senaite.core.browser.samples.view

Complexity

Total Complexity

69

Size/Duplication

Total Lines	752
Duplicated Lines	0 %

Importance

Changes

0

15 Methods

Rating	Name	Duplication	Size	Complexity
F	SamplesView.folderitem()	0	152	29
A	SamplesView.to_datetime_input_value()	0	6	2
A	SamplesView.get_copy_to_new_transition()	0	21	5
A	SamplesView.is_printing_workflow_enabled()	0	4	1
A	SamplesView.flat_listing()	0	3	1
A	SamplesView.before_render()	0	17	3
A	SamplesView.str_date()	0	4	2
A	SamplesView.getDefaultAddCount()	0	2	1
B	SamplesView.add_custom_transitions()	0	29	5
B	SamplesView.__init__()	0	382	1
A	SamplesView.update()	0	17	1
B	SamplesView.purge_review_states()	0	16	6
A	SamplesView.purge_columns()	0	10	4
A	SamplesView.can_create_worksheet()	0	15	5
A	SamplesView.show_partitions()	0	8	3

# -*- coding: utf-8 -*-
#
# This file is part of SENAITE.CORE.
#
# SENAITE.CORE 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 2018-2021 by it's authors.
# Some rights reserved, see README and LICENSE.


import collections

from bika.lims import _
from bika.lims import api
from bika.lims.api.security import check_permission
from bika.lims.config import PRIORITIES
from bika.lims.interfaces import IBatch
from bika.lims.interfaces import IClient
from bika.lims.permissions import AddAnalysisRequest
from bika.lims.permissions import EditWorksheet
from bika.lims.permissions import TransitionSampleSample
from bika.lims.utils import get_image
from bika.lims.utils import get_progress_bar_html
from bika.lims.utils import getUsers
from bika.lims.utils import t
from DateTime import DateTime
from senaite.app.listing import ListingView
from senaite.core.catalog import SAMPLE_CATALOG
from senaite.core.interfaces import ISamples
from senaite.core.interfaces import ISamplesView
from zope.interface import implementer


@implementer(ISamplesView)
class SamplesView(ListingView):
    """Listing View for Samples (AnalysisRequest content type) in the System
    """

    def __init__(self, context, request):
        super(SamplesView, self).__init__(context, request)

        self.catalog = SAMPLE_CATALOG
        self.contentFilter = {
            "sort_on": "created",
            "sort_order": "descending",
            "isRootAncestor": True,  # only root ancestors
        }

        self.title = self.context.translate(_("Samples"))
        self.description = ""

        self.show_select_column = True
        self.form_id = "samples"
        self.context_actions = {}
        self.icon = "{}{}".format(
            self.portal_url, "/senaite_theme/icon/sample")

        self.url = api.get_url(self.context)

        # Toggle some columns if the sampling workflow is enabled
        sampling_enabled = api.get_setup().getSamplingWorkflowEnabled()

        now = DateTime().strftime("%Y-%m-%d %H:%M")

