Module Gnumed.business.gmExportArea
GNUmed export area
Think shopping cart in a web shop.
This is where you want to put documents for further processing by you or someone else, like your secretary.
Expand source code
"""GNUmed export area
Think shopping cart in a web shop.
This is where you want to put documents for further
processing by you or someone else, like your secretary.
"""
#============================================================
__license__ = "GPL v2 or later"
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
import sys
import logging
import shutil
import os
import platform
import hashlib
if __name__ == '__main__':
sys.path.insert(0, '../../')
_ = lambda x:x
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmBusinessDBObject
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmMimeLib
from Gnumed.pycommon import gmDateTime
from Gnumed.pycommon import gmCfgINI
from Gnumed.pycommon import gmCrypto
from Gnumed.business import gmDocuments
from Gnumed.business import gmKeywordExpansion
from Gnumed.business import gmStaff
_log = logging.getLogger('gm.exp_area')
_cfg = gmCfgINI.gmCfgData()
PRINT_JOB_DESIGNATION = 'print'
DOCUMENTS_SUBDIR = 'documents'
DIRENTRY_README_NAME = '.README.GNUmed-DIRENTRY'
#============================================================
# export area item handling
#------------------------------------------------------------
_SQL_get_export_items = "SELECT * FROM clin.v_export_items WHERE %s"
class cExportItem(gmBusinessDBObject.cBusinessDBObject):
"""Represents an item in the export area table"""
_cmd_fetch_payload = _SQL_get_export_items % "pk_export_item = %s"
_cmds_store_payload = [
"""UPDATE clin.export_item SET
fk_identity = %(pk_identity)s,
created_by = gm.nullify_empty_string(%(created_by)s),
created_when = %(created_when)s,
designation = gm.nullify_empty_string(%(designation)s),
description = gm.nullify_empty_string(%(description)s),
fk_doc_obj = %(pk_doc_obj)s,
data = CASE
WHEN %(pk_doc_obj)s IS NULL THEN coalesce(data, 'to be replaced by real data')
ELSE NULL
END,
filename = CASE
WHEN %(pk_doc_obj)s IS NULL THEN gm.nullify_empty_string(%(filename)s)
ELSE NULL
END
WHERE
pk = %(pk_export_item)s
AND
xmin = %(xmin_export_item)s
""",
"SELECT clin.export_item_set_list_position(%(pk_export_item)s, %(list_position)s)",
_SQL_get_export_items % 'pk_export_item = %(pk_export_item)s'
]
_updatable_fields = [
'pk_identity',
'created_when',
'designation',
'description',
'pk_doc_obj',
'filename',
'list_position'
]
#--------------------------------------------------------
def __init__(self, aPK_obj=None, row=None, link_obj=None):
super(cExportItem, self).__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)
# force auto-healing if need be
if self._payload[self._idx['pk_identity_raw_needs_update']]:
_log.warning (
'auto-healing export item [%s] from identity [%s] to [%s] because of document part [%s] seems necessary',
self._payload[self._idx['pk_export_item']],
self._payload[self._idx['pk_identity_raw']],
self._payload[self._idx['pk_identity']],
self._payload[self._idx['pk_doc_obj']]
)
if self._payload[self._idx['pk_doc_obj']] is None:
_log.error('however, .fk_doc_obj is NULL, which should not happen, leaving things alone for manual inspection')
return
# only flag ourselves as modified, do not actually
# modify any values, better safe than sorry
self._is_modified = True
self.save()
self.refetch_payload(ignore_changes = False, link_obj = link_obj)
#--------------------------------------------------------
# def format(self):
# return u'%s' % self
#--------------------------------------------------------
def update_data(self, data=None):
assert (data is not None), '<data> must not be <None>'
if self.is_DIRENTRY or self.is_document_part:
return False
SQL = """
UPDATE clin.export_item SET
data = %(data)s::bytea,
fk_doc_obj = NULL
WHERE pk = %(pk)s"""
args = {'pk': self.pk_obj, 'data': data}
gmPG2.run_rw_queries(queries = [{'cmd': SQL, 'args': args}], return_data = False, get_col_idx = False)
# must update XMIN now ...
self.refetch_payload()
return True
#--------------------------------------------------------
def update_data_from_file(self, filename=None, convert_document_part=False):
if self.is_DIRENTRY:
return False
if self.is_document_part:
if not convert_document_part:
return False
# sanity check
if not (os.access(filename, os.R_OK) and os.path.isfile(filename)):
_log.error('[%s] is not a readable file' % filename)
return False
cmd = """
UPDATE clin.export_item SET
data = %(data)s::bytea,
fk_doc_obj = NULL,
filename = gm.nullify_empty_string(%(fname)s)
WHERE pk = %(pk)s"""
args = {'pk': self.pk_obj, 'fname': filename}
if not gmPG2.file2bytea(query = cmd, filename = filename, args = args):
return False
# must update XMIN now ...
self.refetch_payload()
return True
#--------------------------------------------------------
def save_to_file(self, aChunkSize:int=0, filename:str=None, directory:str=None, passphrase:str=None, convert2pdf:bool=False) -> str:
"""Save this entry to disk.
