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# -*- coding: utf-8 -*- |
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# |
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# This file is part of SENAITE.CORE |
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# |
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# Copyright 2018 by it's authors. |
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# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst. |
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import importlib |
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import inspect |
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import math |
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import re |
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import transaction |
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from AccessControl import ClassSecurityInfo |
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from bika.lims import api |
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from bika.lims import bikaMessageFactory as _ |
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from bika.lims.api import get_object_by_uid |
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from bika.lims.browser.fields import InterimFieldsField |
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from bika.lims.browser.fields.uidreferencefield import UIDReferenceField |
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from bika.lims.browser.fields.uidreferencefield import get_backreferences |
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from bika.lims.browser.widgets import RecordsWidget as BikaRecordsWidget |
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from bika.lims.config import PROJECTNAME |
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from bika.lims.content.bikaschema import BikaSchema |
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from bika.lims.interfaces import IDeactivable |
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from bika.lims.interfaces.calculation import ICalculation |
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from Products.Archetypes.atapi import BaseFolder |
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from Products.Archetypes.atapi import ReferenceWidget |
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from Products.Archetypes.atapi import Schema |
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from Products.Archetypes.atapi import TextAreaWidget |
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from Products.Archetypes.atapi import TextField |
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from Products.Archetypes.atapi import registerType |
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from Products.ATContentTypes.lib.historyaware import HistoryAwareMixin |
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from Products.ATExtensions.field import RecordsField |
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from Products.CMFCore.utils import getToolByName |
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from Products.CMFCore.WorkflowCore import WorkflowException |
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from Products.CMFPlone.utils import safe_unicode |
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from zope.interface import implements |
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schema = BikaSchema.copy() + Schema(( |
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InterimFieldsField( |
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'InterimFields', |
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widget=BikaRecordsWidget( |
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label=_("Calculation Interim Fields"), |
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description=_( |
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"Define interim fields such as vessel mass, dilution factors, " |
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"should your calculation require them. The field title " |
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"specified here will be used as column headers and field " |
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"descriptors where the interim fields are displayed. If " |
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"'Apply wide' is enabled the field will be shown in a " |
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"selection box on the top of the worksheet, allowing to apply " |
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"a specific value to all the corresponding fields on the " |
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"sheet."), |
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) |
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), |
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UIDReferenceField( |
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'DependentServices', |
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required=1, |
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multiValued=1, |
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allowed_types=('AnalysisService',), |
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widget=ReferenceWidget( |
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checkbox_bound=0, |
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visible=False, |
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label=_("Dependent Analyses"), |
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), |
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), |
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RecordsField( |
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'PythonImports', |
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required=False, |
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subfields=('module', 'function'), |
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subfield_labels={'module': _('Module'), 'function': _('Function')}, |
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subfield_readonly={'module': False, 'function': False}, |
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subfield_types={'module': 'string', 'function': 'string'}, |
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default=[ |
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{'module': 'math', 'function': 'ceil'}, |
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{'module': 'math', 'function': 'floor'}, |
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], |
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subfield_validators={ |
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'module': 'importvalidator', |
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}, |
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widget=BikaRecordsWidget( |
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label=_("Additional Python Libraries"), |
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description=_( |
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"If your formula needs a special function from an external " |
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"Python library, you can import it here. E.g. if you want to " |
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"use the 'floor' function from the Python 'math' module, " |
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"you add 'math' to the Module field and 'floor' to the " |
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"function field. The equivalent in Python would be 'from math " |
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"import floor'. In your calculation you could use then " |
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"'floor([Ca] + [Mg])'. " |
