Coverage for cc_modules/cc_tracker.py: 21%
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1"""
2camcops_server/cc_modules/cc_tracker.py
4===============================================================================
6 Copyright (C) 2012, University of Cambridge, Department of Psychiatry.
7 Created by Rudolf Cardinal (rnc1001@cam.ac.uk).
9 This file is part of CamCOPS.
11 CamCOPS is free software: you can redistribute it and/or modify
12 it under the terms of the GNU General Public License as published by
13 the Free Software Foundation, either version 3 of the License, or
14 (at your option) any later version.
16 CamCOPS is distributed in the hope that it will be useful,
17 but WITHOUT ANY WARRANTY; without even the implied warranty of
18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 GNU General Public License for more details.
21 You should have received a copy of the GNU General Public License
22 along with CamCOPS. If not, see <https://www.gnu.org/licenses/>.
24===============================================================================
26**Trackers, showing numerical information over time, and clinical text views,
27showing text that a clinician might care about.**
29"""
31import logging
32from typing import Any, Dict, List, Optional, Set, Tuple, TYPE_CHECKING
34from cardinal_pythonlib.datetimefunc import format_datetime
35from cardinal_pythonlib.logs import BraceStyleAdapter
36from pendulum import DateTime as Pendulum
37from pyramid.renderers import render
39from camcops_server.cc_modules.cc_audit import audit
40from camcops_server.cc_modules.cc_constants import (
41 CssClass,
42 CSS_PAGED_MEDIA,
43 DateFormat,
44 MatplotlibConstants,
45 PlotDefaults,
46)
47from camcops_server.cc_modules.cc_filename import get_export_filename
48from camcops_server.cc_modules.cc_plot import matplotlib
49from camcops_server.cc_modules.cc_pdf import pdf_from_html
50from camcops_server.cc_modules.cc_pyramid import ViewArg, ViewParam
51from camcops_server.cc_modules.cc_simpleobjects import TaskExportOptions
52from camcops_server.cc_modules.cc_task import Task
53from camcops_server.cc_modules.cc_taskcollection import (
54 TaskCollection,
55 TaskFilter,
56 TaskSortMethod,
57)
58from camcops_server.cc_modules.cc_xml import (
59 get_xml_document,
60 XmlDataTypes,
61 XmlElement,
62)
64import matplotlib.dates # delayed until after the cc_plot import
66if TYPE_CHECKING:
67 from camcops_server.cc_modules.cc_patient import Patient # noqa: F401
68 from camcops_server.cc_modules.cc_patientidnum import (
69 PatientIdNum,
70 )
71 from camcops_server.cc_modules.cc_request import (
72 CamcopsRequest,
73 )
74 from camcops_server.cc_modules.cc_trackerhelpers import (
75 TrackerInfo,
76 )
78log = BraceStyleAdapter(logging.getLogger(__name__))
81# =============================================================================
82# Constants
83# =============================================================================
85TRACKER_DATEFORMAT = "%Y-%m-%d"
86WARNING_NO_PATIENT_FOUND = f"""
87 <div class="{CssClass.WARNING}">
88 </div>
89"""
90WARNING_DENIED_INFORMATION = f"""
91 <div class="{CssClass.WARNING}">
92 Other tasks exist for this patient that you do not have access to view.
93 </div>
94"""
96DEBUG_TRACKER_TASK_INCLUSION = False # should be False for production system
99# =============================================================================
100# Helper functions
101# =============================================================================
102# http://stackoverflow.com/questions/11788195
105def consistency(
106 req: "CamcopsRequest",
107 values: List[Any],
108 servervalue: Any = None,
109 case_sensitive: bool = True,
110) -> Tuple[bool, str]:
111 """
112 Checks for consistency in a set of values (e.g. names, dates of birth).
113 (ID numbers are done separately via :func:`consistency_idnums`.)
115 The list of values (with the ``servervalue`` appended, if not ``None``) is
116 checked to ensure that it contains only one unique value (ignoring ``None``
117 values or empty ``""`` values).
