Compatibility with core#2567 (AnalysisCategory to DX) (#107)

* Compatibility with core#2567 (AnalysisCategory to DX)

* Changelog

README.rst

@@ -1,13 +1,26 @@
 Patients for SENAITE
 ====================
 
+.. image:: https://img.shields.io/pypi/v/senaite.patient.svg?style=flat-square
+    :target: https://pypi.python.org/pypi/senaite.patient
+
+.. image:: https://img.shields.io/github/actions/workflow/status/senaite/senaite.patient/build-and-test.yml?branch=2.x
+   :target: https://github.com/senaite/senaite.patient/actions/workflows/build-and-test.yml?query=branch:2.x
+
+.. image:: https://img.shields.io/github/issues-pr/senaite/senaite.patient.svg?style=flat-square
+    :target: https://github.com/senaite/senaite.patient/pulls
+
+.. image:: https://img.shields.io/github/issues/senaite/senaite.patient.svg?style=flat-square
+    :target: https://github.com/senaite/senaite.patient/issues
+
+.. image:: https://img.shields.io/badge/Made%20for%20SENAITE-%E2%AC%A1-lightgrey.svg
+   :target: https://www.senaite.com
+
 About
 -----
 
 SENAITE.PATIENT adds Patient handling to `SENAITE LIMS`_.
 
-NOTE: This Add-on requires `senaite.lims >= 2.2.0`
-
 
 License
 -------

buildout.cfg

@@ -1,109 +1,3 @@
 [buildout]
-index = https://pypi.org/simple/
-extends = https://dist.plone.org/release/5.2-latest/versions.cfg
-find-links =
-    https://dist.plone.org/release/5.2-latest/
-    https://dist.plone.org/thirdparty/
-
-parts =
-    instance
-    test
-    omelette
-    i18ndude
-    zopepy
-    update_translations
-    update_sources
-    write_code_headers
-
-eggs =
-    senaite.core
-    senaite.app.listing
-    senaite.app.spotlight
-    senaite.app.supermodel
-    senaite.patient
-    senaite.impress
-    senaite.jsonapi
-    senaite.lims
-    plone.reload
-    Products.PrintingMailHost
-
-extensions = mr.developer
-
+extends = https://raw.githubusercontent.com/senaite/senaite.core/2.x/buildout.base.cfg
 package-name = senaite.patient
-
-versions = versions
-show-picked-versions = true
-
-plone-user = admin:admin
-
-develop = .
-sources = sources
-auto-checkout = *
-
-[sources]
-senaite.core = git https://github.com/senaite/senaite.core.git pushurl[email protected]:senaite/senaite.core.git branch=2.x
-senaite.app.listing = git https://github.com/senaite/senaite.app.listing.git pushurl[email protected]:senaite/senaite.app.listing.git branch=2.x
-senaite.app.spotlight = git https://github.com/senaite/senaite.app.spotlight.git pushurl[email protected]:senaite/senaite.app.spotlight.git branch=2.x
-senaite.app.supermodel = git https://github.com/senaite/senaite.app.supermodel.git pushurl[email protected]:senaite/senaite.app.supermodel.git branch=2.x
-senaite.impress = git https://github.com/senaite/senaite.impress.git pushurl[email protected]:senaite/senaite.impress.git branch=2.x
-senaite.jsonapi = git https://github.com/senaite/senaite.jsonapi.git pushurl[email protected]:senaite/senaite.jsonapi.git branch=2.x
-senaite.lims = git https://github.com/senaite/senaite.lims.git pushurl[email protected]:senaite/senaite.lims.git branch=2.x
-
-[instance]
-recipe = plone.recipe.zope2instance
-http-address = 127.0.0.1:8080
-user = ${buildout:plone-user}
-wsgi = off
-eggs =
-    Plone
-    plone.app.upgrade
-    ${buildout:package-name}
-    ${buildout:eggs}
-deprecation-warnings = on
-environment-vars =
-    zope_i18n_compile_mo_files true
-zcml =
-
-[i18ndude]
-unzip = true
-recipe = zc.recipe.egg
-eggs = i18ndude
-
-[update_translations]
-recipe = collective.recipe.template
-output = ${buildout:directory}/bin/update_translations
-input = ${buildout:directory}/templates/update_translations.in
-mode = 755
-
-[update_sources]
-recipe = collective.recipe.template
-output = ${buildout:directory}/bin/update_sources
-input = ${buildout:directory}/templates/update_sources.in
-mode = 755
-
-[write_code_headers]
-recipe = collective.recipe.template
-output = ${buildout:directory}/bin/write_code_headers
-input = ${buildout:directory}/templates/write_code_headers.py.in
-mode = 755
-
-[test]
-recipe = zc.recipe.testrunner
-defaults = ['--auto-color', '--auto-progress']
-eggs =
-    senaite.patient [test]
-
-[omelette]
-recipe = collective.recipe.omelette
-eggs = ${buildout:eggs}
-
-[zopepy]
-recipe = zc.recipe.egg
-eggs = ${instance:eggs}
-interpreter = zopepy
-scripts = zopepy
-
-[versions]
-# versions taken from requirements.txt
-setuptools =
-zc.buildout =