        self.columns = collections.OrderedDict((
            ("Priority", {
                "title": "",
                "index": "getPrioritySortkey",
                "sortable": True, }),
            ("Progress", {
                "title": "Progress",
                "index": "getProgress",
                "sortable": True,
                "toggle": True}),
            ("getId", {
                "title": _("Sample ID"),
                "attr": "getId",
                "replace_url": "getURL",
                "index": "getId"}),
            ("getClientOrderNumber", {
                "title": _("Client Order"),
                "sortable": True,
                "toggle": False}),
            ("Creator", {
                "title": _("Creator"),
                "index": "getCreatorFullName",
                "sortable": True,
                "toggle": True}),
            ("Created", {
                "title": _("Date Registered"),
                "index": "created",
                "toggle": False}),
            ("SamplingDate", {
                "title": _("Expected Sampling Date"),
                "index": "getSamplingDate",
                "toggle": sampling_enabled}),
            ("getDateSampled", {
                "title": _("Date Sampled"),
                "toggle": True,
                "type": "datetime",
                "max": now,
                "sortable": True}),
            ("getDatePreserved", {
                "title": _("Date Preserved"),
                "toggle": False,
                "type": "datetime",
                "max": now,
                "sortable": False}),  # no datesort without index
            ("getDateReceived", {
                "title": _("Date Received"),
                "toggle": False}),
            ("getDueDate", {
                "title": _("Due Date"),
                "toggle": False}),
            ("getDateVerified", {
                "title": _("Date Verified"),
                "input_width": "10",
                "toggle": False}),
            ("getDatePublished", {
                "title": _("Date Published"),
                "toggle": False}),
            ("BatchID", {
                "title": _("Batch ID"),
                "index": "getBatchID",
                "sortable": True,
                "toggle": False}),
            ("Client", {
                "title": _("Client"),
                "index": "getClientTitle",
                "attr": "getClientTitle",
                "replace_url": "getClientURL",
                "toggle": True}),
            ("ClientID", {
                "title": _("Client ID"),
                "index": "getClientID",
                "attr": "getClientID",
                "replace_url": "getClientURL",
                "toggle": True}),
            ("Province", {
                "title": _("Province"),
                "sortable": True,
                "index": "getProvince",
                "attr": "getProvince",
                "toggle": False}),
            ("District", {
                "title": _("District"),
                "sortable": True,
                "index": "getDistrict",
                "attr": "getDistrict",
                "toggle": False}),
            ("getClientReference", {
                "title": _("Client Ref"),
                "sortable": True,
                "index": "getClientReference",
                "toggle": False}),
            ("getClientSampleID", {
                "title": _("Client SID"),
                "toggle": False}),
            ("ClientContact", {
                "title": _("Contact"),
                "sortable": True,
                "index": "getContactFullName",
                "toggle": False}),
            ("getSampleTypeTitle", {
                "title": _("Sample Type"),
                "sortable": True,
                "toggle": True}),
            ("getSamplePointTitle", {
                "title": _("Sample Point"),
                "sortable": True,
                "index": "getSamplePointTitle",
                "toggle": False}),
            ("getStorageLocation", {
                "title": _("Storage Location"),
                "sortable": True,
                "index": "getStorageLocationTitle",
                "toggle": False}),
            ("SamplingDeviation", {
                "title": _("Sampling Deviation"),
                "sortable": True,
                "index": "getSamplingDeviationTitle",
                "toggle": False}),
            ("getSampler", {
                "title": _("Sampler"),
                "toggle": sampling_enabled}),
            ("getPreserver", {
                "title": _("Preserver"),
                "sortable": False,
                "toggle": False}),
            ("getProfilesTitle", {
                "title": _("Profile"),
                "sortable": True,
                "index": "getProfilesTitle",
                "toggle": False}),
            ("getAnalysesNum", {
                "title": _("Number of Analyses"),
                "sortable": True,
                "index": "getAnalysesNum",
                "toggle": False}),
            ("getTemplateTitle", {
                "title": _("Template"),
                "sortable": True,
                "index": "getTemplateTitle",
                "toggle": False}),
            ("Printed", {
                "title": _("Printed"),
                "sortable": False,
                "index": "getPrinted",
                "toggle": False}),
            ("state_title", {
                "title": _("State"),
                "sortable": True,
                "index": "review_state"}),
        ))

        # custom print transition
        print_stickers = {
            "id": "print_stickers",
            "title": _("Print stickers"),
            "url": "{}/workflow_action?action=print_stickers".format(self.url)
        }