119 Returns:
120 the tuple ``consistent, msg``, where ``consistent`` is a bool and
121 ``msg`` is a descriptive HTML message
122 """
123 if case_sensitive:
124 vallist = [str(v) if v is not None else v for v in values]
125 if servervalue is not None:
126 vallist.append(str(servervalue))
127 else:
128 vallist = [str(v).upper() if v is not None else v for v in values]
129 if servervalue is not None:
130 vallist.append(str(servervalue).upper())
131 # Replace "" with None, so we only have a single "not-present" value
132 vallist = [None if x == "" else x for x in vallist]
133 unique = list(set(vallist))
134 _ = req.gettext
135 if len(unique) == 0:
136 return True, _("consistent (no values)")
137 if len(unique) == 1:
138 return True, f"{_('consistent')} ({unique[0]})"
139 if len(unique) == 2:
140 if None in unique:
141 return (
142 True,
143 (
144 f"{_('consistent')} "
145 f"({_('all blank or')} {unique[1 - unique.index(None)]})"
146 ),
147 )
148 return (
149 False,
150 (
151 f"<b>{_('INCONSISTENT')} "
152 f"({_('contains values')} {', '.join(unique)})</b>"
153 ),
154 )
157def consistency_idnums(
158 req: "CamcopsRequest", idnum_lists: List[List["PatientIdNum"]]
159) -> Tuple[bool, str]:
160 """
161 Checks the consistency of a set of :class:`PatientIdNum` objects.
162 "Are all these records from the same patient?"
164 Args:
165 req:
166 a :class:`camcops_server.cc_modules.cc_request.CamcopsRequest`
167 idnum_lists:
168 a list of lists (one per task/patient instance) of
169 :class:`PatientIdNum` objects
171 Returns:
172 the tuple ``consistent, msg``, where ``consistent`` is a bool and
173 ``msg`` is a descriptive HTML message
175 """
176 # 1. Generate "known", mapping which_idnum -> set of observed non-NULL
177 # idnum_values
178 known = {} # type: Dict[int, Set[int]]
179 for task_idnum_list in idnum_lists:
180 for idnum in task_idnum_list:
181 idnum_value = idnum.idnum_value
182 if idnum_value is not None:
183 which_idnum = idnum.which_idnum
184 if which_idnum not in known:
185 known[which_idnum] = set()
186 known[which_idnum].add(idnum_value)
188 # 2. For every observed which_idnum, was it observed in all tasks?
189 present_in_all = {} # type: Dict[int, bool]
190 for which_idnum in known.keys():
191 present_for_all_tasks = all(
192 # "For all tasks..."
193 (
194 # "At least one ID number record relates to this which_idnum".
195 any(
196 idnum.which_idnum == which_idnum # type: ignore[arg-type]
197 and idnum.idnum_value is not None
198 )
199 for idnum in task_idnum_list
200 )
201 for task_idnum_list in idnum_lists
202 )
203 present_in_all[which_idnum] = present_for_all_tasks
205 # 3. Summarize
206 failures = [] # type: List[str]
207 successes = [] # type: List[str]
208 _ = req.gettext
209 for which_idnum, encountered_values in known.items():
210 value_str = ", ".join(str(v) for v in sorted(list(encountered_values)))
211 if len(encountered_values) > 1:
212 failures.append(
213 f"idnum{which_idnum} {_('contains values')} {value_str}"
214 )
215 else:
216 if present_in_all[which_idnum]:
217 successes.append(
218 f"idnum{which_idnum} {_('consistent')} ({value_str})"
219 )
220 else:
221 successes.append(
222 f"idnum{which_idnum} {_('all blank or')} {value_str}"
223 )
224 if failures:
225 return (
226 False,
227 (
228 f"<b>{_('INCONSISTENT')} "
229 f"({'; '.join(failures + successes)})</b>"
230 ),
231 )
232 else:
233 return True, f"{_('consistent')} ({'; '.join(successes)})"
236def format_daterange(
237 start: Optional[Pendulum], end: Optional[Pendulum]
238) -> str:
239 """
240 Textual representation of an inclusive-to-exclusive date range.
242 Arguments are datetime values.
243 """
244 start_str = format_datetime(
245 start, DateFormat.ISO8601_DATE_ONLY, default="−∞"
246 )
247 end_str = format_datetime(end, DateFormat.ISO8601_DATE_ONLY, default="+∞")
248 return f"[{start_str}, {end_str})"
251# =============================================================================
252# ConsistencyInfo class
253# =============================================================================
256class ConsistencyInfo(object):
257 """