Args:
filename: The filename to save into, unless this is a DIRENTRY.
directory: The directory to save the DIRENTRY _content into, if this is a DIRENTRY.
passphrase: Encrypt file(s) with this passphrase, if not _None_.
convert2pdf: Convert file(s) to PDF on the way out. Before encryption, that is.
Returns:
Directory for DIRENTRIES, or filename, or None on failure.
"""
if self.is_DIRENTRY and convert2pdf:
# cannot convert dir entries to PDF
return None
# data linked from archive ?
part_fname = self.__save_doc_obj (
filename = filename,
directory = directory,
passphrase = passphrase,
convert2pdf = convert2pdf
)
if part_fname is False:
return None
if part_fname is not None:
return part_fname
# valid DIRENTRY ?
if self.is_valid_DIRENTRY:
target_dir = self.__save_direntry (
directory,
passphrase = passphrase
)
if target_dir is False:
return None
if target_dir is not None:
return target_dir
# but still a DIRENTRY ?
if self.is_DIRENTRY:
# yes, but apparently not valid (anymore), say,
# other machine or dir not found locally
return None
# normal item with data in export area table
return self.__save_normal_item (
filename = filename,
directory = directory,
passphrase = passphrase,
convert2pdf = convert2pdf
)
#--------------------------------------------------------
def display_via_mime(self, chunksize=0, block=None):
# document part
if self._payload[self._idx['pk_doc_obj']] is not None:
return self.document_part.display_via_mime(chunksize = chunksize, block = block)
# DIR entry
if self._payload[self._idx['filename']].startswith('DIR::'):
# FIXME: error handling with malformed entries
tag, node, path = self._payload[self._idx['filename']].split('::', 2)
if node != platform.node():
msg = _(
'This item points to a directory on the computer named:\n'
' %s\n'
'You are, however, currently using another computer:\n'
' %s\n'
'Directory items can only be viewed/saved/exported\n'
'on the computer they are pointing to.'
) % (node, platform.node())
return False, msg
success, msg = gmMimeLib.call_viewer_on_file(path, block = block)
return success, msg
# data -> save
fname = self.save_to_file(aChunkSize = chunksize)
if fname is None:
return False, ''
success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
if not success:
return False, msg
return True, ''
#--------------------------------------------------------
def get_useful_filename(self, patient=None, directory=None):
patient_part = ''
if patient is not None:
patient_part = '-%s' % patient.subdir_name
# preserve original filename extension if available
suffix = '.dat'
if self._payload[self._idx['filename']] is not None:
tmp, suffix = os.path.splitext (
gmTools.fname_sanitize(self._payload[self._idx['filename']]).casefold()
)
if suffix == '':
suffix = '.dat'
fname = gmTools.get_unique_filename (
prefix = '%s-gm-export_item%s-' % (self._payload[self._idx['list_position']], patient_part),
suffix = suffix,
tmp_dir = directory
)
return fname
#--------------------------------------------------------
# helpers
#--------------------------------------------------------
def __save_normal_item(self, filename:str=None, directory:str=None, passphrase:str=None, convert2pdf:bool=False) -> str:
_SQL = 'SELECT substring(data FROM %(start)s FOR %(size)s) FROM clin.export_item WHERE pk = %(pk)s'
tmp_fname = gmTools.get_unique_filename()
success = gmPG2.bytea2file (
data_query = {'cmd': _SQL, 'args': {'pk': self.pk_obj}},
filename = tmp_fname,
data_size = self._payload[self._idx['size']]
)
if not success:
return None
tmp_fname = gmMimeLib.adjust_extension_by_mimetype(tmp_fname)
if convert2pdf:
tmp_fname = gmMimeLib.convert_file(filename = tmp_fname, target_mime = 'application/pdf', target_extension = '.pdf')
if filename is None:
target_fname = self.get_useful_filename(directory = directory)
else:
target_fname = filename
if passphrase is None:
if not gmTools.rename_file(tmp_fname, target_fname, overwrite = True, allow_symlink = True):
return None
if filename is None:
return gmMimeLib.adjust_extension_by_mimetype(target_fname)
return target_fname
enc_fname = gmCrypto.encrypt_file (
filename = tmp_fname,
passphrase = passphrase,
verbose = _cfg.get(option = 'debug'),
remove_unencrypted = True,
convert2pdf = False # already done, if desired
)
removed = gmTools.remove_file(tmp_fname)
if enc_fname is None:
_log.error('cannot encrypt or, possibly, convert')
return None
if not removed:
_log.error('cannot remove unencrypted file')
gmTools.remove_file(enc_fname)
return None
return enc_fname
#--------------------------------------------------------
def __save_doc_obj(self, filename=None, directory=None, passphrase=None, convert2pdf:bool=False):
"""Save doc object part into target.
