Source code for camcops_server.cc_modules.cc_tracker

#!/usr/bin/env python



    Copyright (C) 2012-2020 Rudolf Cardinal ([email protected]).

    This file is part of CamCOPS.

    CamCOPS 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, either version 3 of the License, or
    (at your option) any later version.

    CamCOPS is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with CamCOPS. If not, see <>.


**Trackers, showing numerical information over time, and clinical text views,
showing text that a clinician might care about.**


import logging
from typing import Any, Dict, List, Optional, Set, Tuple, TYPE_CHECKING

from cardinal_pythonlib.datetimefunc import format_datetime
from cardinal_pythonlib.logs import BraceStyleAdapter
from pendulum import DateTime as Pendulum
from pyramid.renderers import render

from camcops_server.cc_modules.cc_audit import audit
from camcops_server.cc_modules.cc_constants import (
from camcops_server.cc_modules.cc_filename import get_export_filename
from camcops_server.cc_modules.cc_plot import matplotlib
from camcops_server.cc_modules.cc_pdf import pdf_from_html
from camcops_server.cc_modules.cc_pyramid import ViewArg, ViewParam
from camcops_server.cc_modules.cc_simpleobjects import (
from camcops_server.cc_modules.cc_task import Task
from camcops_server.cc_modules.cc_taskcollection import (
from camcops_server.cc_modules.cc_unittest import DemoDatabaseTestCase
from camcops_server.cc_modules.cc_xml import (

import matplotlib.dates  # delayed until after the cc_plot import

    from camcops_server.cc_modules.cc_patient import Patient  # noqa: F401
    from camcops_server.cc_modules.cc_patientidnum import PatientIdNum  # noqa: E501,F401
    from camcops_server.cc_modules.cc_request import CamcopsRequest  # noqa: E501,F401
    from camcops_server.cc_modules.cc_trackerhelpers import TrackerInfo  # noqa: E501,F401

log = BraceStyleAdapter(logging.getLogger(__name__))

# =============================================================================
# Constants
# =============================================================================

    <div class="{CssClass.WARNING}">
    <div class="{CssClass.WARNING}">
        Other tasks exist for this patient that you do not have access to view.

DEBUG_TRACKER_TASK_INCLUSION = False  # should be False for production system

# =============================================================================
# Helper functions
# =============================================================================