258 Represents ID consistency information about a set of tasks.
259 """
261 def __init__(self, req: "CamcopsRequest", tasklist: List[Task]) -> None:
262 """
263 Initialize values, from a list of task instances.
264 """
265 self.request = req
266 self.consistent_forename, self.msg_forename = consistency(
267 req,
268 [task.get_patient_forename() for task in tasklist],
269 servervalue=None,
270 case_sensitive=False,
271 )
272 self.consistent_surname, self.msg_surname = consistency(
273 req,
274 [task.get_patient_surname() for task in tasklist],
275 servervalue=None,
276 case_sensitive=False,
277 )
278 self.consistent_dob, self.msg_dob = consistency(
279 req, [task.get_patient_dob_first11chars() for task in tasklist]
280 )
281 self.consistent_sex, self.msg_sex = consistency(
282 req, [task.get_patient_sex() for task in tasklist]
283 )
284 self.consistent_idnums, self.msg_idnums = consistency_idnums(
285 req, [task.get_patient_idnum_objects() for task in tasklist]
286 )
287 self.all_consistent = (
288 self.consistent_forename
289 and self.consistent_surname
290 and self.consistent_dob
291 and self.consistent_sex
292 and self.consistent_idnums
293 )
295 def are_all_consistent(self) -> bool:
296 """
297 Is all the ID information consistent?
298 """
299 return self.all_consistent
301 def get_description_list(self) -> List[str]:
302 """
303 Textual representation of ID information, indicating consistency or
304 lack of it.
305 """
306 _ = self.request.gettext
307 cons = [
308 f"{_('Forename:')} {self.msg_forename}",
309 f"{_('Surname:')} {self.msg_surname}",
310 f"{_('DOB:')} {self.msg_dob}",
311 f"{_('Sex:')} {self.msg_sex}",
312 f"{_('ID numbers:')} {self.msg_idnums}",
313 ]
314 return cons
316 def get_xml_root(self) -> XmlElement:
317 """
318 XML tree (as root :class:`camcops_server.cc_modules.cc_xml.XmlElement`)
319 of consistency information.
320 """
321 branches = [
322 XmlElement(
323 name="all_consistent",
324 value=self.are_all_consistent(),
325 datatype="boolean",
326 )
327 ]
328 for c in self.get_description_list():
329 branches.append(XmlElement(name="consistency_check", value=c))
330 return XmlElement(name="_consistency", value=branches)
333# =============================================================================
334# TrackerCtvCommon class:
335# =============================================================================
338class TrackerCtvCommon(object):
339 """
340 Base class for :class:`camcops_server.cc_modules.cc_tracker.Tracker` and
341 :class:`camcops_server.cc_modules.cc_tracker.ClinicalTextView`.
342 """
344 def __init__(
345 self,
346 req: "CamcopsRequest",
347 taskfilter: TaskFilter,
348 as_ctv: bool,
349 via_index: bool = True,
350 ) -> None:
351 """
352 Initialize, fetching applicable tasks.
353 """
355 # Record input variables at this point (for URL regeneration)
356 self.req = req
357 self.taskfilter = taskfilter
358 self.as_ctv = as_ctv
359 assert taskfilter.tasks_with_patient_only
361 self.collection = TaskCollection(
362 req=req,
363 taskfilter=taskfilter,
364 sort_method_by_class=TaskSortMethod.CREATION_DATE_ASC,
365 sort_method_global=TaskSortMethod.CREATION_DATE_ASC,
366 via_index=via_index,
367 )
368 all_tasks = self.collection.all_tasks
369 if all_tasks:
370 self.earliest = all_tasks[0].when_created
371 self.latest = all_tasks[-1].when_created
372 self.patient = all_tasks[0].patient
373 else:
374 self.earliest = None # type: ignore[no-redef]
375 self.latest = None # type: ignore[no-redef]
376 self.patient = None # type: ignore[no-redef]
378 # Summary information
379 self.summary = ""
380 if DEBUG_TRACKER_TASK_INCLUSION:
381 first = True
382 for cls in self.taskfilter.task_classes:
383 if not first:
384 self.summary += " // "
385 self.summary += cls.tablename
386 first = False
387 task_instances = self.collection.tasks_for_task_class(cls)
388 if not task_instances:
389 if DEBUG_TRACKER_TASK_INCLUSION:
390 self.summary += " (no instances)"
391 continue
392 for task in task_instances:
393 if DEBUG_TRACKER_TASK_INCLUSION:
394 self.summary += f" / PK {task.pk}"
395 self.summary += " ~~~ "
396 self.summary += " — ".join(
397 [
398 "; ".join(
399 [
400 f"({task.tablename},{task.pk},"
401 f"{task.get_patient_server_pk()})"
402 for task in self.collection.tasks_for_task_class(cls)
403 ]
404 )
405 for cls in self.taskfilter.task_classes
406 ]
407 )
409 # Consistency information
410 self.consistency_info = ConsistencyInfo(req, all_tasks)
412 # -------------------------------------------------------------------------
413 # Required for implementation
414 # -------------------------------------------------------------------------
416 def get_xml(
417 self,
418 indent_spaces: int = 4,
419 eol: str = "\n",
420 include_comments: bool = False,
421 ) -> str:
422 """