None: not a doc obj
True: success
False: failure (to save/convert/encrypt/remove unencrypted)
"""
if self._payload[self._idx['pk_doc_obj']] is None:
return None
part = self.document_part
if filename is None:
filename = part.get_useful_filename (
make_unique = False,
directory = directory,
include_gnumed_tag = False,
date_before_type = True,
name_first = False
)
path, name = os.path.split(filename)
filename = os.path.join(path, '%s-%s' % (self._payload[self._idx['list_position']], name))
if convert2pdf:
target_mime = 'application/pdf'
target_ext = '.pdf'
else:
target_mime = None
target_ext = None
part_fname = part.save_to_file (
filename = filename,
target_mime = target_mime,
target_extension = target_ext,
ignore_conversion_problems = False
)
if part_fname is None:
_log.error('cannot save document part to file')
return False
if passphrase is None:
return part_fname
enc_filename = gmCrypto.encrypt_file (
filename = part_fname,
passphrase = passphrase,
verbose = _cfg.get(option = 'debug'),
remove_unencrypted = True
)
removed = gmTools.remove_file(part_fname)
if enc_filename is None:
_log.error('cannot encrypt')
return False
if removed:
return enc_filename
_log.error('cannot remove unencrypted file')
gmTools.remove_file(enc_filename)
return False
#--------------------------------------------------------
def __save_direntry(self, directory=None, passphrase=None):
"""Move DIRENTRY source into target.
None: not a DIRENTRY
True: success
False: failure
"""
# do not process malformed entries
try:
tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2)
except ValueError:
_log.exception('malformed DIRENTRY: [%s]', self._payload[self._idx['filename']])
return False
# source and target paths must not overlap
if directory is None:
directory = gmTools.mk_sandbox_dir(prefix = 'exp-')
if directory.startswith(local_fs_path):
_log.error('cannot dump DIRENTRY item [%s]: must not be subdirectory of target dir [%s]', self._payload[self._idx['filename']], directory)
return False
if local_fs_path.startswith(directory):
_log.error('cannot dump DIRENTRY item [%s]: target dir [%s] must not be subdirectory of DIRENTRY', self._payload[self._idx['filename']], directory)
return False
_log.debug('dumping DIRENTRY item [%s] into [%s]', self._payload[self._idx['filename']], directory)
sandbox_dir = gmTools.mk_sandbox_dir()
_log.debug('sandbox: %s', sandbox_dir)
tmp = gmTools.copy_tree_content(local_fs_path, sandbox_dir)
if tmp is None:
_log.error('cannot dump DIRENTRY item [%s] into [%s]: copy error', self._payload[self._idx['filename']], sandbox_dir)
return False
gmTools.remove_file(os.path.join(tmp, DIRENTRY_README_NAME))
if passphrase is not None:
_log.debug('encrypting sandbox: %s', sandbox_dir)
encrypted = gmCrypto.encrypt_directory_content (
directory = sandbox_dir,
passphrase = passphrase,
verbose = _cfg.get(option = 'debug'),
remove_unencrypted = True
)
if not encrypted:
_log.error('cannot dump DIRENTRY item [%s]: encryption problem in [%s]', self._payload[self._idx['filename']], sandbox_dir)
return False
tmp = gmTools.copy_tree_content(sandbox_dir, directory)
if tmp is None:
_log.debug('cannot dump DIRENTRY item [%s] into [%s]: copy error', self._payload[self._idx['filename']], directory)
return False
return directory
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def _get_is_doc_part(self):
return self._payload[self._idx['pk_doc_obj']] is not None
is_document_part = property(_get_is_doc_part)
#--------------------------------------------------------
def _get_doc_part(self):
if self._payload[self._idx['pk_doc_obj']] is None:
return None
return gmDocuments.cDocumentPart(aPK_obj = self._payload[self._idx['pk_doc_obj']])
document_part = property(_get_doc_part)
#--------------------------------------------------------
def _get_is_print_job(self):
return self._payload[self._idx['designation']] == PRINT_JOB_DESIGNATION
def _set_is_print_job(self, is_print_job):
desig = gmTools.bool2subst(is_print_job, PRINT_JOB_DESIGNATION, None, None)
if self._payload[self._idx['designation']] == desig:
return
self['designation'] = desig
self.save()
is_print_job = property(_get_is_print_job, _set_is_print_job)
#--------------------------------------------------------
def _is_DIRENTRY(self):
"""Check whether this item looks like a DIRENTRY."""