[docs]def consistency(req: "CamcopsRequest", values: List[Any], servervalue: Any = None, case_sensitive: bool = True) -> Tuple[bool, str]: """ Checks for consistency in a set of values (e.g. ID numbers, names). The list of values (with the ``servervalue`` appended, if not ``None``) is checked to ensure that it contains only one unique value (ignoring ``None`` values or empty ``""`` values). Returns: the tuple ``consistent, msg``, where ``consistent`` is a bool and ``msg`` is a descriptive HTML message """ if case_sensitive: vallist = [str(v) if v is not None else v for v in values] if servervalue is not None: vallist.append(str(servervalue)) else: vallist = [str(v).upper() if v is not None else v for v in values] if servervalue is not None: vallist.append(str(servervalue).upper()) # Replace "" with None, so we only have a single "not-present" value vallist = [None if x == "" else x for x in vallist] unique = list(set(vallist)) _ = req.gettext if len(unique) == 0: return True, _("consistent (no values)") if len(unique) == 1: return True, f"{_('consistent')} ({unique[0]})" if len(unique) == 2: if None in unique: return True, ( f"{_('consistent')} " f"({_('all blank or')} {unique[1 - unique.index(None)]})" ) return False, ( f"<b>{_('INCONSISTENT')} " f"({_('contains values')} {', '.join(unique)})</b>" )
[docs]def consistency_idnums(req: "CamcopsRequest", idnum_lists: List[List["PatientIdNum"]]) \ -> Tuple[bool, str]: """ Checks the consistency of a set of :class:`PatientIdNum` objects. "Are all these records from the same patient?" Args: req: a :class:`camcops_server.cc_modules.cc_request.CamcopsRequest` idnum_lists: a list of lists (one per :class:`camcops_server.cc_modules.cc_patient.Patient` instance) of :class:`PatientIdNum` objects Returns: the tuple ``consistent, msg``, where ``consistent`` is a bool and ``msg`` is a descriptive HTML message """ known = {} # type: Dict[int, Set[int]] # maps which_idnum -> set of idnum_values # noqa for idnum_list in idnum_lists: for idnum in idnum_list: idnum_value = idnum.idnum_value if idnum_value is not None: which_idnum = idnum.which_idnum if which_idnum not in known: known[which_idnum] = set() # type: Set[int] known[which_idnum].add(idnum_value) failures = [] # type: List[str] successes = [] # type: List[str] _ = req.gettext for which_idnum, encountered_values in known.items(): value_str = ", ".join(str(v) for v in sorted(list(encountered_values))) if len(encountered_values) > 1: failures.append( f"idnum{which_idnum} {_('contains values')} {value_str}") else: successes.append( f"idnum{which_idnum} {_('all blank or')} {value_str}") if failures: return False, ( f"<b>{_('INCONSISTENT')} ({'; '.join(failures + successes)})</b>" ) else: return True, f"{_('consistent')} ({'; '.join(successes)})"
[docs]def format_daterange(start: Optional[Pendulum], end: Optional[Pendulum]) -> str: """ Textual representation of an inclusive-to-exclusive date range. Arguments are datetime values. """ start_str = format_datetime(start, DateFormat.ISO8601_DATE_ONLY, default="−∞") end_str = format_datetime(end, DateFormat.ISO8601_DATE_ONLY, default="+∞") return f"[{start_str}, {end_str})"
# ============================================================================= # ConsistencyInfo class # =============================================================================
[docs]class ConsistencyInfo(object): """ Represents ID consistency information about a set of tasks. """ def __init__(self, req: "CamcopsRequest", tasklist: List[Task]) -> None: """ Initialize values, from a list of task instances. """ self.request = req self.consistent_forename, self.msg_forename = consistency( req, [task.get_patient_forename() for task in tasklist], servervalue=None, case_sensitive=False) self.consistent_surname, self.msg_surname = consistency( req, [task.get_patient_surname() for task in tasklist], servervalue=None, case_sensitive=False) self.consistent_dob, self.msg_dob = consistency( req, [task.get_patient_dob_first11chars() for task in tasklist]) self.consistent_sex, self.msg_sex = consistency( req, [task.get_patient_sex() for task in tasklist]) self.consistent_idnums, self.msg_idnums = consistency_idnums( req, [task.get_patient_idnum_objects() for task in tasklist]) self.all_consistent = ( self.consistent_forename and self.consistent_surname and self.consistent_dob and self.consistent_sex and self.consistent_idnums )
[docs] def are_all_consistent(self) -> bool: """ Is all the ID information consistent? """ return self.all_consistent
[docs] def get_description_list(self) -> List[str]: """ Textual representation of ID information, indicating consistency or lack of it. """ _ = self.request.gettext cons = [ f"{_('Forename:')} {self.msg_forename}", f"{_('Surname:')} {self.msg_surname}", f"{_('DOB:')} {self.msg_dob}", f"{_('Sex:')} {self.msg_sex}", f"{_('ID numbers:')} {self.msg_idnums}", ] return cons
