from miabis_model import NetworkOrganization +from miabis_model.observation import Observation +from miabis_model import Sample +from miabis_model import SampleDonor +from miabis_model import StorageTemperature +from blaze_client import NonExistentResourceException +from blaze_client.blaze_client import BlazeClient class TestBlazeService(unittest.TestCase): diff --git a/test/unit/model/test_biobank.py b/test/unit/model/test_biobank.py index a5edaa1..d5105a7 100644 --- a/test/unit/model/test_biobank.py +++ b/test/unit/model/test_biobank.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.biobank import Biobank +from miabis_model import Biobank class TestBiobank(unittest.TestCase): diff --git a/test/unit/model/test_collection.py b/test/unit/model/test_collection.py index cf7d313..8ac52aa 100644 --- a/test/unit/model/test_collection.py +++ b/test/unit/model/test_collection.py @@ -2,9 +2,9 @@ from fhirclient.models.group import Group -from src.MIABIS_on_FHIR.collection import Collection -from src.MIABIS_on_FHIR.gender import Gender -from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature +from miabis_model import Collection +from miabis_model import Gender +from miabis_model import StorageTemperature class TestCollection(unittest.TestCase): diff --git a/test/unit/model/test_collection_org.py b/test/unit/model/test_collection_org.py index d5a1b4c..bdb2613 100644 --- a/test/unit/model/test_collection_org.py +++ b/test/unit/model/test_collection_org.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.collection_organization import CollectionOrganization +from miabis_model.collection_organization import CollectionOrganization class TestCollectionOrganization(unittest.TestCase): diff --git a/test/unit/model/test_condition.py b/test/unit/model/test_condition.py index 2840770..c4d843a 100644 --- a/test/unit/model/test_condition.py +++ b/test/unit/model/test_condition.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.condition import Condition +from miabis_model import Condition class TestCondition(unittest.TestCase): diff --git a/test/unit/model/test_diagnosis_report.py b/test/unit/model/test_diagnosis_report.py index a9d37a7..9983b12 100644 --- a/test/unit/model/test_diagnosis_report.py +++ b/test/unit/model/test_diagnosis_report.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.diagnosis_report import DiagnosisReport +from miabis_model import DiagnosisReport class TestDiagnosisReport(unittest.TestCase): diff --git a/test/unit/model/test_network.py b/test/unit/model/test_network.py index 8590782..3910ddf 100644 --- a/test/unit/model/test_network.py +++ b/test/unit/model/test_network.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.network import Network +from miabis_model import Network class TestNetwork(unittest.TestCase): diff --git a/test/unit/model/test_network_org.py b/test/unit/model/test_network_org.py index e1f9486..78d59f7 100644 --- a/test/unit/model/test_network_org.py +++ b/test/unit/model/test_network_org.py @@ -1,6 +1,6 @@ import unittest -from src.MIABIS_on_FHIR.network_organization import NetworkOrganization +from miabis_model import NetworkOrganization class TestNetworkOrganization(unittest.TestCase): diff --git a/test/unit/model/test_observation.py b/test/unit/model/test_observation.py index 9d014dd..f18af9d 100644 --- a/test/unit/model/test_observation.py +++ b/test/unit/model/test_observation.py @@ -1,7 +1,7 @@ import datetime import unittest -from src.MIABIS_on_FHIR.observation import Observation +from miabis_model.observation import Observation class TestObservation(unittest.TestCase): diff --git a/test/unit/model/test_sample.py b/test/unit/model/test_sample.py index b102e31..04a59c9 100644 --- a/test/unit/model/test_sample.py +++ b/test/unit/model/test_sample.py @@ -1,8 +1,8 @@ import unittest from datetime import datetime -from src.MIABIS_on_FHIR.sample import Sample -from src.MIABIS_on_FHIR.storage_temperature import StorageTemperature +from miabis_model import Sample +from miabis_model import StorageTemperature class TestSample(unittest.TestCase): diff --git a/test/unit/model/test_sample_donor.py b/test/unit/model/test_sample_donor.py index e5a5fc3..15a3294 100644 --- a/test/unit/model/test_sample_donor.py +++ b/test/unit/model/test_sample_donor.py @@ -1,8 +1,8 @@ import unittest from datetime import datetime -from src.MIABIS_on_FHIR.sample_donor import SampleDonor -from src.MIABIS_on_FHIR.gender import Gender +from miabis_model import SampleDonor +from miabis_model import Gender class TestSampleDonor(unittest.TestCase):