if self._payload[self._idx['filename']] is None:
return False
if not self._payload[self._idx['filename']].startswith('DIR::'):
return False
if len(self._payload[self._idx['filename']].split('::', 2)) != 3:
return False
return True
is_DIRENTRY = property(_is_DIRENTRY)
#--------------------------------------------------------
def _is_valid_DIRENTRY(self):
"""Check whether this item is a _valid_ DIRENTRY."""
if not self.is_DIRENTRY:
return False
# malformed ?
try:
tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2)
except ValueError:
# should not happen because structure already checked in .is_DIRENTRY,
# better safe than sorry
_log.exception('DIRENTRY [%s]: malformed', self._payload[self._idx['filename']])
return False
# this machine ?
if node != platform.node():
_log.warning('DIRENTRY [%s]: not on this machine (%s)', self._payload[self._idx['filename']], platform.node())
return False
# valid path ?
if not os.path.isdir(local_fs_path):
_log.warning('DIRENTRY [%s]: directory not found (old DIRENTRY ?)', self._payload[self._idx['filename']])
return False
return True
is_valid_DIRENTRY = property(_is_valid_DIRENTRY)
#--------------------------------------------------------
def _is_DICOM_directory(self):
"""Check whether this item points to a DICOMDIR."""
if not self.is_valid_DIRENTRY:
return False
tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2)
found_DICOMDIR = False
for fs_entry in os.listdir(local_fs_path):
# found a subdir
if os.path.isdir(os.path.join(local_fs_path, fs_entry)):
# allow for any number of subdirs
continue
# found a file
if fs_entry != 'DICOMDIR':
# not named "DICOMDIR" -> not a DICOMDIR DIRENTRY
return False
# must be named DICOMDIR -> that's the only file allowed (and required) in ./
found_DICOMDIR = True
return found_DICOMDIR
is_DICOM_directory = property(_is_DICOM_directory)
#--------------------------------------------------------
def _has_files_in_root(self):
"""True if there are files in the root directory."""
tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2)
for fs_entry in os.listdir(local_fs_path):
if os.path.isfile(fs_entry):
_log.debug('has files in top level: %s', local_fs_path)
return True
return False
has_files_in_root = property(_has_files_in_root)
#------------------------------------------------------------
def get_export_items(order_by=None, pk_identity=None, designation=None, return_pks=False):
args = {
'pat': pk_identity,
'desig': gmTools.coalesce(designation, PRINT_JOB_DESIGNATION)
}
where_parts = []
if pk_identity is not None:
where_parts.append('pk_identity = %(pat)s')
# note that invalidly linked items will be
# auto-healed when instantiated
if designation is None:
where_parts.append("designation IS DISTINCT FROM %(desig)s")
else:
where_parts.append('designation = %(desig)s')
if order_by is None:
order_by = 'pk_identity, list_position'
order_by = ' ORDER BY %s' % order_by
cmd = (_SQL_get_export_items % ' AND '.join(where_parts)) + order_by
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
if return_pks:
return [ r['pk_export_item'] for r in rows ]
return [ cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) for r in rows ]
#------------------------------------------------------------
def get_print_jobs(order_by=None, pk_identity=None):
return get_export_items(order_by = order_by, pk_identity = pk_identity, designation = PRINT_JOB_DESIGNATION)
#------------------------------------------------------------
def create_export_item(description=None, pk_identity=None, pk_doc_obj=None, filename=None):
args = {
'desc': description,
'pk_obj': pk_doc_obj,
'pk_pat': pk_identity,
'fname': filename
}
cmd = """
INSERT INTO clin.export_item (
description,
fk_doc_obj,
fk_identity,
data,
filename
) VALUES (
gm.nullify_empty_string(%(desc)s),
%(pk_obj)s,
%(pk_pat)s,
(CASE
WHEN %(pk_obj)s IS NULL THEN %(fname)s::bytea
ELSE NULL::bytea
END),
(CASE
WHEN %(pk_obj)s IS NULL THEN gm.nullify_empty_string(%(fname)s)
ELSE NULL
END)
)
RETURNING pk
"""
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
return cExportItem(aPK_obj = rows[0]['pk'])
#------------------------------------------------------------
def delete_export_item(pk_export_item=None):
args = {'pk': pk_export_item}
cmd = "DELETE FROM clin.export_item WHERE pk = %(pk)s"
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#============================================================
#============================================================
_FRONTPAGE_HTML_CONTENT = """<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"https://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<link rel="icon" type="image/x-icon" href="gnumed.ico">
<title>%(html_title_header)s %(html_title_patient)s</title>
</head>
<body>
<h1>%(title)s</h1>
<p>
(%(date)s)<br>
</p>
<h2><a href="patient.vcf">Patient</a></h2>
<p>
%(pat_name)s<br>
%(pat_dob)s
</p>
<p><img src="%(mugshot_url)s" alt="%(mugshot_alt)s" title="%(mugshot_title)s" width="200" border="2"></p>
<h2>%(docs_title)s</h2>
<ul>
<li><a href="./">%(browse_root)s</a></li>
<li><a href="%(doc_subdir)s/">%(browse_docs)s</a></li>
%(browse_dicomdir)s
%(run_dicom_viewer)s
</ul>
<ul>
%(docs_list)s
</ul>
<h2><a href="praxis.vcf">Praxis</a></h2>
<p>
%(branch)s @ %(praxis)s
%(adr)s
</p>
<p>(<a href="https://www.gnumed.de">GNUmed</a> version %(gm_ver)s)</p>
</body>
</html>
"""
_INDEX_HTML_CONTENT = """<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"https://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<link rel="icon" type="image/x-icon" href="gnumed.ico">
<title>%(html_title_header)s</title>
</head>
<body>
<h1>%(title)s</h1>
<p>
(%(date)s)<br>
</p>
This is an encrypted patient data excerpt created by the GNUmed Electronic Medical Record.