[docs] def get_xml_root(self) -> XmlElement: """ XML tree (as root :class:`camcops_server.cc_modules.cc_xml.XmlElement`) of consistency information. """ branches = [ XmlElement( name="all_consistent", value=self.are_all_consistent(), datatype="boolean" ) ] for c in self.get_description_list(): branches.append(XmlElement( name="consistency_check", value=c, )) return XmlElement(name="_consistency", value=branches)
# ============================================================================= # TrackerCtvCommon class: # =============================================================================
[docs]class TrackerCtvCommon(object): """ Base class for :class:`camcops_server.cc_modules.cc_tracker.Tracker` and :class:`camcops_server.cc_modules.cc_tracker.ClinicalTextView`. """ def __init__(self, req: "CamcopsRequest", taskfilter: TaskFilter, as_ctv: bool, via_index: bool = True) -> None: """ Initialize, fetching applicable tasks. """ # Record input variables at this point (for URL regeneration) self.req = req self.taskfilter = taskfilter self.as_ctv = as_ctv assert taskfilter.tasks_with_patient_only self.collection = TaskCollection( req=req, taskfilter=taskfilter, sort_method_by_class=TaskSortMethod.CREATION_DATE_ASC, sort_method_global=TaskSortMethod.CREATION_DATE_ASC, via_index=via_index ) all_tasks = self.collection.all_tasks if all_tasks: self.earliest = all_tasks[0].when_created self.latest = all_tasks[-1].when_created self.patient = all_tasks[0].patient else: self.earliest = None # type: Optional[Pendulum] self.latest = None # type: Optional[Pendulum] self.patient = None # type: Optional[Patient] # Summary information self.summary = "" if DEBUG_TRACKER_TASK_INCLUSION: first = True for cls in self.taskfilter.task_classes: if not first: self.summary += " // " self.summary += cls.tablename first = False task_instances = self.collection.tasks_for_task_class(cls) if not task_instances: if DEBUG_TRACKER_TASK_INCLUSION: self.summary += " (no instances)" continue for task in task_instances: if DEBUG_TRACKER_TASK_INCLUSION: # noinspection PyProtectedMember self.summary += f" / PK {task._pk}" self.summary += " ~~~ " self.summary += " — ".join([ "; ".join([ f"({task.tablename},{task.get_pk()}," f"{task.get_patient_server_pk()})" for task in self.collection.tasks_for_task_class(cls) ]) for cls in self.taskfilter.task_classes ]) # Consistency information self.consistency_info = ConsistencyInfo(req, all_tasks) # ------------------------------------------------------------------------- # Required for implementation # -------------------------------------------------------------------------
[docs] def get_xml(self, indent_spaces: int = 4, eol: str = '\n', include_comments: bool = False) -> str: """ Returns an XML representation. Args: indent_spaces: number of spaces to indent formatted XML eol: end-of-line string include_comments: include comments describing each field? Returns: an XML UTF-8 document representing our object. """ raise NotImplementedError("implement in subclass")
def _get_html(self) -> str: """ Returns an HTML representation. """ raise NotImplementedError("implement in subclass") def _get_pdf_html(self) -> str: """ Returns HTML used for making PDFs. """ raise NotImplementedError("implement in subclass") # ------------------------------------------------------------------------- # XML view # ------------------------------------------------------------------------- def _get_xml(self, audit_string: str, xml_name: str, indent_spaces: int = 4, eol: str = '\n', include_comments: bool = False) -> str: """ Returns an XML document representing this object. Args: audit_string: description used to audit access to this information xml_name: name of the root XML element indent_spaces: number of spaces to indent formatted XML eol: end-of-line string include_comments: include comments describing each field? Returns: an XML UTF-8 document representing the task. """ iddef = self.taskfilter.get_only_iddef() if not iddef: raise ValueError("Tracker/CTV doesn't have a single ID number " "criterion") branches = [ self.consistency_info.get_xml_root(), XmlElement( name="_search_criteria", value=[ XmlElement( name="task_tablename_list", value=",".join(self.taskfilter.task_tablename_list) ), XmlElement( name=ViewParam.WHICH_IDNUM, value=iddef.which_idnum, datatype=XmlDataTypes.INTEGER ), XmlElement( name=ViewParam.IDNUM_VALUE, value=iddef.idnum_value, datatype=XmlDataTypes.INTEGER ), XmlElement( name=ViewParam.START_DATETIME, value=format_datetime(self.taskfilter.start_datetime, DateFormat.ISO8601), datatype=XmlDataTypes.DATETIME ), XmlElement( name=ViewParam.END_DATETIME, value=format_datetime(self.taskfilter.end_datetime, DateFormat.ISO8601), datatype=XmlDataTypes.DATETIME ), ] ) ] options = TaskExportOptions(xml_include_plain_columns=True, xml_include_calculated=True, include_blobs=False) for t in self.collection.all_tasks: branches.append(t.get_xml_root(self.req, options)) audit( self.req, audit_string, table=t.tablename, server_pk=t.get_pk(), patient_server_pk=t.get_patient_server_pk() ) tree = XmlElement(name=xml_name, value=branches) return get_xml_document( tree, indent_spaces=indent_spaces, eol=eol, include_comments=include_comments ) # ------------------------------------------------------------------------- # HTML view # -------------------------------------------------------------------------