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), |
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allowDelete=True, |
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), |
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), |
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TextField( |
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'Formula', |
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validators=('formulavalidator',), |
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default_content_type='text/plain', |
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allowable_content_types=('text/plain',), |
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widget=TextAreaWidget( |
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label=_("Calculation Formula"), |
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description=_( |
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"<p>The formula you type here will be dynamically calculated " |
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"when an analysis using this calculation is displayed.</p>" |
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"<p>To enter a Calculation, use standard maths operators, " |
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"+ - * / ( ), and all keywords available, both from other " |
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"Analysis Services and the Interim Fields specified here, " |
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"as variables. Enclose them in square brackets [ ].</p>" |
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"<p>E.g, the calculation for Total Hardness, the total of " |
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"Calcium (ppm) and Magnesium (ppm) ions in water, is entered " |
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"as [Ca] + [Mg], where Ca and MG are the keywords for those " |
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"two Analysis Services.</p>"), |
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) |
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), |
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RecordsField( |
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'TestParameters', |
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required=False, |
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subfields=('keyword', 'value'), |
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subfield_labels={'keyword': _('Keyword'), 'value': _('Value')}, |
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subfield_readonly={'keyword': True, 'value': False}, |
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subfield_types={'keyword': 'string', 'value': 'float'}, |
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default=[{'keyword': '', 'value': 0}], |
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widget=BikaRecordsWidget( |
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label=_("Test Parameters"), |
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description=_("To test the calculation, enter values here for all " |
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"calculation parameters. This includes Interim " |
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"fields defined above, as well as any services that " |
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"this calculation depends on to calculate results."), |
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allowDelete=False, |
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), |
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), |
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TextField( |
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'TestResult', |
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default_content_type='text/plain', |
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allowable_content_types=('text/plain',), |
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widget=TextAreaWidget( |
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label=_('Test Result'), |
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description=_("The result after the calculation has taken place " |
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"with test values. You will need to save the " |
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"calculation before this value will be calculated."), |
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) |
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), |
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)) |
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schema['title'].widget.visible = True |
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schema['description'].widget.visible = True |
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class Calculation(BaseFolder, HistoryAwareMixin): |
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"""Calculation for Analysis Results |
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""" |
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implements(ICalculation, IDeactivable) |
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security = ClassSecurityInfo() |
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displayContentsTab = False |
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schema = schema |
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_at_rename_after_creation = True |
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def _renameAfterCreation(self, check_auto_id=False): |
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from bika.lims.idserver import renameAfterCreation |
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renameAfterCreation(self) |
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def setInterimFields(self, value): |
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new_value = [] |
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for x in range(len(value)): |
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row = dict(value[x]) |
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keys = row.keys() |
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if 'value' not in keys: |
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row['value'] = 0 |
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new_value.append(row) |
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# extract the keywords from the new calculation interims |
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calculation_interim_keys = map(lambda i: i.get("keyword"), value) |
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# update all service interims |
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for service in self.getCalculationDependants(): |
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# get the interims of the dependant service |
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service_interims = service.getInterimFields() |
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# extract the keywords from the service interims |
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service_interim_keys = map(lambda i: i.get("keyword"), |
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service_interims) |
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# sync new interims from the calculation -> service |
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new_interims = set(calculation_interim_keys).difference( |
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set(service_interim_keys)) |
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for key in new_interims: |
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new_interim = value[calculation_interim_keys.index(key)] |
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service_interims.append(new_interim) |