423 Returns an XML representation.
425 Args:
426 indent_spaces: number of spaces to indent formatted XML
427 eol: end-of-line string
428 include_comments: include comments describing each field?
430 Returns:
431 an XML UTF-8 document representing our object.
432 """
433 raise NotImplementedError("implement in subclass")
435 def _get_html(self) -> str:
436 """
437 Returns an HTML representation.
438 """
439 raise NotImplementedError("implement in subclass")
441 def _get_pdf_html(self) -> str:
442 """
443 Returns HTML used for making PDFs.
444 """
445 raise NotImplementedError("implement in subclass")
447 # -------------------------------------------------------------------------
448 # XML view
449 # -------------------------------------------------------------------------
451 def _get_xml(
452 self,
453 audit_string: str,
454 xml_name: str,
455 indent_spaces: int = 4,
456 eol: str = "\n",
457 include_comments: bool = False,
458 ) -> str:
459 """
460 Returns an XML document representing this object.
462 Args:
463 audit_string: description used to audit access to this information
464 xml_name: name of the root XML element
465 indent_spaces: number of spaces to indent formatted XML
466 eol: end-of-line string
467 include_comments: include comments describing each field?
469 Returns:
470 an XML UTF-8 document representing the task.
471 """
472 iddef = self.taskfilter.get_only_iddef()
473 if not iddef:
474 raise ValueError(
475 "Tracker/CTV doesn't have a single ID number " "criterion"
476 )
477 branches = [
478 self.consistency_info.get_xml_root(),
479 XmlElement(
480 name="_search_criteria",
481 value=[
482 XmlElement(
483 name="task_tablename_list",
484 value=",".join(self.taskfilter.task_tablename_list),
485 ),
486 XmlElement(
487 name=ViewParam.WHICH_IDNUM,
488 value=iddef.which_idnum,
489 datatype=XmlDataTypes.INTEGER,
490 ),
491 XmlElement(
492 name=ViewParam.IDNUM_VALUE,
493 value=iddef.idnum_value,
494 datatype=XmlDataTypes.INTEGER,
495 ),
496 XmlElement(
497 name=ViewParam.START_DATETIME,
498 value=format_datetime(
499 self.taskfilter.start_datetime, DateFormat.ISO8601
500 ),
501 datatype=XmlDataTypes.DATETIME,
502 ),
503 XmlElement(
504 name=ViewParam.END_DATETIME,
505 value=format_datetime(
506 self.taskfilter.end_datetime, DateFormat.ISO8601
507 ),
508 datatype=XmlDataTypes.DATETIME,
509 ),
510 ],
511 ),
512 ]
513 options = TaskExportOptions(
514 xml_include_plain_columns=True,
515 xml_include_calculated=True,
516 include_blobs=False,
517 )
518 for t in self.collection.all_tasks:
519 branches.append(t.get_xml_root(self.req, options))
520 audit(
521 self.req,
522 audit_string,
523 table=t.tablename,
524 server_pk=t.pk,
525 patient_server_pk=t.get_patient_server_pk(),
526 )
527 tree = XmlElement(name=xml_name, value=branches)
528 return get_xml_document(
529 tree,
530 indent_spaces=indent_spaces,
531 eol=eol,
532 include_comments=include_comments,
533 )
535 # -------------------------------------------------------------------------
536 # HTML view
537 # -------------------------------------------------------------------------
539 def get_html(self) -> str:
540 """