<p>
For decryption you will need to
<ul>
<li>install decryption software and</li>
<li>obtain relevant passwords from the creator or holder of this media</li>
</ul>
<h2>Decryption software</h2>
For files ending in
<ul>
<li>.asc: install <a href="https://gnupg.org">GNU Privacy Guard</a></li>
<li>.7z: install <a href="https://www.7-zip.org">7-zip</a> or <a href="https://www.winzip.com">WinZip</a></li>
</ul>
<h2>%(docs_title)s</h2>
<ul>
<li><a href="./frontpage.html">front page (after decryption)</a></li>
<li><a href="./%(frontpage_fname)s">front page (if decryption from browser is supported)</a></li>
<li><a href="./">%(browse_root)s</a></li>
<li><a href="%(doc_subdir)s/">%(browse_docs)s</a></li>
</ul>
<h2><a href="praxis.vcf">Praxis</a></h2>
<p>
%(branch)s @ %(praxis)s
%(adr)s
</p>
<p>(<a href="https://www.gnumed.de">GNUmed</a> version %(gm_ver)s)</p>
</body>
</html>
"""
#------------------------------------------------------------
class cExportArea(object):
def __init__(self, pk_identity):
self.__pk_identity = pk_identity
#--------------------------------------------------------
def add_form(self, form=None, designation=None):
if len(form.final_output_filenames) == 0:
return True
items = []
for fname in form.final_output_filenames:
item = self.add_file(filename = fname)
if item is None:
for prev_item in items:
delete_export_item(pk_export_item = prev_item['pk_export_item'])
return False
items.append(item)
item['description'] = _('form: %s %s (%s)') % (form.template['name_long'], form.template['external_version'], fname)
item['designation'] = designation
item.save()
return True
#--------------------------------------------------------
def add_forms(self, forms=None, designation=None):
all_ok = True
for form in forms:
all_ok = all_ok and self.add_form(form = form, designation = designation)
return all_ok
#--------------------------------------------------------
def add_path(self, path, comment=None):
"""Add a DIR entry to the export area.
This sort of entry points to a certain directory on a
certain machine. The content of the the directory
will be included in exports, the directory *itself*
will not. For *that*, use a disposable top-level
directory into which you put the directory to include
as a subdirectory.
