Merge branch 'master' of github.com:senaite/senaite.ast into fix-no-registry-found

Author: xispa

ci_flake8.cfg

@@ -0,0 +1,7 @@
+[flake8]
+# temporarily disable violations for existing code until they are cleaned up
+per-file-ignores =
+    # C901 'AnalysisGuardAdapter.guard_submit' is too complex (14)
+    src/senaite/ast/adapters/guards.py:C901
+    # C901 'get_sensitivity_category' is too complex (14)
+    src/senaite/ast/utils.py:C901

docs/conf.py

@@ -1,5 +1,5 @@
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -9,7 +9,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -27,7 +27,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -47,41 +47,41 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ['_build']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output ----------------------------------------------
@@ -93,26 +93,26 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -122,93 +122,92 @@
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'senaiteastdoc'
 
-
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'senaiteast.tex', u'senaite.ast Documentation',
-   u'Riding Bytes & Naralabs', 'manual'),
+    ('index', 'senaiteast.tex', u'senaite.ast Documentation',
+     u'Riding Bytes & Naralabs', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ---------------------------------------
@@ -221,7 +220,7 @@
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -230,20 +229,20 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'senaiteast', u'senaite.ast Documentation',
-   u'Riding Bytes & Naralabs', 'senaiteast',
-   'Antibiotic Sensitivity Testing (AST) for SENAITE',
-   'Miscellaneous'),
+    ('index', 'senaiteast', u'senaite.ast Documentation',
+     u'Riding Bytes & Naralabs', 'senaiteast',
+     'Antibiotic Sensitivity Testing (AST) for SENAITE',
+     'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False

src/senaite/ast/behaviors/astpanel.py

@@ -70,8 +70,8 @@ class IASTPanelBehavior(model.Schema):
         description=_(
             u"Default clinical breakpoints table to use for this panel. If "
             u"set, the system will automatically calculate the susceptibility "
-            u"testing category as soon as the zone diameter in mm is submitted "
-            u"by the user."
+            u"testing category as soon as the zone diameter in mm is "
+            u"submitted by the user."
         ),
         allowed_types=("BreakpointsTable", ),
         multi_valued=False,
@@ -120,9 +120,9 @@ class IASTPanelBehavior(model.Schema):
     disk_content = schema.Bool(
         title=_(u"Include disk content in μg"),
         description=_(
-            u"When enabled, an additional row for the introduction of the disk "
-            u"content (potency) in μg is displayed in the results entry view, "
-            u"above resistance call options"
+            u"When enabled, an additional row for the introduction of the "
+            u"disk content (potency) in μg is displayed in the results entry "
+            u"view, above resistance call options"
         ),
         required=False,
         default=False,
@@ -164,8 +164,8 @@ class IASTPanelBehavior(model.Schema):
         title=_(u"Selective reporting"),
         description=_(
             u"When enabled, an additional row to indicate whether the "
-            u"resistance result for each microorganism-antibiotic tuple has to "
-            u"be reported in results report or not"
+            u"resistance result for each microorganism-antibiotic tuple has "
+            u"to be reported in results report or not"
         ),
         required=False,
         default=False,
@@ -210,7 +210,8 @@ def _get_breakpoints_table(self):
         breakpoints_table = getattr(self.context, "breakpoints_table", None)
         return copy(breakpoints_table)
 
-    breakpoints_table = property(_get_breakpoints_table, _set_breakpoints_table)
+    breakpoints_table = property(_get_breakpoints_table,
+                                 _set_breakpoints_table)
 
     def _set_disk_content(self, value):
         self.context.disk_content = value
@@ -234,10 +235,11 @@ def _set_selective_reporting(self, value):
         self.context.selective_reporting = value
 
     def _get_selective_reporting(self):
-        selective_reporting = getattr(self.context, "selective_reporting", None)
+        selective_reporting = getattr(self.context, "selective_reporting")
         return selective_reporting
 
-    selective_reporting = property(_get_selective_reporting, _set_selective_reporting)
+    selective_reporting = property(_get_selective_reporting,
+                                   _set_selective_reporting)
 
     def _set_method(self, value):
         self.context.method = value

src/senaite/ast/browser/addpanel.py

@@ -59,7 +59,9 @@ def __call__(self):
 
             # Create/Update the breakpoints table analysis
             if panel.breakpoints_table:
-                self.add_breakpoints_analysis(panel, microorganism, antibiotics)
+                self.add_breakpoints_analysis(
+                    panel, microorganism, antibiotics
+                )
 
             if panel.method == METHOD_DIFFUSION_DISK_ID:
                 # Create/Update the disk content (potency) analysis
@@ -121,7 +123,8 @@ def add_ast_analysis(self, keyword, microorganism, antibiotics):
 
         # Create a new analysis
         sample = self.context
-        return utils.create_ast_analysis(sample, keyword, microorganism, antibiotics)
+        return utils.create_ast_analysis(sample, keyword, microorganism,
+                                         antibiotics)
 
     def add_breakpoints_analysis(self, panel, microorganism, antibiotics):
         """Updates or creates an analysis for the selection of the clinical

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

@@ -23,7 +23,6 @@
 
 from bika.lims import api
 from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile
-from senaite.ast import logger
 from senaite.ast import utils
 from senaite.ast.calc import update_sensitivity_result
 from senaite.ast.config import NOT_TESTED

src/senaite/ast/browser/panel.py

@@ -209,7 +209,8 @@ def render_checkbox(self, item, microorganism, antibiotic):
             if not isinstance(disabled, (list, tuple)):
                 item["disabled"] = []
 
-            if has_analysis and not self.is_editable(microorganism, antibiotic):
+            if has_analysis and not self.is_editable(microorganism,
+                                                     antibiotic):
                 item.setdefault("disabled", []).append(uid)
 
     def is_editable(self, microorganism, antibiotic):

src/senaite/ast/calc.py

@@ -253,9 +253,9 @@ def update_sensitivity_result(analysis):
     """Updates the sensitivity "final" result of the sensitivity category
     analysis based on the values set to the AST siblings.
 
-    The sensitivity category results for antibiotics of this analysis are stored
-    as interim values, while the "final" result of the analysis is a list of
-    result options, that is only used for reporting purposes.
+    The sensitivity category results for antibiotics of this analysis are
+    stored as interim values, while the "final" result of the analysis is a
+    list of result options, that is only used for reporting purposes.
     """
     # Get the analysis (keyword: analysis) from same sample and microorganism
     analyses = utils.get_ast_group(analysis)
@@ -315,10 +315,7 @@ def get_reportable_antibiotics(analysis):
     extrapolated = analyses.get(REPORT_EXTRAPOLATED_KEY)
     if extrapolated:
         for interim in extrapolated.getInterimFields():
-            try:
-                selected = json.loads(interim.get("value", "[]"))
-            except:
-                selected = []
+            selected = api.parse_json(interim.get("value"), default=[])
             reportable[interim.get("uid")] = selected
 
     def is_reportable(interim):