        self.review_states = [
            {
                "id": "default",
                "title": _("Active"),
                "contentFilter": {
                    "review_state": (
                        "sample_registered",
                        "scheduled_sampling",
                        "to_be_sampled",
                        "sample_due",
                        "sample_received",
                        "to_be_preserved",
                        "to_be_verified",
                        "verified",
                    ),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "to_be_sampled",
                "title": _("To Be Sampled"),
                "contentFilter": {
                    "review_state": ("to_be_sampled",),
                    "sort_on": "created",
                    "sort_order": "descending"},
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys()
            }, {
                "id": "to_be_preserved",
                "title": _("To Be Preserved"),
                "contentFilter": {
                    "review_state": ("to_be_preserved",),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "scheduled_sampling",
                "title": _("Scheduled sampling"),
                "contentFilter": {
                    "review_state": ("scheduled_sampling",),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "sample_due",
                "title": _("Due"),
                "contentFilter": {
                    "review_state": (
                        "to_be_sampled",
                        "to_be_preserved",
                        "sample_due"),
                    "sort_on": "created",
                    "sort_order": "descending"},
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "sample_received",
                "title": _("Received"),
                "contentFilter": {
                    "review_state": "sample_received",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "to_be_verified",
                "title": _("To be verified"),
                "contentFilter": {
                    "review_state": "to_be_verified",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "verified",
                "title": _("Verified"),
                "contentFilter": {
                    "review_state": "verified",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "published",
                "title": _("Published"),
                "contentFilter": {
                    "review_state": ("published"),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [],
                "columns": self.columns.keys(),
            }, {
                "id": "dispatched",
                "title": _("Dispatched"),
                "flat_listing": True,
                "confirm_transitions": ["restore"],
                "contentFilter": {
                    "review_state": ("dispatched"),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [],
                "columns": self.columns.keys(),
            }, {
                "id": "cancelled",
                "title": _("Cancelled"),
                "contentFilter": {
                    "review_state": "cancelled",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [],
                "columns": self.columns.keys(),
            }, {
                "id": "invalid",
                "title": _("Invalid"),
                "contentFilter": {
                    "review_state": "invalid",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "all",
                "title": _("All"),
                "contentFilter": {
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "rejected",
                "title": _("Rejected"),
                "contentFilter": {
                    "review_state": "rejected",
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "assigned",
                "title": get_image("assigned.png",
                                   title=t(_("Assigned"))),
                "contentFilter": {
                    "assigned_state": "assigned",
                    "review_state": ("sample_received",),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "unassigned",
                "title": get_image("unassigned.png",
                                   title=t(_("Unsassigned"))),
                "contentFilter": {
                    "assigned_state": "unassigned",
                    "review_state": (
                        "sample_received",
                    ),
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }, {
                "id": "late",
                "title": get_image("late.png",
                                   title=t(_("Late"))),
                "contentFilter": {
                    # Query only for unpublished ARs that are late
                    "review_state": (
                        "sample_received",
                        "to_be_verified",
                        "verified",
                    ),
                    "getDueDate": {
                        "query": DateTime(),
                        "range": "max",
                    },
                    "sort_on": "created",
                    "sort_order": "descending",
                },
                "custom_transitions": [print_stickers],
                "columns": self.columns.keys(),
            }
        ]

    def update(self):
        """Called before the listing renders
        """
        super(SamplesView, self).update()

        self.workflow = api.get_tool("portal_workflow")
        self.member = self.mtool.getAuthenticatedMember()
        self.roles = self.member.getRoles()

        # Remove unnecessary filters
        self.purge_review_states()

        # Remove unnecessary columns
        self.purge_columns()

        # Additional custom transitions
        self.add_custom_transitions()

    def before_render(self):
        """Before template render hook
        """
        # If the current user is a client contact, display those analysis
        # requests that belong to same client only
        super(SamplesView, self).before_render()
        client = api.get_current_client()
        if client:
            self.contentFilter['path'] = {
                "query": "/".join(client.getPhysicalPath()),
                "level": 0}
            # No need to display the Client column
            self.remove_column('Client')

        # remove query filter for root samples when listing is flat
        if self.flat_listing:
            self.contentFilter.pop("isRootAncestor", None)

    def folderitem(self, obj, item, index):
        # Additional info from AnalysisRequest to be added in the item
        # generated by default by bikalisting.
        # Call the folderitem method from the base class
        item = super(SamplesView, self).folderitem(obj, item, index)
        if not item:
            return None

        item["Creator"] = self.user_fullname(obj.Creator)
        # If we redirect from the folderitems view we should check if the
        # user has permissions to medify the element or not.
        priority_sort_key = obj.getPrioritySortkey
        if not priority_sort_key:
            # Default priority is Medium = 3.
            # The format of PrioritySortKey is <priority>.<created>
            priority_sort_key = "3.%s" % obj.created.ISO8601()
        priority = priority_sort_key.split(".")[0]
        priority_text = PRIORITIES.getValue(priority)
        priority_div = """<div class="priority-ico priority-%s">
                          <span class="notext">%s</span><div>
                       """
        item["replace"]["Priority"] = priority_div % (priority, priority_text)
        item["replace"]["getProfilesTitle"] = obj.getProfilesTitleStr

        analysesnum = obj.getAnalysesNum
        if analysesnum:
            num_verified = str(analysesnum[0])
            num_total = str(analysesnum[1])
            item["getAnalysesNum"] = "{0}/{1}".format(num_verified, num_total)
        else:
            item["getAnalysesNum"] = ""

