Merge branch 'master' of github.com:senaite/senaite.ast into fix-smal…

…ler-decimals

.github/workflows/build-and-test.yml

@@ -0,0 +1,30 @@
+name: build and test senaite.ast
+on:
+  - push
+  - pull_request
+env:
+  PLONE_VERSION: "5.2"
+jobs:
+  build-and-test:
+    runs-on: 'ubuntu-20.04'
+    container:
+      image: python:2.7.18-buster
+    steps:
+      - uses: actions/checkout@v3
+      - name: cache eggs
+        uses: actions/cache@v3
+        with:
+          key: eggs-cache-${{ hashFiles('buildout.cfg', 'requirements.txt') }}
+          path: |
+            eggs/
+      - name: install
+        run: |
+          pip install virtualenv
+          virtualenv -p `which python` .
+          bin/pip install --upgrade pip
+          bin/pip install -r requirements.txt
+          bin/buildout -N -t 3 annotate
+          bin/buildout -N -t 3
+      - name: test
+        run: |
+          bin/test -s senaite.ast.tests

.readthedocs.yaml

@@ -0,0 +1,15 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py

README.rst

@@ -4,8 +4,8 @@ Antibiotic Sensitivity Testing (AST) for SENAITE
 .. image:: https://img.shields.io/pypi/v/senaite.ast.svg?style=flat-square
     :target: https://pypi.python.org/pypi/senaite.ast
 
-.. image:: https://img.shields.io/travis/com/senaite/senaite.ast/master.svg?style=flat-square
-    :target: https://app.travis-ci.com/github/senaite/senaite.ast
+.. image:: https://img.shields.io/github/actions/workflow/status/senaite/senaite.ast/build-and-test.yml?branch=2.x
+   :target: https://github.com/senaite/senaite.ast/actions/workflows/build-and-test.yml?query=branch:2.x
 
 .. image:: https://readthedocs.org/projects/pip/badge/
     :target: https://senaiteast.readthedocs.org

buildout.cfg

@@ -1,105 +1,7 @@
 [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
-    write_code_headers
-
-eggs =
-    senaite.core
-    senaite.app.listing
-    senaite.app.spotlight
-    senaite.app.supermodel
-    senaite.impress
-    senaite.jsonapi
-    senaite.lims
-    senaite.abx
-    senaite.microorganism
-    senaite.ast
-    plone.reload
-    Products.PrintingMailHost
-
-extensions = mr.developer
-
+extends = https://raw.githubusercontent.com/senaite/senaite.core/2.x/buildout.base.cfg
 package-name = senaite.ast
 
-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 branch=2.x
-senaite.app.listing = git https://github.com/senaite/senaite.app.listing.git branch=2.x
-senaite.app.spotlight = git https://github.com/senaite/senaite.app.spotlight.git branch=2.x
-senaite.app.supermodel = git https://github.com/senaite/senaite.app.supermodel.git branch=2.x
-senaite.impress = git https://github.com/senaite/senaite.impress.git branch=2.x
-senaite.jsonapi = git https://github.com/senaite/senaite.jsonapi.git branch=2.x
-senaite.lims = git https://github.com/senaite/senaite.lims.git branch=2.x
 senaite.abx = git https://github.com/senaite/senaite.abx.git
 senaite.microorganism = git https://github.com/senaite/senaite.microorganism.git
-
-[instance]
-recipe = plone.recipe.zope2instance
-http-address = 127.0.0.1:8080
-user = ${buildout:plone-user}
-wsgi = on
-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
-
-[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.ast [test]
-
-[omelette]
-recipe = collective.recipe.omelette
-eggs = ${buildout:eggs}
-
-[zopepy]
-recipe = zc.recipe.egg
-eggs = ${instance:eggs}
-interpreter = zopepy
-scripts = zopepy
-
-[versions]
-setuptools =
-zc.buildout =

docs/changelog.rst

@@ -4,6 +4,14 @@ Changelog
 1.2.0 (unreleased)
 ------------------
 
+- #37 Compatibility with core#2567 (AnalysisCategory to DX)
+- #37 Compatibility with core#2471 (Department to DX)
+- #36 Fix user can edit ast built-in services after upgrades
+- #35 Compatibility with core#2521 - AT2DX ARTemplate/SampleTemplate
+- #34 Add transition "Reject antibiotics"
+- #33 Display the Antibiotic Sensitivity section only when necessary
+- #32 Compatibility with senaite.core#2492 (AnalysisProfile to DX)
+
 
 1.1.0 (2024-01-04)
 ------------------
@@ -17,6 +25,7 @@ Changelog
 - #21 Fix AST entry is empty when analyses categorization for sample is checked
 - #20 Compatibility with senaite.app.listing#87
 
+
 1.0.0 (2022-06-18)
 ------------------
 

docs/quickstart.rst

@@ -175,7 +175,30 @@ From this view, user can choose the tuples Microorganism-Antibiotic to be
 reported in results. Once the button "Save" is pressed, the value for analyses
 with name "Report" for all microorganisms are updated accordingly.
 