541 Get HTML representing this object.
542 """
543 self.req.prepare_for_html_figures()
544 return self._get_html()
546 # -------------------------------------------------------------------------
547 # PDF view
548 # -------------------------------------------------------------------------
550 def get_pdf_html(self) -> str:
551 """
552 Returns HTML to be made into a PDF representing this object.
553 """
554 self.req.prepare_for_pdf_figures()
555 return self._get_pdf_html()
557 def get_pdf(self) -> bytes:
558 """
559 Get PDF representing tracker/CTV.
560 """
561 req = self.req
562 html = self.get_pdf_html() # main content
563 if CSS_PAGED_MEDIA:
564 return pdf_from_html(req, html)
565 else:
566 return pdf_from_html(
567 req,
568 html=html,
569 header_html=render(
570 "wkhtmltopdf_header.mako",
571 dict(
572 inner_text=render(
573 "tracker_ctv_header.mako",
574 dict(tracker=self),
575 request=req,
576 )
577 ),
578 request=req,
579 ),
580 footer_html=render(
581 "wkhtmltopdf_footer.mako",
582 dict(
583 inner_text=render(
584 "tracker_ctv_footer.mako",
585 dict(tracker=self),
586 request=req,
587 )
588 ),
589 request=req,
590 ),
591 extra_wkhtmltopdf_options={"orientation": "Portrait"},
592 )
594 def suggested_pdf_filename(self) -> str:
595 """
596 Get suggested filename for tracker/CTV PDF.
597 """
598 cfg = self.req.config
599 return get_export_filename(
600 req=self.req,
601 patient_spec_if_anonymous=cfg.patient_spec_if_anonymous,
602 patient_spec=cfg.patient_spec,
603 filename_spec=(
604 cfg.ctv_filename_spec
605 if self.as_ctv
606 else cfg.tracker_filename_spec
607 ),
608 filetype=ViewArg.PDF,
609 is_anonymous=self.patient is None,
610 surname=self.patient.get_surname() if self.patient else "",
611 forename=self.patient.get_forename() if self.patient else "",
612 dob=self.patient.get_dob() if self.patient else None,
613 sex=self.patient.get_sex() if self.patient else None,
614 idnum_objects=(
615 self.patient.get_idnum_objects() if self.patient else None
616 ),
617 creation_datetime=None,
618 basetable=None,
619 serverpk=None,
620 )
623# =============================================================================
624# Tracker class
625# =============================================================================
628class Tracker(TrackerCtvCommon):
629 """
630 Class representing a numerical tracker.
631 """
633 def __init__(
634 self,
635 req: "CamcopsRequest",
636 taskfilter: TaskFilter,
637 via_index: bool = True,
638 ) -> None:
639 super().__init__(
640 req=req, taskfilter=taskfilter, as_ctv=False, via_index=via_index
641 )
643 def get_xml(
644 self,
645 indent_spaces: int = 4,
646 eol: str = "\n",
647 include_comments: bool = False,
648 ) -> str:
649 return self._get_xml(
650 audit_string="Tracker XML accessed",
651 xml_name="tracker",
652 indent_spaces=indent_spaces,
653 eol=eol,
654 include_comments=include_comments,
655 )
657 def _get_html(self) -> str:
658 return render(
659 "tracker.mako",
660 dict(tracker=self, viewtype=ViewArg.HTML),
661 request=self.req,
662 )
664 def _get_pdf_html(self) -> str:
665 return render(
666 "tracker.mako",
667 dict(tracker=self, pdf_landscape=False, viewtype=ViewArg.PDF),
668 request=self.req,
669 )
671 # -------------------------------------------------------------------------
672 # Plotting
673 # -------------------------------------------------------------------------
675 def get_all_plots_for_one_task_html(self, tasks: List[Task]) -> str:
676 """