docs/changelog.rst

@@ -4,6 +4,7 @@ Changelog
 1.5.0 (unreleased)
 ------------------
 
+- #107 Compatibility with core#2567 (AnalysisCategory to DX)
 - #106 Skip patient creation if the user has no permissions
 - #95  Support for dynamic analysis specs with MinAge, MaxAge and Sex columns
 - #98  Allow to flag patients as deceased

src/senaite/patient/tests/base.py

@@ -19,108 +19,42 @@
 # Some rights reserved, see README and LICENSE.
 
 import transaction
-import unittest2 as unittest
-from plone.app.testing import PLONE_FIXTURE
-from plone.app.testing import TEST_USER_ID
-from plone.app.testing import TEST_USER_NAME
-from plone.app.testing import TEST_USER_PASSWORD
-from plone.app.testing import FunctionalTesting
-from plone.app.testing import PloneSandboxLayer
 from plone.app.testing import applyProfile
-from plone.app.testing import setRoles
+from plone.app.testing import FunctionalTesting
 from plone.testing import zope
-from plone.testing.z2 import Browser
+from senaite.core.tests.base import BaseTestCase
+from senaite.core.tests.layers import BaseLayer
 
 
-class SimpleTestLayer(PloneSandboxLayer):
-    """Setup Plone with installed AddOn only
-    """
-    defaultBases = (PLONE_FIXTURE,)
+class SimpleTestLayer(BaseLayer):
 
     def setUpZope(self, app, configurationContext):
         super(SimpleTestLayer, self).setUpZope(app, configurationContext)
 
-        import bika.lims
-        import senaite.app.listing
-        import senaite.app.spotlight
-        import senaite.core
-        import senaite.impress
-        import senaite.lims
-        import senaite.patient
-
         # Load ZCML
-        self.loadZCML(package=bika.lims)
-        self.loadZCML(package=senaite.lims)
-        self.loadZCML(package=senaite.core)
-        self.loadZCML(package=senaite.app.listing)
-        self.loadZCML(package=senaite.impress)
-        self.loadZCML(package=senaite.app.spotlight)
+        import senaite.patient
         self.loadZCML(package=senaite.patient)
 
         # Install product and call its initialize() function
-        zope.installProduct(app, "bika.lims")
-        zope.installProduct(app, "senaite.lims")
-        zope.installProduct(app, "senaite.core")
-        zope.installProduct(app, "senaite.app.listing")
-        zope.installProduct(app, "senaite.impress")
-        zope.installProduct(app, "senaite.app.spotlight")
         zope.installProduct(app, "senaite.patient")
 
     def setUpPloneSite(self, portal):
         super(SimpleTestLayer, self).setUpPloneSite(portal)
-        applyProfile(portal, "senaite.core:default")
         applyProfile(portal, "senaite.patient:default")
         transaction.commit()
 
 
-###
-# Use for simple tests (w/o contents)
-###
-SIMPLE_FIXTURE = SimpleTestLayer()
+SIMPLE_TEST_LAYER_FIXTURE = SimpleTestLayer()
 SIMPLE_TESTING = FunctionalTesting(
-    bases=(SIMPLE_FIXTURE, ),
+    bases=(SIMPLE_TEST_LAYER_FIXTURE, ),
     name="senaite.patient:SimpleTesting"
 )
 