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if new_interims: |
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service.setInterimFields(service_interims) |
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self.getField('InterimFields').set(self, new_value) |
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def setFormula(self, Formula=None): |
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"""Set the Dependent Services from the text of the calculation Formula |
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""" |
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bsc = getToolByName(self, 'bika_setup_catalog') |
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if Formula is None: |
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self.setDependentServices(None) |
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self.getField('Formula').set(self, Formula) |
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else: |
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keywords = re.compile(r"\[([^.^\]]+)\]").findall(Formula) |
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brains = bsc(portal_type='AnalysisService', |
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getKeyword=keywords) |
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services = [brain.getObject() for brain in brains] |
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self.getField('DependentServices').set(self, services) |
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self.getField('Formula').set(self, Formula) |
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def getMinifiedFormula(self): |
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"""Return the current formula value as text. |
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The result will have newlines and additional spaces stripped out. |
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""" |
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value = " ".join(self.getFormula().splitlines()) |
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return value |
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def getCalculationDependencies(self, flat=False, deps=None): |
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""" Recursively calculates all dependencies of this calculation. |
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The return value is dictionary of dictionaries (of dictionaries...) |
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{service_UID1: |
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{service_UID2: |
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{service_UID3: {}, |
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service_UID4: {}, |
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}, |
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}, |
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} |
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set flat=True to get a simple list of AnalysisService objects |
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""" |
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if deps is None: |
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deps = [] if flat is True else {} |
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for service in self.getDependentServices(): |
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calc = service.getCalculation() |
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if calc: |
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calc.getCalculationDependencies(flat, deps) |
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if flat: |
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deps.append(service) |
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else: |
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deps[service.UID()] = {} |
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return deps |
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def getCalculationDependants(self, deps=None): |
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"""Return a flat list of services who depend on this calculation. |
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This refers only to services who's Calculation UIDReferenceField have |
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the value set to point to this calculation. |
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It has nothing to do with the services referenced in the calculation's |
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Formula. |
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""" |
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if deps is None: |
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deps = [] |
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backrefs = get_backreferences(self, 'AnalysisServiceCalculation') |
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services = map(get_object_by_uid, backrefs) |
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for service in services: |
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calc = service.getCalculation() |
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if calc and calc.UID() != self.UID(): |
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calc.getCalculationDependants(deps) |
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deps.append(service) |
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return deps |
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def setTestParameters(self, form_value): |
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"""This is called from the objectmodified subscriber, to ensure |
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correct population of the test-parameters field. |
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It collects Keywords for all services that are direct dependencies of |
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this calculatioin, and all of this calculation's InterimFields, |
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and gloms them together. |
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""" |
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params = [] |
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# Set default/existing values for InterimField keywords |
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for interim in self.getInterimFields(): |
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keyword = interim.get('keyword') |
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ex = [x.get('value') for x in form_value if |
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x.get('keyword') == keyword] |
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params.append({'keyword': keyword, |
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'value': ex[0] if ex else interim.get('value')}) |
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# Set existing/blank values for service keywords |
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for service in self.getDependentServices(): |
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keyword = service.getKeyword() |
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ex = [x.get('value') for x in form_value if |
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x.get('keyword') == keyword] |
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params.append({'keyword': keyword, |
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'value': ex[0] if ex else ''}) |
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self.Schema().getField('TestParameters').set(self, params) |
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# noinspection PyUnusedLocal |
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def setTestResult(self, form_value): |