"""
assert (os.path.isdir(path)), '<path> must exist: %s' % path
path_item_data = 'DIR::%s::%s/' % (platform.node(), path.rstrip('/'))
_log.debug('attempting to add path item [%s]', path_item_data)
item = self.path_item_exists(path_item_data)
if item is not None:
_log.debug('[%s] already in export area', path)
return item
if comment is None:
comment = _('path [%s/] on computer "%s"') % (
path.rstrip('/'),
platform.node()
)
else:
comment += _(' (on "%s")') % platform.node()
item = create_export_item (
description = comment,
pk_identity = self.__pk_identity,
filename = path_item_data
)
try:
README = open(os.path.join(path, DIRENTRY_README_NAME), mode = 'wt', encoding = 'utf8')
README.write('GNUmed DIRENTRY information\n')
README.write('created: %s\n' % gmDateTime.pydt_now_here())
README.write('machine: %s\n' % platform.node())
README.write('path: %s\n' % path)
README.close()
except OSError:
_log.exception('READONLY DIRENTRY [%s]', path)
return item
#--------------------------------------------------------
def path_item_exists(self, path_item_data):
assert (path_item_data.startswith('DIR::')), 'invalid <path_item_data> [%s]' % path_item_data
where_parts = [
'pk_identity = %(pat)s',
'filename = %(fname)s',
'pk_doc_obj IS NULL'
]
args = {
'pat': self.__pk_identity,
'fname': path_item_data
}
SQL = _SQL_get_export_items % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}], get_col_idx = True)
if len(rows) == 0:
return None
r = rows[0]
return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'})
#--------------------------------------------------------
def add_file(self, filename=None, hint=None):
try:
open(filename).close()
except Exception:
_log.exception('cannot open file <%s>', filename)
return None
file_md5 = gmTools.file2md5(filename = filename, return_hex = True)
existing_item = self.md5_exists(md5 = file_md5, include_document_parts = False)
if existing_item is not None:
_log.debug('md5 match (%s): %s already in export area', file_md5, filename)
return existing_item
path, basename = os.path.split(filename)
item = create_export_item (
description = '%s: %s (%s/)' % (
gmTools.coalesce(hint, _('file'), '%s'),
basename,
path
),
pk_identity = self.__pk_identity,
filename = filename
)
if item.update_data_from_file(filename = filename):
return item
# failed to insert data, hence remove export item entry
delete_export_item(pk_export_item = item['pk_export_item'])
return None
#--------------------------------------------------------
def add_files(self, filenames=None, hint=None):
all_ok = True
for fname in filenames:
all_ok = all_ok and (self.add_file(filename = fname, hint = hint) is not None)
return all_ok
#--------------------------------------------------------
def add_documents(self, documents=None):
for doc in documents:
doc_tag = _('%s (%s)%s') % (
doc['l10n_type'],
gmDateTime.pydt_strftime(doc['clin_when'], '%Y %b %d'),
gmTools.coalesce(doc['comment'], '', ' "%s"')
)
for obj in doc.parts:
if self.document_part_item_exists(pk_part = obj['pk_obj']):
continue
f_ext = ''
if obj['filename'] is not None:
f_ext = os.path.splitext(obj['filename'])[1].strip('.').strip()
if f_ext != '':
f_ext = ' .' + f_ext.upper()
obj_tag = _('part %s (%s%s)%s') % (
obj['seq_idx'],
gmTools.size2str(obj['size']),
f_ext,
gmTools.coalesce(obj['obj_comment'], '', ' "%s"')
)
create_export_item (
description = '%s - %s' % (doc_tag, obj_tag),
pk_doc_obj = obj['pk_obj']
)
#--------------------------------------------------------
def document_part_item_exists(self, pk_part=None):
cmd = "SELECT EXISTS (SELECT 1 FROM clin.export_item WHERE fk_doc_obj = %(pk_obj)s)"
args = {'pk_obj': pk_part}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
return rows[0][0]
#--------------------------------------------------------
def md5_exists(self, md5=None, include_document_parts=False):
where_parts = [
'pk_identity = %(pat)s',
'md5_sum = %(md5)s'
]
args = {
'pat': self.__pk_identity,
'md5': md5
}
if not include_document_parts:
where_parts.append('pk_doc_obj IS NULL')
cmd = _SQL_get_export_items % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
if len(rows) == 0:
return None
r = rows[0]
return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'})
#--------------------------------------------------------
def remove_item(self, item):
if item.is_valid_DIRENTRY:
tag, node, local_fs_path = item['filename'].split('::', 2)
gmTools.remove_file(os.path.join(local_fs_path, DIRENTRY_README_NAME))
elif item.is_DIRENTRY:
return False
return delete_export_item(pk_export_item = item['pk_export_item'])
#--------------------------------------------------------
def dump_items_to_disk(self, base_dir:str=None, items:list=None, passphrase:str=None, convert2pdf:bool=False) -> str:
"""Dump export area items to disk.
Args:
base_dir: directory into which to dump the items, defaults to a new sandbox directory
items: which items to dump, defaults to all items
passphrase: used to symmetrically encrypt dumped files, if set
convert2pdf: attempt to convert items into PDF before dumping them
Returns:
The base_dir into which items were dumped, or None.
"""
if items is None:
items = self.items
if len(items) == 0:
return None
if base_dir is None:
base_dir = gmTools.mk_sandbox_dir()
else:
gmTools.mkdir(base_dir)
_log.debug('dumping export items to: %s', base_dir)
for item in items:
saved_fname = item.save_to_file(directory = base_dir, passphrase = passphrase, convert2pdf = convert2pdf)
if saved_fname is None:
return None
if passphrase:
store_passphrase_of_file(filename = saved_fname, passphrase = passphrase, hash_type = 'sha256')
return base_dir
#--------------------------------------------------------
def dump_items_to_disk_as_zip(self, base_dir:str=None, items:list=None, passphrase:str=None) -> str:
"""Dump items to disk into a zip archive.