 
-class SimpleTestCase(unittest.TestCase):
+class SimpleTestCase(BaseTestCase):
+    """Use for test cases which do not rely on demo data
+    """
     layer = SIMPLE_TESTING
 
     def setUp(self):
         super(SimpleTestCase, self).setUp()
-
-        self.app = self.layer["app"]
-        self.portal = self.layer["portal"]
-        self.request = self.layer["request"]
-        self.request["ACTUAL_URL"] = self.portal.absolute_url()
-        setRoles(self.portal, TEST_USER_ID, ["LabManager", "Manager"])
-
-    def getBrowser(self,
-                   username=TEST_USER_NAME,
-                   password=TEST_USER_PASSWORD,
-                   loggedIn=True):
-
-        # Instantiate and return a testbrowser for convenience
-        browser = Browser(self.portal)
-        browser.addHeader("Accept-Language", "en-US")
-        browser.handleErrors = False
-        if loggedIn:
-            browser.open(self.portal.absolute_url())
-            browser.getControl("Login Name").value = username
-            browser.getControl("Password").value = password
-            browser.getControl("Log in").click()
-            self.assertTrue("You are now logged in" in browser.contents)
-        return browser
-
-
-class FunctionalTestCase(unittest.TestCase):
-    layer = SIMPLE_TESTING
-
-    def setUp(self):
-        super(FunctionalTestCase, self).setUp()
-
-        self.app = self.layer["app"]
-        self.portal = self.layer["portal"]
-        self.request = self.layer["request"]
-        self.request["ACTUAL_URL"] = self.portal.absolute_url()
-        setRoles(self.portal, TEST_USER_ID, ["LabManager", "Member"])

src/senaite/patient/tests/doctests/API.rst

@@ -15,6 +15,8 @@ Needed Imports:
     >>> from bika.lims.api import get_review_status
     >>> from datetime import date
     >>> from dateutil.relativedelta import relativedelta
+    >>> from plone.app.testing import setRoles
+    >>> from plone.app.testing import TEST_USER_ID
     >>> from senaite.core.api import dtime
     >>> from senaite.patient import api
 
@@ -23,6 +25,9 @@ Variables:
     >>> portal = self.portal
     >>> request = self.request
 
+Assign default roles for the user to test with:
+
+    >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
 
 Test fixture:
 

src/senaite/patient/tests/doctests/AgeDateOfBirthField.rst

@@ -14,6 +14,8 @@ Needed Imports:
     >>> from bika.lims.utils.analysisrequest import create_analysisrequest
     >>> from DateTime import DateTime
     >>> from datetime import datetime
+    >>> from plone.app.testing import setRoles
+    >>> from plone.app.testing import TEST_USER_ID
     >>> from senaite.core.api import dtime
     >>> from senaite.patient.api import to_ymd
 
@@ -39,6 +41,10 @@ Variables:
     >>> sampled = DateTime("2020-12-01")
     >>> birth_date = DateTime("1979-12-07")
 
+Assign default roles for the user to test with:
+
+    >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
+
 Test fixture:
 
     >>> import os
@@ -51,7 +57,7 @@ We need to create some basic objects for the test:
     >>> sampletype = api.create(bika_setup.bika_sampletypes, "SampleType", title="Blood", Prefix="B")
     >>> labcontact = api.create(bika_setup.bika_labcontacts, "LabContact", Firstname="Lab", Lastname="Manager")
     >>> department = api.create(setup.departments, "Department", title="Clinical Lab", Manager=labcontact)
-    >>> category = api.create(bika_setup.bika_analysiscategories, "AnalysisCategory", title="Blood", Department=department)
+    >>> category = api.create(setup.analysiscategories, "AnalysisCategory", title="Blood", Department=department)
     >>> malaria = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Malaria Count", Keyword="MC", Price="10", Category=category.UID(), Accredited=True)
     >>> sample = new_sample([malaria], client, contact, sampletype, sampled, DateOfBirth=birth_date)
 