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"""Calculate formula with TestParameters and enter result into |
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TestResult field. |
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""" |
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# Create mapping from TestParameters |
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mapping = {x['keyword']: x['value'] for x in self.getTestParameters()} |
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# Gather up and parse formula |
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formula = self.getMinifiedFormula() |
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test_result_field = self.Schema().getField('TestResult') |
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# Flush the TestResult field and return |
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if not formula: |
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return test_result_field.set(self, "") |
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formula = formula.replace('[', '{').replace(']', '}').replace(' ', '') |
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result = 'Failure' |
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try: |
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# print "pre: {}".format(formula) |
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formula = formula.format(**mapping) |
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# print "formatted: {}".format(formula) |
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result = eval(formula, self._getGlobals()) |
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# print "result: {}".format(result) |
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except TypeError as e: |
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# non-numeric arguments in interim mapping? |
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result = "TypeError: {}".format(str(e.args[0])) |
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except ZeroDivisionError as e: |
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result = "Division by 0: {}".format(str(e.args[0])) |
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except KeyError as e: |
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result = "Key Error: {}".format(str(e.args[0])) |
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except ImportError as e: |
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result = "Import Error: {}".format(str(e.args[0])) |
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except Exception as e: |
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result = "Unspecified exception: {}".format(str(e.args[0])) |
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test_result_field.set(self, str(result)) |
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def _getGlobals(self, **kwargs): |
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"""Return the globals dictionary for the formula calculation |
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""" |
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# Default globals |
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globs = { |
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"__builtins__": None, |
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"all": all, |
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"any": any, |
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"bool": bool, |
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"chr": chr, |
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"cmp": cmp, |
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"complex": complex, |
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"divmod": divmod, |
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"enumerate": enumerate, |
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"float": float, |
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"format": format, |
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"frozenset": frozenset, |
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"hex": hex, |
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"int": int, |
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"len": len, |
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"list": list, |
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"long": long, |
|
|
|
|
355
|
|
|
"math": math, |
356
|
|
|
"max": max, |
357
|
|
|
"min": min, |
358
|
|
|
"oct": oct, |
359
|
|
|
"ord": ord, |
360
|
|
|
"pow": pow, |
361
|
|
|
"range": range, |
362
|
|
|
"reversed": reversed, |
363
|
|
|
"round": round, |
364
|
|
|
"str": str, |
365
|
|
|
"sum": sum, |
366
|
|
|
"tuple": tuple, |
367
|
|
|
"xrange": xrange, |
|
|
|
|
368
|
|
|
} |
369
|
|
|
# Update with keyword arguments |
370
|
|
|
globs.update(kwargs) |
371
|
|
|
# Update with additional Python libraries |
372
|
|
|
for imp in self.getPythonImports(): |
373
|
|
|
mod = imp["module"] |
374
|
|
|
func = imp["function"] |
375
|
|
|
member = self._getModuleMember(mod, func) |
376
|
|
|
if member is None: |
377
|
|
|
raise ImportError( |
378
|
|
|
"Could not find member {} of module {}".format( |
379
|
|
|
func, mod)) |
380
|
|
|
globs[func] = member |
381
|
|
|
return globs |
382
|
|
|
|
383
|
|
|
def _getModuleMember(self, dotted_name, member): |
384
|
|
|
"""Get the member object of a module. |
385
|
|
|
|
386
|
|
|
:param dotted_name: The dotted name of the module, e.g. 'scipy.special' |
387
|
|
|
:type dotted_name: string |
388
|
|
|
:param member: The name of the member function, e.g. 'gammaincinv' |
389
|
|
|
:type member: string |
390
|
|
|
:returns: member object or None |
391
|
|
|
""" |
392
|
|
|
try: |
393
|
|
|
mod = importlib.import_module(dotted_name) |
394
|
|
|
except ImportError: |
395
|
|
|
return None |
396
|
|
|
|
397
|
|
|
members = dict(inspect.getmembers(mod)) |
398
|
|
|
return members.get(member) |
399
|
|
|
|
400
|
|
|
def workflow_script_activate(self): |
401
|
|
|
pu = getToolByName(self, 'plone_utils') |
402
|
|
|
# A calculation cannot be re-activated if services it depends on |
403
|
|
|
# are deactivated. |
404
|
|
|
services = self.getDependentServices() |
405
|
|
|
inactive_services = [] |
406
|
|
|
for service in services: |
407
|
|
|
if not api.is_active(service): |
408
|
|
|
inactive_services.append(service.Title()) |
409
|
|
|
if inactive_services: |
410
|
|
|
msg = _("Cannot activate calculation, because the following " |
411
|
|
|
"service dependencies are inactive: ${inactive_services}", |
412
|
|
|
mapping={'inactive_services': safe_unicode( |
413
|
|
|
", ".join(inactive_services))}) |
414
|
|
|
pu.addPortalMessage(msg, 'error') |
415
|
|
|
transaction.get().abort() |
416
|
|
|
raise WorkflowException |
417
|
|
|
|
418
|
|
|
def workflow_script_deactivate(self): |
419
|
|
|
bsc = getToolByName(self, 'bika_setup_catalog') |
420
|
|
|
pu = getToolByName(self, 'plone_utils') |
421
|
|
|
# A calculation cannot be deactivated if active services are using it. |
422
|
|
|
services = bsc(portal_type="AnalysisService", is_active=True) |
423
|
|
|
calc_services = [] |
424
|
|
|
for service in services: |
425
|
|
|
service = service.getObject() |
426
|
|
|
calc = service.getCalculation() |
427
|
|
|
if calc and calc.UID() == self.UID(): |
428
|
|
|
calc_services.append(service.Title()) |
429
|
|
|
if calc_services: |
430
|
|
|
msg = _( |
431
|
|
|
'Cannot deactivate calculation, because it is in use by the ' |
432
|
|
|
'following services: ${calc_services}', |
433
|
|
|
mapping={ |
434
|
|
|
'calc_services': safe_unicode(", ".join(calc_services))}) |
435
|
|
|
pu.addPortalMessage(msg, 'error') |
436
|
|
|
transaction.get().abort() |
437
|
|
|
raise WorkflowException |
438
|
|
|
|
439
|
|
|
|
440
|
|
|
registerType(Calculation, PROJECTNAME) |
441
|
|
|
|