Calls dump_items_to_disk().
Args:
base_dir: directory into which to dump the items, defaults to a new sandbox directory
items: which items to dump, defaults to all items
passphrase: used to symmetrically encrypt dumped files, if set
Returns:
Zip archive name, or None.
"""
_log.debug('target dir: %s', base_dir)
dump_dir = self.dump_items_to_disk(base_dir = base_dir, items = items)
if dump_dir is None:
_log.error('cannot dump export area items')
return None
if passphrase:
zip_file = gmCrypto.create_encrypted_zip_archive_from_dir (
source_dir = dump_dir,
comment = _('GNUmed Patient Media'),
overwrite = True,
passphrase = passphrase,
verbose = _cfg.get(option = 'debug')
)
if zip_file:
store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256')
else:
_log.error('cannot zip+encrypt export area items dump')
return zip_file
zip_file = gmCrypto.create_zip_archive_from_dir (
dump_dir,
comment = _('GNUmed Patient Media'),
overwrite = True,
verbose = _cfg.get(option = 'debug')
)
if not zip_file:
_log.error('cannot zip export area items dump')
return zip_file
#--------------------------------------------------------
def export(self, base_dir=None, items=None, passphrase=None):
"""Export items as structured patient media.
Args:
base_dir: directory into which to store the export, defaults to a new sandbox directory based on patient name
items: which items to dump, defaults to all items
passphrase: used to symmetrically encrypt dumped files, if set
Returns:
Base_dir name, else None or False on failure.
"""
if items is None:
items = self.items
if len(items) == 0:
return None
from Gnumed.business.gmPerson import cPatient
pat = cPatient(aPK_obj = self.__pk_identity)
target_base_dir = base_dir
if target_base_dir is None:
target_base_dir = gmTools.mk_sandbox_dir(prefix = '%s-' % pat.subdir_name)
gmTools.mkdir(target_base_dir)
_log.debug('patient media base dir: %s', target_base_dir)
if not gmTools.dir_is_empty(target_base_dir):
_log.error('patient media base dir is not empty')
return False
from Gnumed.business.gmPraxis import gmCurrentPraxisBranch
prax = gmCurrentPraxisBranch()
html_data = {}
# 1) assemble everything in a sandbox
# - setup sandbox
sandbox_dir = gmTools.mk_sandbox_dir()
_log.debug('sandbox dir: %s', sandbox_dir)
doc_dir = os.path.join(sandbox_dir, DOCUMENTS_SUBDIR)
gmTools.mkdir(doc_dir)
# - export mugshot
mugshot = pat.document_folder.latest_mugshot
if mugshot is not None:
mugshot_fname = mugshot.save_to_file(directory = doc_dir)
fname = os.path.split(mugshot_fname)[1]
html_data['mugshot_url'] = os.path.join(DOCUMENTS_SUBDIR, fname)
html_data['mugshot_alt'] =_('patient photograph from %s') % gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y')
html_data['mugshot_title'] = gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y')
# - export patient demographics as GDT/XML/VCF/MCF
pat.export_as_gdt(filename = os.path.join(sandbox_dir, 'patient.gdt'))
pat.export_as_xml_linuxmednews(filename = os.path.join(sandbox_dir, 'patient.xml'))
pat.export_as_vcard(filename = os.path.join(sandbox_dir, 'patient.vcf'))
pat.export_as_mecard(filename = os.path.join(sandbox_dir, u'patient.mcf'))
# - create CD.INF
self._create_cd_inf(pat, sandbox_dir)
# - export items
docs_list = []
for item in items:
# if it is a dicomdir - put it into the root of the target media
if item.is_DICOM_directory:
_log.debug('exporting DICOMDIR DIRENTRY')
# save into base dir
item_fname = item.save_to_file(directory = sandbox_dir)
# do not include into ./documents/ listing
continue
if item.is_valid_DIRENTRY:
_log.debug('exporting DIRENTRY')
# if there are files in the root dir: put it into a
# subdir of ./documents/ where subdir is the leaf
# of the item .filename
if item.has_files_in_root:
tag, node, local_fs_path = item['filename'].split('::', 2)
subdir = local_fs_path.rstrip('/').split('/')[-1]
subdir = os.path.join(doc_dir, subdir)
gmTools.mkdir(subdir)
item_fname = item.save_to_file(directory = subdir)
# if it is subdirs only - put it into documents/ directly
else:
item_fname = item.save_to_file(directory = doc_dir)
# include into ./documents/ listing
fname = os.path.split(item_fname)[1]
docs_list.append([fname, gmTools.html_escape_string(item['description'])])
continue
if item.is_DIRENTRY:
# DIRENTRY but not valid: skip
continue
# normal entry, doc obj links or data item
item_fname = item.save_to_file(directory = doc_dir)