src/senaite/patient/tests/doctests/DynamicResultRanges.rst

@@ -137,7 +137,7 @@ Create some baseline objects for the test:
     >>> sampletype = api.create(bika_setup.bika_sampletypes, "SampleType", title="EDTA", Prefix="EDTA")
     >>> labcontact = api.create(bika_setup.bika_labcontacts, "LabContact", Firstname="Lab", Lastname="Manager")
     >>> department = api.create(setup.departments, "Department", title="Biochemistry", Manager=labcontact)
-    >>> category = api.create(bika_setup.bika_analysiscategories, "AnalysisCategory", title="Biochemistry", Department=department)
+    >>> category = api.create(setup.analysiscategories, "AnalysisCategory", title="Biochemistry", Department=department)
     >>> Ht = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Hematocrit", Keyword="Ht", Category=category)
 
 Create a default specification for the Sample type `EDTA`:

src/senaite/patient/tests/doctests/Patient.rst

@@ -12,6 +12,8 @@ Test Setup
 Needed Imports:
 
     >>> from bika.lims import api
+    >>> from plone.app.testing import setRoles
+    >>> from plone.app.testing import TEST_USER_ID
 
 Variables:
 
@@ -20,6 +22,10 @@ Variables:
     >>> setup = api.get_setup()
     >>> patients = portal.patients
 
+Assign default roles for the user to test with:
+
+    >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
+
 
 Patients
 --------

src/senaite/patient/tests/doctests/PatientSample.rst

@@ -61,20 +61,23 @@ Variables:
     >>> birthdate = DateTime("1980-02-25")
     >>> sampled = DateTime("2023-05-19")
 
+Assign default roles for the user to test with:
+
+    >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
+
 Test fixture:
 
     >>> import os
     >>> os.environ["TZ"] = "CET"
 
 We need to create some basic objects for the test:
 
-    >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
     >>> client = api.create(portal.clients, "Client", Name="General Hospital", ClientID="GH", MemberDiscountApplies=False)
     >>> contact = api.create(client, "Contact", Firstname="Rita", Lastname="Mohale")
     >>> sampletype = api.create(bika_setup.bika_sampletypes, "SampleType", title="Blood", Prefix="B")
     >>> labcontact = api.create(bika_setup.bika_labcontacts, "LabContact", Firstname="Lab", Lastname="Manager")
     >>> department = api.create(setup.departments, "Department", title="Clinical Lab", Manager=labcontact)
-    >>> category = api.create(bika_setup.bika_analysiscategories, "AnalysisCategory", title="Blood", Department=department)
+    >>> category = api.create(setup.analysiscategories, "AnalysisCategory", title="Blood", Department=department)
     >>> MC = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Malaria Count", Keyword="MC", Price="10", Category=category.UID(), Accredited=True)
     >>> MS = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Malaria Species", Keyword="MS", Price="10", Category=category.UID(), Accredited=True)
 

src/senaite/patient/tests/doctests/PatientWorkflow.rst

@@ -61,15 +61,18 @@ Variables:
     >>> bika_setup = api.get_bika_setup()
     >>> patients = portal.patients
 
-We need to create some basic objects for the test:
+Assign default roles for the user to test with:
 
     >>> setRoles(portal, TEST_USER_ID, ['LabManager',])
+
+We need to create some basic objects for the test:
+
     >>> client = api.create(portal.clients, "Client", Name="General Hospital", ClientID="GH", MemberDiscountApplies=False)
     >>> contact = api.create(client, "Contact", Firstname="Rita", Lastname="Mohale")
     >>> sampletype = api.create(bika_setup.bika_sampletypes, "SampleType", title="Blood", Prefix="B")
     >>> labcontact = api.create(bika_setup.bika_labcontacts, "LabContact", Firstname="Lab", Lastname="Manager")
     >>> department = api.create(setup.departments, "Department", title="Clinical Lab", Manager=labcontact)
-    >>> category = api.create(bika_setup.bika_analysiscategories, "AnalysisCategory", title="Blood", Department=department)
+    >>> category = api.create(setup.analysiscategories, "AnalysisCategory", title="Blood", Department=department)
     >>> MC = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Malaria Count", Keyword="MC", Price="10", Category=category.UID(), Accredited=True)
     >>> MS = api.create(bika_setup.bika_analysisservices, "AnalysisService", title="Malaria Species", Keyword="MS", Price="10", Category=category.UID(), Accredited=True)