677 HTML for all plots for a given task type.
678 """
679 html = ""
680 ntasks = len(tasks)
681 if ntasks == 0:
682 return html
683 if not tasks[0].provides_trackers:
684 # ask the first of the task instances
685 return html
686 alltrackers = [task.get_trackers(self.req) for task in tasks]
687 datetimes = [task.get_creation_datetime() for task in tasks]
688 ntrackers = len(alltrackers[0])
689 # ... number of trackers supplied by the first task (and all tasks)
690 for tracker in range(ntrackers):
691 values = [
692 alltrackers[tasknum][tracker].value
693 for tasknum in range(ntasks)
694 ]
695 html += self.get_single_plot_html(
696 datetimes, values, specimen_tracker=alltrackers[0][tracker]
697 )
698 for task in tasks:
699 audit(
700 self.req,
701 "Tracker data accessed",
702 table=task.tablename,
703 server_pk=task.pk,
704 patient_server_pk=task.get_patient_server_pk(),
705 )
706 return html
708 def get_single_plot_html(
709 self,
710 datetimes: List[Pendulum],
711 values: List[Optional[float]],
712 specimen_tracker: "TrackerInfo",
713 ) -> str:
714 """
715 HTML for a single figure.
716 """
717 nonblank_values = [x for x in values if x is not None]
718 # NB DIFFERENT to list(filter(None, values)), which implements the
719 # test "if x", not "if x is not None" -- thus eliminating zero values!
720 # We don't want that.
721 if not nonblank_values:
722 return ""
724 plot_label = specimen_tracker.plot_label
725 axis_label = specimen_tracker.axis_label
726 axis_min = specimen_tracker.axis_min
727 axis_max = specimen_tracker.axis_max
728 axis_ticks = specimen_tracker.axis_ticks
729 horizontal_lines = specimen_tracker.horizontal_lines
730 horizontal_labels = specimen_tracker.horizontal_labels
731 aspect_ratio = specimen_tracker.aspect_ratio
733 figsize = (
734 PlotDefaults.FULLWIDTH_PLOT_WIDTH,
735 (1.0 / float(aspect_ratio)) * PlotDefaults.FULLWIDTH_PLOT_WIDTH,
736 )
737 fig = self.req.create_figure(figsize=figsize)
738 ax = fig.add_subplot(MatplotlibConstants.WHOLE_PANEL)
739 x = [matplotlib.dates.date2num(t) for t in datetimes]
740 datelabels = [dt.strftime(TRACKER_DATEFORMAT) for dt in datetimes]
742 # Plot lines and markers (on top of lines)
743 ax.plot(
744 x, # x
745 values, # y
746 color=MatplotlibConstants.COLOUR_BLUE, # line colour
747 linestyle=MatplotlibConstants.LINESTYLE_SOLID,
748 marker=MatplotlibConstants.MARKER_PLUS, # point shape
749 markeredgecolor=MatplotlibConstants.COLOUR_RED, # point colour
750 markerfacecolor=MatplotlibConstants.COLOUR_RED, # point colour
751 label=None,
752 zorder=PlotDefaults.ZORDER_DATA_LINES_POINTS,
753 )
755 # x axis
756 ax.set_xlabel("Date/time", fontdict=self.req.fontdict)
757 ax.set_xticks(x)
758 ax.set_xticklabels(datelabels, fontdict=self.req.fontdict)
759 if (
760 self.earliest is not None
761 and self.latest is not None
762 and self.earliest != self.latest
763 ):
764 xlim = matplotlib.dates.date2num((self.earliest, self.latest))
765 margin = (2.5 / 95.0) * (xlim[1] - xlim[0])
766 xlim[0] -= margin
767 xlim[1] += margin
768 ax.set_xlim(xlim)
769 xlim = ax.get_xlim()
770 fig.autofmt_xdate(rotation=90)
771 # ... autofmt_xdate must be BEFORE twinx:
772 # http://stackoverflow.com/questions/8332395
773 if axis_ticks is not None and len(axis_ticks) > 0:
774 tick_positions = [m.y for m in axis_ticks]
775 tick_labels = [m.label for m in axis_ticks]
776 ax.set_yticks(tick_positions)
777 ax.set_yticklabels(tick_labels, fontdict=self.req.fontdict)
779 # y axis
780 ax.set_ylabel(axis_label, fontdict=self.req.fontdict)
781 axis_min = (
782 min(axis_min, min(nonblank_values))
783 if axis_min is not None
784 else min(nonblank_values)