[docs] def get_html(self) -> str: """ Get HTML representing this object. """ self.req.prepare_for_html_figures() return self._get_html()
# ------------------------------------------------------------------------- # PDF view # -------------------------------------------------------------------------
[docs] def get_pdf_html(self) -> str: """ Returns HTML to be made into a PDF representing this object. """ self.req.prepare_for_pdf_figures() return self._get_pdf_html()
[docs] def get_pdf(self) -> bytes: """ Get PDF representing tracker/CTV. """ req = self.req html = self.get_pdf_html() # main content if CSS_PAGED_MEDIA: return pdf_from_html(req, html) else: return pdf_from_html( req, html=html, header_html=render( "wkhtmltopdf_header.mako", dict(inner_text=render("tracker_ctv_header.mako", dict(tracker=self), request=req)), request=req ), footer_html=render( "wkhtmltopdf_footer.mako", dict(inner_text=render("tracker_ctv_footer.mako", dict(tracker=self), request=req)), request=req ), extra_wkhtmltopdf_options={ "orientation": "Portrait" } )
[docs] def suggested_pdf_filename(self) -> str: """ Get suggested filename for tracker/CTV PDF. """ cfg = self.req.config return get_export_filename( req=self.req, patient_spec_if_anonymous=cfg.patient_spec_if_anonymous, patient_spec=cfg.patient_spec, filename_spec=cfg.ctv_filename_spec if self.as_ctv else cfg.tracker_filename_spec, # noqa filetype=ViewArg.PDF, is_anonymous=self.patient is None, surname=self.patient.get_surname() if self.patient else "", forename=self.patient.get_forename() if self.patient else "", dob=self.patient.get_dob() if self.patient else None, sex=self.patient.get_sex() if self.patient else None, idnum_objects=self.patient.get_idnum_objects() if self.patient else None, # noqa creation_datetime=None, basetable=None, serverpk=None )
# ============================================================================= # Tracker class # =============================================================================
[docs]class Tracker(TrackerCtvCommon): """ Class representing a numerical tracker. """ def __init__(self, req: "CamcopsRequest", taskfilter: TaskFilter, via_index: bool = True) -> None: super().__init__( req=req, taskfilter=taskfilter, as_ctv=False, via_index=via_index )
[docs] def get_xml(self, indent_spaces: int = 4, eol: str = '\n', include_comments: bool = False) -> str: return self._get_xml( audit_string="Tracker XML accessed", xml_name="tracker", indent_spaces=indent_spaces, eol=eol, include_comments=include_comments )
def _get_html(self) -> str: return render("tracker.mako", dict(tracker=self, viewtype=ViewArg.HTML), request=self.req) def _get_pdf_html(self) -> str: return render("tracker.mako", dict(tracker=self, pdf_landscape=False, viewtype=ViewArg.PDF), request=self.req) # ------------------------------------------------------------------------- # Plotting # -------------------------------------------------------------------------
[docs] def get_all_plots_for_one_task_html(self, tasks: List[Task]) -> str: """ HTML for all plots for a given task type. """ html = "" ntasks = len(tasks) if ntasks == 0: return html if not tasks[0].provides_trackers: # ask the first of the task instances return html alltrackers = [task.get_trackers(self.req) for task in tasks] datetimes = [task.get_creation_datetime() for task in tasks] ntrackers = len(alltrackers[0]) # ... number of trackers supplied by the first task (and all tasks) for tracker in range(ntrackers): values = [ alltrackers[tasknum][tracker].value for tasknum in range(ntasks) ] html += self.get_single_plot_html( datetimes, values, specimen_tracker=alltrackers[0][tracker] ) for task in tasks: # noinspection PyProtectedMember audit(self.req, "Tracker data accessed", table=task.tablename, server_pk=task._pk, patient_server_pk=task.get_patient_server_pk()) return html
[docs] def get_single_plot_html(self, datetimes: List[Pendulum], values: List[Optional[float]], specimen_tracker: "TrackerInfo") -> str: """ HTML for a single figure. """ nonblank_values = [x for x in values if x is not None] # NB DIFFERENT to list(filter(None, values)), which implements the # test "if x", not "if x is not None" -- thus eliminating zero values! # We don't want that. if not nonblank_values: return "" plot_label = specimen_tracker.plot_label axis_label = specimen_tracker.axis_label axis_min = specimen_tracker.axis_min axis_max = specimen_tracker.axis_max axis_ticks = specimen_tracker.axis_ticks horizontal_lines = specimen_tracker.horizontal_lines horizontal_labels = specimen_tracker.horizontal_labels aspect_ratio = specimen_tracker.aspect_ratio figsize = (FULLWIDTH_PLOT_WIDTH, (1.0/float(aspect_ratio)) * FULLWIDTH_PLOT_WIDTH) fig = self.req.create_figure(figsize=figsize) ax = fig.add_subplot(WHOLE_PANEL) x = [matplotlib.dates.date2num(t) for t in datetimes] datelabels = [dt.strftime(TRACKER_DATEFORMAT) for dt in