        # Progress
        progress_perc = obj.getProgress
        item["Progress"] = progress_perc
        item["replace"]["Progress"] = get_progress_bar_html(progress_perc)

        item["BatchID"] = obj.getBatchID
        if obj.getBatchID:
            item['replace']['BatchID'] = "<a href='%s'>%s</a>" % \
                                         (obj.getBatchURL, obj.getBatchID)
        # TODO: SubGroup ???
        # val = obj.Schema().getField('SubGroup').get(obj)
        # item['SubGroup'] = val.Title() if val else ''

        item["SamplingDate"] = self.str_date(obj.getSamplingDate)
        item["getDateSampled"] = self.str_date(obj.getDateSampled)
        item["getDateReceived"] = self.str_date(obj.getDateReceived)
        item["getDueDate"] = self.str_date(obj.getDueDate)
        item["getDatePublished"] = self.str_date(obj.getDatePublished)
        item["getDateVerified"] = self.str_date(obj.getDateVerified)

        if self.is_printing_workflow_enabled:
            item["Printed"] = ""
            printed = obj.getPrinted if hasattr(obj, "getPrinted") else "0"
            print_icon = ""
            if printed == "0":
                print_icon = get_image("delete.png",
                                       title=t(_("Not printed yet")))
            elif printed == "1":
                print_icon = get_image("ok.png",
                                       title=t(_("Printed")))
            elif printed == "2":
                print_icon = get_image(
                    "exclamation.png",
                    title=t(_("Republished after last print")))
            item["after"]["Printed"] = print_icon
        item["SamplingDeviation"] = obj.getSamplingDeviationTitle

        item["getStorageLocation"] = obj.getStorageLocationTitle

        after_icons = ""
        if obj.assigned_state == 'assigned':
            after_icons += get_image("worksheet.png",
                                     title=t(_("All analyses assigned")))
        if item["review_state"] == 'invalid':
            after_icons += get_image("delete.png",
                                     title=t(_("Results have been withdrawn")))

        due_date = obj.getDueDate
        if due_date and due_date < (obj.getDatePublished or DateTime()):
            due_date_str = self.ulocalized_time(due_date)
            img_title = "{}: {}".format(t(_("Late Analyses")), due_date_str)
            after_icons += get_image("late.png", title=img_title)

        if obj.getSamplingDate and obj.getSamplingDate > DateTime():
            after_icons += get_image("calendar.png",
                                     title=t(_("Future dated sample")))
        if obj.getInvoiceExclude:
            after_icons += get_image("invoice_exclude.png",
                                     title=t(_("Exclude from invoice")))
        if obj.getHazardous:
            after_icons += get_image("hazardous.png",
                                     title=t(_("Hazardous")))

        if obj.getInternalUse:
            after_icons += get_image("locked.png", title=t(_("Internal use")))

        if after_icons:
            item['after']['getId'] = after_icons

        item['Created'] = self.ulocalized_time(obj.created, long_format=1)
        if obj.getContactUID:
            item['ClientContact'] = obj.getContactFullName
            item['replace']['ClientContact'] = "<a href='%s'>%s</a>" % \
                                               (obj.getContactURL, obj.getContactFullName)
        else:
            item["ClientContact"] = ""
        # TODO-performance: If SamplingWorkflowEnabled, we have to get the
        # full object to check the user permissions, so far this is
        # a performance hit.
        if obj.getSamplingWorkflowEnabled:

            sampler = obj.getSampler
            if sampler:
                item["getSampler"] = obj.getSampler
                item["replace"]["getSampler"] = obj.getSamplerFullName

            # sampling workflow - inline edits for Sampler and Date Sampled
            if item["review_state"] == "to_be_sampled":
                # We need to get the full object in order to check
                # the permissions
                full_object = api.get_object(obj)
                if check_permission(TransitionSampleSample, full_object):
                    # make fields required and editable
                    item["required"] = ["getSampler", "getDateSampled"]
                    item["allow_edit"] = ["getSampler", "getDateSampled"]
                    date = obj.getDateSampled or DateTime()
                    # provide date and time in a valid input format
                    item["getDateSampled"] = self.to_datetime_input_value(date)
                    sampler_roles = ["Sampler", "LabManager", ""]
                    samplers = getUsers(full_object, sampler_roles)
                    users = [({
                        "ResultValue": u,
                        "ResultText": samplers.getValue(u)}) for u in samplers]
                    item["choices"] = {"getSampler": users}
                    # preselect the current user as sampler
                    if not sampler and "Sampler" in self.roles:
                        sampler = self.member.getUserName()
                        item["getSampler"] = sampler

