def as_r(self) -> str:
"""
Returns data as an R script.
This could be more sophisticated, e.g. creating factors with
appropriate levels (etc.).
"""
now = format_datetime(
get_now_localtz_pendulum(),
DateFormat.ISO8601_HUMANIZED_TO_SECONDS_TZ,
)
table_definition_str = "\n\n".join(page.r_data_table_definition()
for page in self.pages)
script = f"""#!/usr/bin/env Rscript
# R script generated by CamCOPS at {now}
# =============================================================================
# Libraries
# =============================================================================
library(data.table)
# =============================================================================
# Data
# =============================================================================
{table_definition_str}
"""
return script
def nlprp_datetime_now(as_local: bool = True) -> str:
"""
Returns the time now, as a string suitable for use with NLPRP.
Args:
as_local: use local timezone? (Otherwise, use UTC.)
"""
now = get_now_localtz_pendulum() if as_local else get_now_utc_pendulum()
return pendulum_to_nlprp_datetime(now)
def get_changelog() -> str:
now = get_now_localtz_pendulum()
return """camcops-server ({CAMCOPS_SERVER_VERSION_STRING}) all; urgency=low
* Change date: {CAMCOPS_SERVER_CHANGEDATE}.
* PLEASE SEE docs/source/changelog.rst FOR ALL CHANGES, or the online version
at https://camcops.readthedocs.io/.
* This file (changelog.Debian) has a very precise format:
https://www.debian.org/doc/debian-policy/ch-source.html#s-dpkgchangelog
* Note that newer entries are at the top.
-- Rudolf Cardinal <*****@*****.**> {now}
""".format(
CAMCOPS_SERVER_VERSION_STRING=CAMCOPS_SERVER_VERSION_STRING,
CAMCOPS_SERVER_CHANGEDATE=CAMCOPS_SERVER_CHANGEDATE,
now=now.strftime(DEBIAN_DATETIME_FORMAT),
)
def __init__(self,
from_addr: str,
date: str = None,
sender: str = "",
reply_to: str = "",
to: str = "",
cc: str = "",
bcc: str = "",
subject: str = "",
body: str = "",
content_type: str = "text/plain",
charset: str = "utf8",
attachment_filenames: Sequence[str] = None,
attachments_binary: Sequence[Tuple[str, bytes]] = None,
save_msg_string: bool = False) -> None:
"""
Args:
from_addr: name of the sender for the "From:" field
date: e-mail date in RFC 2822 format, or ``None`` for "now"
sender: name of the sender for the "Sender:" field
reply_to: name of the sender for the "Reply-To:" field
to: e-mail address(es) of the recipients for "To:" field, as a
CSV list
cc: e-mail address(es) of the recipients for "Cc:" field, as a
CSV list
bcc: e-mail address(es) of the recipients for "Bcc:" field, as a
CSV list
subject: e-mail subject
body: e-mail body
content_type: MIME type for body content, default ``text/plain``
charset: character set for body; default ``utf8``
charset:
attachment_filenames: filenames of attachments to add
attachments_binary: binary attachments to add, as a list of
``filename, bytes`` tuples
save_msg_string: save the encoded message string? (May take
significant space in the database).