785 )
786 axis_max = (
787 max(axis_max, max(nonblank_values))
788 if axis_max is not None
789 else max(nonblank_values)
790 )
791 # ... the supplied values are stretched if the data are outside them
792 # ... but min(something, None) is None, so beware
793 # If we get something with no sense of scale whatsoever, then what
794 # we do is arbitrary. Matplotlib does its own thing, but we could do:
795 if axis_min == axis_max:
796 if axis_min == 0:
797 axis_min, axis_min = -1.0, 1.0
798 else:
799 singlevalue = axis_min
800 axis_min = 0.9 * singlevalue
801 axis_max = 1.1 * singlevalue
802 if axis_min > axis_max:
803 axis_min, axis_max = axis_max, axis_min
804 ax.set_ylim(axis_min, axis_max)
806 # title
807 ax.set_title(plot_label, fontdict=self.req.fontdict)
809 # Horizontal lines
810 stupid_jitter = 0.001
811 if horizontal_lines is not None:
812 for y in horizontal_lines:
813 ax.plot(
814 xlim, # x
815 [y, y + stupid_jitter], # y
816 color=MatplotlibConstants.COLOUR_GREY_50,
817 linestyle=MatplotlibConstants.LINESTYLE_DOTTED,
818 zorder=PlotDefaults.ZORDER_PRESET_LINES,
819 )
820 # PROBLEM: horizontal lines becoming invisible
821 # (whether from ax.axhline or plot)
823 # Horizontal labels
824 if horizontal_labels is not None:
825 label_left = xlim[0] + 0.01 * (xlim[1] - xlim[0])
826 for lab in horizontal_labels:
827 y = lab.y
828 l_ = lab.label
829 va = lab.vertical_alignment.value
830 ax.text(
831 label_left, # x
832 y, # y
833 l_, # text
834 verticalalignment=va,
835 # alpha=0.5,
836 # ... was "0.5" rather than 0.5, which led to a
837 # tricky-to-find "TypeError: a float is required" exception
838 # after switching to Python 3.
839 # ... and switched to grey colour with zorder on 2020-06-28
840 # after wkhtmltopdf 0.12.5 had problems rendering
841 # opacity=0.5 with SVG lines
842 color=MatplotlibConstants.COLOUR_GREY_50,
843 fontdict=self.req.fontdict,
844 zorder=PlotDefaults.ZORDER_PRESET_LABELS,
845 )
847 self.req.set_figure_font_sizes(ax)
849 fig.tight_layout()
850 # ... stop the labels dropping off
851 # (only works properly for LEFT labels...)
853 # http://matplotlib.org/faq/howto_faq.html
854 # ... tried it - didn't work (internal numbers change fine,
855 # check the logger, but visually doesn't help)
856 # - http://stackoverflow.com/questions/9126838
857 # - http://matplotlib.org/examples/pylab_examples/finance_work2.html
858 return self.req.get_html_from_pyplot_figure(fig) + "<br>"
859 # ... extra line break for the PDF rendering
862# =============================================================================
863# ClinicalTextView class
864# =============================================================================
867class ClinicalTextView(TrackerCtvCommon):
868 """
869 Class representing a clinical text view.
870 """
872 def __init__(
873 self,
874 req: "CamcopsRequest",
875 taskfilter: TaskFilter,
876 via_index: bool = True,
877 ) -> None:
878 super().__init__(
879 req=req, taskfilter=taskfilter, as_ctv=True, via_index=via_index
880 )
882 def get_xml(
883 self,
884 indent_spaces: int = 4,
885 eol: str = "\n",
886 include_comments: bool = False,
887 ) -> str:
888 return self._get_xml(
889 audit_string="Clinical text view XML accessed",
890 xml_name="ctv",
891 indent_spaces=indent_spaces,
892 eol=eol,
893 include_comments=include_comments,
894 )
896 def _get_html(self) -> str:
897 return render(
898 "ctv.mako",
899 dict(tracker=self, viewtype=ViewArg.HTML),
900 request=self.req,
901 )
903 def _get_pdf_html(self) -> str:
904 return render(
905 "ctv.mako",
906 dict(tracker=self, pdf_landscape=False, viewtype=ViewArg.PDF),
907 request=self.req,
908 )