datetimes] # First plot ax.plot(x, values, color="b", linestyle="-", marker="+", markeredgecolor="r", markerfacecolor="r", label=None) # ... NB command performed twice, see below # x axis ax.set_xlabel("Date/time", fontdict=self.req.fontdict) ax.set_xticks(x) ax.set_xticklabels(datelabels, fontdict=self.req.fontdict) if (self.earliest is not None and self.latest is not None and self.earliest != self.latest): xlim = matplotlib.dates.date2num((self.earliest, self.latest)) margin = (2.5 / 95.0) * (xlim[1] - xlim[0]) xlim[0] -= margin xlim[1] += margin ax.set_xlim(xlim) xlim = ax.get_xlim() fig.autofmt_xdate(rotation=90) # ... autofmt_xdate must be BEFORE twinx: # if axis_ticks is not None and len(axis_ticks) > 0: tick_positions = [m.y for m in axis_ticks] tick_labels = [m.label for m in axis_ticks] ax.set_yticks(tick_positions) ax.set_yticklabels(tick_labels, fontdict=self.req.fontdict) # y axis ax.set_ylabel(axis_label, fontdict=self.req.fontdict) axis_min = min(axis_min, min(nonblank_values)) if axis_min else min(nonblank_values) # noqa axis_max = max(axis_max, max(nonblank_values)) if axis_max else max(nonblank_values) # noqa # ... the supplied values are stretched if the data are outside them # ... but min(something, None) is None, so beware # If we get something with no sense of scale whatsoever, then what # we do is arbitrary. Matplotlib does its own thing, but we could do: if axis_min == axis_max: if axis_min == 0: axis_min, axis_min = -1.0, 1.0 else: singlevalue = axis_min axis_min = 0.9 * singlevalue axis_max = 1.1 * singlevalue if axis_min > axis_max: axis_min, axis_max = axis_max, axis_min ax.set_ylim(axis_min, axis_max) # title ax.set_title(plot_label, fontdict=self.req.fontdict) # Horizontal lines stupid_jitter = 0.001 if horizontal_lines is not None: for y in horizontal_lines: ax.plot(xlim, [y, y + stupid_jitter], color="0.5", linestyle=":") # PROBLEM: horizontal lines becoming invisible # (whether from ax.axhline or plot) # Horizontal labels if horizontal_labels is not None: label_left = xlim[0] + 0.01 * (xlim[1] - xlim[0]) for lab in horizontal_labels: y = lab.y l_ = lab.label va = lab.vertical_alignment.value ax.text(label_left, y, l_, verticalalignment=va, alpha=0.5, fontdict=self.req.fontdict) # was "0.5" rather than 0.5, which led to a tricky-to-find # "TypeError: a float is required" exception after switching # to Python 3. # replot so the data are on top of the rest: ax.plot(x, values, color="b", linestyle="-", marker="+", markeredgecolor="r", markerfacecolor="r", label=None) # ... NB command performed twice, see above self.req.set_figure_font_sizes(ax) fig.tight_layout() # ... stop the labels dropping off # (only works properly for LEFT labels...) # # ... tried it - didn't work (internal numbers change fine, # check the logger, but visually doesn't help) # - # - return self.req.get_html_from_pyplot_figure(fig) + "<br>"
# ... extra line break for the PDF rendering # ============================================================================= # ClinicalTextView class # =============================================================================
[docs]class ClinicalTextView(TrackerCtvCommon): """ Class representing a clinical text view. """ def __init__(self, req: "CamcopsRequest", taskfilter: TaskFilter, via_index: bool = True) -> None: super().__init__( req=req, taskfilter=taskfilter, as_ctv=True, via_index=via_index )
[docs] def get_xml(self, indent_spaces: int = 4, eol: str = '\n', include_comments: bool = False) -> str: return self._get_xml( audit_string="Clinical text view XML accessed", xml_name="ctv", indent_spaces=indent_spaces, eol=eol, include_comments=include_comments )
def _get_html(self) -> str: return render("ctv.mako", dict(tracker=self, viewtype=ViewArg.HTML), request=self.req) def _get_pdf_html(self) -> str: return render("ctv.mako", dict(tracker=self, pdf_landscape=False, viewtype=ViewArg.PDF), request=self.req)
# ============================================================================= # Unit tests # =============================================================================
[docs]class TrackerCtvTests(DemoDatabaseTestCase): """ Unit tests. """
[docs] def setUp(self) -> None: super().setUp() self.taskfilter = TaskFilter() idnum_ref = IdNumReference(which_idnum=0, idnum_value=0) self.taskfilter.idnum_criteria = [idnum_ref] self.taskfilter.tasks_with_patient_only = True
def test_tracker(self) -> None: self.announce("test_tracker") req = self.req t = Tracker(req, self.taskfilter) self.assertIsInstance(t.get_html(), str) self.assertIsInstance(t.get_pdf(), bytes) self.assertIsInstance(t.get_pdf_html(), str) self.assertIsInstance(t.get_xml(), str) self.assertIsInstance(t.suggested_pdf_filename(), str) def test_ctv(self) -> None: self.announce("test_ctv") req = self.req c = ClinicalTextView(req, self.taskfilter) self.assertIsInstance(c.get_html(), str) self.assertIsInstance(c.get_pdf(), bytes) self.assertIsInstance(c.get_pdf_html(), str) self.assertIsInstance(c.get_xml(), str) self.assertIsInstance(c.suggested_pdf_filename(), str)