"""
# ---------------------------------------------------------------------
# Timestamp
# ---------------------------------------------------------------------
now_local = get_now_localtz_pendulum()
self.created_at_utc = convert_datetime_to_utc(now_local)
# -------------------------------------------------------------------------
# Arguments
# -------------------------------------------------------------------------
if not date:
date = email.utils.format_datetime(now_local)
attachment_filenames = attachment_filenames or [] # type: List[str]
attachments_binary = attachments_binary or [
] # type: List[Tuple[str, bytes]] # noqa
attachment_binary_filenames, attachment_binaries = zip(
*attachments_binary) # noqa
# ... https://stackoverflow.com/questions/13635032/what-is-the-inverse-function-of-zip-in-python # noqa
# Other checks performed by our e-mail function below
# ---------------------------------------------------------------------
# Transient fields
# ---------------------------------------------------------------------
self.password = None
self.msg = make_email(
from_addr=from_addr,
date=date,
sender=sender,
reply_to=reply_to,
to=to,
cc=cc,
bcc=bcc,
subject=subject,
body=body,
content_type=content_type,
attachment_filenames=attachment_filenames,
attachment_binaries=attachment_binaries,
attachment_binary_filenames=attachment_binary_filenames,
)
# ---------------------------------------------------------------------
# Database fields
# ---------------------------------------------------------------------
self.date = date
self.from_addr = from_addr
self.sender = sender
self.reply_to = reply_to
self.to = to
self.cc = cc
self.bcc = bcc
self.subject = subject
self.body = body
self.content_type = content_type
self.charset = charset
if save_msg_string:
self.msg_string = self.msg.as_string()
def get_export_filename(
req: "CamcopsRequest",
patient_spec_if_anonymous: str,
patient_spec: str,
filename_spec: str,
filetype: str,
is_anonymous: bool = False,
surname: str = None,
forename: str = None,
dob: Date = None,
sex: str = None,
idnum_objects: List["PatientIdNum"] = None,
creation_datetime: Pendulum = None,
basetable: str = None,
serverpk: int = None,
skip_conversion_to_safe_filename: bool = False,
) -> str:
"""
Get filename, for file exports/transfers.
Also used for e-mail headers and bodies.
Args:
req: :class:`camcops_server.cc_modules.cc_request.CamcopsRequest`
patient_spec_if_anonymous:
patient specification to be used for anonymous tasks
patient_spec:
patient specification to be used for patient-identifiable tasks
filename_spec:
specification to use to create the filename (may include
patient information from the patient specification)
filetype:
task output format and therefore file type (e.g. HTML, PDF, XML)
is_anonymous: is it an anonymous task?
surname: patient's surname
forename: patient's forename
dob: patient's date of birth
sex: patient's sex
idnum_objects: list of :class:`PatientIdNum` objects for the patient
creation_datetime: date/time the task was created
basetable: name of the task's base table
serverpk: server PK of the task
skip_conversion_to_safe_filename: don't bother converting the result
to a safe filename (because it'll be used for something else, like
an e-mail subject)
Returns:
the generated filename
"""
idnum_objects = idnum_objects or [] # type: List['PatientIdNum']
pse = PatientSpecElementForFilename
fse = FilenameSpecElement
d = {
pse.SURNAME:
surname or "",
pse.FORENAME:
forename or "",
pse.DOB: (format_datetime(dob, DateFormat.FILENAME_DATE_ONLY, "")
if dob else ""),
pse.SEX:
sex or "",
}
all_id_components = []
for idobj in idnum_objects:
if idobj.which_idnum is not None:
nstr = str(idobj.which_idnum)
has_num = idobj.idnum_value is not None
d[pse.IDNUM_PREFIX +
nstr] = (str(idobj.idnum_value) if has_num else "")
d[pse.IDSHORTDESC_PREFIX + nstr] = (idobj.short_description(req)
or "")
if has_num and idobj.short_description(req):
all_id_components.append(idobj.get_filename_component(req))
d[pse.ALLIDNUMS] = "_".join(all_id_components)
if is_anonymous:
patient = patient_spec_if_anonymous
else:
try:
patient = str(patient_spec).format(**d)
except STR_FORMAT_EXCEPTIONS:
log.warning("Bad patient_spec: {!r}; dictionary was {!r}",
patient_spec, d)
patient = "invalid_patient_spec"
d.update({
fse.PATIENT:
patient,
fse.CREATED:
format_datetime(creation_datetime, DateFormat.FILENAME, ""),
fse.NOW:
format_datetime(get_now_localtz_pendulum(), DateFormat.FILENAME),
fse.TASKTYPE:
str(basetable or ""),
fse.SERVERPK:
str(serverpk or ""),
fse.FILETYPE:
filetype.lower(),
fse.ANONYMOUS:
patient_spec_if_anonymous if is_anonymous else "",
})
try:
formatted = str(filename_spec).format(**d)
except STR_FORMAT_EXCEPTIONS:
log.warning("Bad filename_spec: {!r}", filename_spec)
formatted = "invalid_filename_spec"
if skip_conversion_to_safe_filename:
return formatted
return convert_string_for_filename(formatted, allow_paths=True)