-.. Links
+
+.. _RejectAntibiotics:
+
+Flag antibiotics as Not Tested
+------------------------------
+
+Quite often, laboratory manager will want to report "Not tested" for some
+antibiotics and microorganisms, while keeping them in the AST panel. This can
+be easily achieved with the transition "Reject antibiotics". This transition is
+available for analyses that are part of a sensitivity testing panel. Once
+clicked, a modal view is displayed, where user can choose the antibiotics to be
+flagged as "Not Tested":
+
+.. image:: static/reject_antibiotics.png
+  :width: 640
+  :alt: Reject antibiotics
+
+Once done, "NT" is displayed as a result for the selected antibiotics, both in
+results entry and in results report:
+
+.. image:: static/not_tested.png
+  :width: 640
+  :alt: Antibiotics flagged as Not Tested
+
 
 .. _SENAITE LIMS: https://www.senaite.com
 .. _senaite.ast: https://pypi.python.org/pypi/senaite.ast

requirements.txt

@@ -1,3 +1,3 @@
-setuptools==42.0.2
+setuptools==44.1.1
 zc.buildout==2.13.3
 wheel

src/senaite/ast/adapters/configure.zcml

@@ -23,15 +23,15 @@
    AST-like analyses are always added manually afterwards, based on the result
    oif the "Microorganism Identification" analysis -->
   <subscriber
-    for="bika.lims.browser.widgets.analysisprofileanalyseswidget.AnalysisProfileAnalysesView
-         bika.lims.interfaces.IAnalysisProfile"
+    for="senaite.core.browser.widgets.analysisprofileswidget.AnalysisProfilesWidget
+         senaite.core.interfaces.IAnalysisProfile"
     provides="senaite.app.listing.interfaces.IListingViewAdapter"
     factory=".listing.services.NonASTServicesViewAdapter" />
 
-  <!-- Do not display AST-type services for selection in Analysis Template -->
+  <!-- Do not display AST-type services for selection in Sample Template -->
   <subscriber
-    for="bika.lims.browser.widgets.artemplateanalyseswidget.ARTemplateAnalysesView
-         bika.lims.interfaces.IARTemplate"
+    for="senaite.core.browser.widgets.sampletemplate_services_widget.SampleTemplateServicesWidget
+         senaite.core.interfaces.ISampleTemplate"
     provides="senaite.app.listing.interfaces.IListingViewAdapter"
     factory=".listing.services.NonASTServicesViewAdapter" />
 

src/senaite/ast/adapters/guards.py

@@ -26,6 +26,7 @@
 from senaite.ast.config import DISK_CONTENT_KEY
 from senaite.ast.config import MIC_KEY
 from senaite.ast.config import ZONE_SIZE_KEY
+from senaite.ast.utils import is_ast_analysis
 from zope.interface import implementer
 
 OPERATORS = ["<=", ">=", "<", ">"]
@@ -103,6 +104,10 @@ def guard_submit(self):
                 # Skip extrapolated antibiotics
                 continue
 
+            if utils.is_rejected_interim(antibiotic):
+                # Skip rejected antibiotics
+                continue
+
             if utils.is_interim_empty(antibiotic):
                 # Cannot submit if no result
                 return False
@@ -135,3 +140,9 @@ def guard_submit(self):
                     return False
 
         return True
+
+    def guard_reject_antibiotics(self):
+        """Rejection of antibiotics is only possible for sensitivity testing
+        (AST) analyses
+        """
+        return is_ast_analysis(self.context)

src/senaite/ast/browser/configure.zcml

@@ -6,6 +6,7 @@
 
   <!-- Package includes -->
   <include package=".content"/>
+  <include package=".modals"/>
   <include package=".theme"/>
 
   <!-- Static directory for js, css and image resources -->

src/senaite/ast/browser/modals/__init__.py

@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+#
+# This file is part of SENAITE.AST.
+#
+# SENAITE.AST is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, version 2.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program; if not, write to the Free Software Foundation, Inc., 51
+# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Copyright 2020-2024 by it's authors.
+# Some rights reserved, see README and LICENSE.

src/senaite/ast/browser/modals/configure.zcml

@@ -0,0 +1,13 @@
+<configure
+    xmlns="http://namespaces.zope.org/zope"
+    xmlns:browser="http://namespaces.zope.org/browser">
+
+  <!-- Modal for antibiotic rejection -->
+  <browser:page
+      name="reject_antibiotics"
+      for="*"
+      class=".rejectantibiotics.RejectAntibioticsModal"
+      permission="zope2.View"
+      layer="senaite.ast.interfaces.ISenaiteASTLayer" />
+
+</configure>