        # These don't exist on ARs
        # XXX This should be a list of preservers...
        item["getPreserver"] = ""
        item["getDatePreserved"] = ""

        # Assign parent and children partitions of this sample
        if self.show_partitions:
            item["parent"] = obj.getRawParentAnalysisRequest
            item["children"] = obj.getDescendantsUIDs or []

        return item

    def purge_review_states(self):
        """Purges unnecessary review statuses
        """
        remove_filters = []
        setup = api.get_bika_setup()
        if not setup.getSamplingWorkflowEnabled():
            remove_filters.append("to_be_sampled")
        if not setup.getScheduleSamplingEnabled():
            remove_filters.append("scheduled_sampling")
        if not setup.getSamplePreservationEnabled():
            remove_filters.append("to_be_preserved")
        if not setup.getRejectionReasons():
            remove_filters.append("rejected")

        self.review_states = filter(lambda r: r.get("id") not in remove_filters,
                                    self.review_states)

    def purge_columns(self):
        """Purges unnecessary columns
        """
        remove_columns = []
        if not self.is_printing_workflow_enabled:
            remove_columns.append("Printed")

        for rv in self.review_states:
            cols = rv.get("columns", [])
            rv["columns"] = filter(lambda c: c not in remove_columns, cols)

    def add_custom_transitions(self):
        """Adds custom transitions as required
        """
        custom_transitions = []
        if self.is_printing_workflow_enabled:
            custom_transitions.append({
                "id": "print_sample",
                "title": _("Print"),
                "url": "{}/workflow_action?action={}".format(
                    self.url, "print_sample")
            })

        copy_to_new = self.get_copy_to_new_transition()
        if copy_to_new:
            custom_transitions.append(copy_to_new)

        # Allow to create a worksheet for the selected samples
        if self.can_create_worksheet():
            custom_transitions.append({
                "id": "modal_create_worksheet",
                "title": _("Create Worksheet"),
                "url": "{}/create_worksheet_modal".format(
                    api.get_url(self.context)),
                "css_class": "btn btn-outline-secondary",
                "help": _("Create a new worksheet for the selected samples")
            })

        for rv in self.review_states:
            rv.setdefault("custom_transitions", []).extend(custom_transitions)

    def get_copy_to_new_transition(self):
        """Returns the copy to new custom transition if the current has enough
        privileges. Returns None otherwise
        """
        base_url = None
        mtool = api.get_tool("portal_membership")
        if mtool.checkPermission(AddAnalysisRequest, self.context):
            base_url = self.url
        else:
            client = api.get_current_client()
            if client and mtool.checkPermission(AddAnalysisRequest, client):
                base_url = api.get_url(client)

        if base_url:
            return {
                "id": "copy_to_new",
                "title": _("Copy to new"),
                "url": "{}/workflow_action?action=copy_to_new".format(base_url)
            }

        return None

    def can_create_worksheet(self):
        """Checks if the create worksheet transition should be rendered or not
        """
        if not check_permission(EditWorksheet, self.context):
            return False

        # restrict contexts to well known places
        if ISamples.providedBy(self.context):
            return True
        elif IBatch.providedBy(self.context):
            return True
        elif IClient.providedBy(self.context):
            return True
        else:
            return False

    @property
    def is_printing_workflow_enabled(self):
        setup = api.get_setup()
        return setup.getPrintingWorkflowEnabled()

    def str_date(self, date, long_format=1, default=""):
        if not date:
            return default
        return self.ulocalized_time(date, long_format=long_format)

    def to_datetime_input_value(self, date):
        """Converts to a compatible datetime format
        """
        if not isinstance(date, DateTime):
            return ""
        return date.strftime("%Y-%m-%d %H:%M")

    def getDefaultAddCount(self):
        return self.context.bika_setup.getDefaultNumberOfARsToAdd()

    @property
    def show_partitions(self):
        if self.flat_listing:
            return False
        if api.get_current_client():
            # If current user is a client contact, delegate to ShowPartitions
            return api.get_setup().getShowPartitions()
        return True

    @property
    def flat_listing(self):
        return self.review_state.get("flat_listing", False)