fname = os.path.split(item_fname)[1]
# collect items so we can later correlate items and descriptions
# actually we should link to encrypted items, and to unencrypted ones
docs_list.append([fname, gmTools.html_escape_string(item['description'])])
# - link to DICOMDIR if exists
if 'DICOMDIR' in os.listdir(sandbox_dir): # in root path
has_dicomdir = True
html_data['browse_dicomdir'] = '<li><a href="./DICOMDIR">%s</a></li>' % _('show DICOMDIR file')
else:
has_dicomdir = False
# - include DWV link if there is a DICOMDIR
if has_dicomdir:
# do not clone into media base to avoid encryption,
# DWV will be cloned to there later on
dwv_sandbox_dir = self._clone_dwv()
if dwv_sandbox_dir is not None:
html_data['run_dicom_viewer'] = '<li><a href="./dwv/viewers/mobile-local/index.html">%s</a></li>' % _('run Radiology Images (DICOM) Viewer')
# - create frontpage.html
frontpage_fname = self._create_frontpage_html(pat, prax, sandbox_dir, html_data, docs_list)
# - start.html (just a convenience copy of frontpage.html)
# (later overwritten, if encryption is requested)
start_fname = os.path.join(sandbox_dir, 'start.html')
try:
shutil.copy2(frontpage_fname, start_fname)
except Exception:
_log.exception('cannot copy %s to %s', frontpage_fname, start_fname)
# - index.html (just a convenience copy of frontpage.html)
# (later overwritten if encryption is requested)
index_fname = os.path.join(sandbox_dir, 'index.html')
try:
shutil.copy2(frontpage_fname, index_fname)
except Exception:
_log.exception('cannot copy %s to %s', frontpage_fname, index_fname)
# 2) encrypt content of sandbox
if passphrase is not None:
encrypted = gmCrypto.encrypt_directory_content (
directory = sandbox_dir,
receiver_key_ids = None,
passphrase = passphrase,
comment = None,
verbose = _cfg.get(option = 'debug'),
remove_unencrypted = True,
store_passphrase_cb = store_passphrase_of_file_callback
)
if not encrypted:
_log.errror('cannot encrypt data in sandbox dir')
return False
# 3) add never-to-be-encrypted data
# - AUTORUN.INF
# - README
if passphrase:
self._create_autorun_inf(None, sandbox_dir)
self._create_readme(None, sandbox_dir)
else:
self._create_autorun_inf(pat, sandbox_dir)
self._create_readme(pat, sandbox_dir)
# - praxis VCF/MCF
shutil.move(prax.vcf, os.path.join(sandbox_dir, 'praxis.vcf'))
prax.export_as_mecard(filename = os.path.join(sandbox_dir, u'praxis.mcf'))
# - include DWV code
if has_dicomdir:
self._clone_dwv(target_dir = sandbox_dir)
# - index.html as boilerplate for decryption
if passphrase:
index_fname = self._create_index_html(prax, sandbox_dir, html_data)
# 4) move sandbox to target dir
target_dir = gmTools.copy_tree_content(sandbox_dir, target_base_dir)
if target_dir is None:
_log.error('cannot fill target base dir')
return False
return target_dir
#--------------------------------------------------------
def export_as_zip(self, base_dir=None, items=None, passphrase=None):
_log.debug('target dir: %s', base_dir)
export_dir = self.export(base_dir = base_dir, items = items)
if export_dir is None:
_log.debug('cannot export items')
return None
if passphrase:
zip_file = gmCrypto.create_encrypted_zip_archive_from_dir (
export_dir,
comment = _('GNUmed Patient Media'),
overwrite = True,
passphrase = passphrase,
verbose = _cfg.get(option = 'debug')
)
if zip_file:
store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256')
else:
_log.debug('cannot create zip archive')
return zip_file
zip_file = gmCrypto.create_zip_archive_from_dir (
export_dir,
comment = _('GNUmed Patient Media'),
overwrite = True,
verbose = _cfg.get(option = 'debug')
)
if not zip_file:
_log.debug('cannot create zip archive')
return zip_file
#--------------------------------------------------------
def _create_index_html(self, praxis, directory, data):
# header part
_HTML_data = {
'html_title_header': _('Patient data'),
'title': _('Patient data excerpt'),
'docs_title': _('Documents'),
'browse_root': _('browse storage medium'),
'browse_docs': _('browse documents area'),
'doc_subdir': DOCUMENTS_SUBDIR,
'date' : gmTools.html_escape_string(gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y %B %d'))
}
frontpage_fname_enc = 'frontpage.html.asc'
if os.path.isfile(os.path.join(directory, frontpage_fname_enc)):
_HTML_data['frontpage_fname'] = frontpage_fname_enc
frontpage_fname_enc = 'frontpage.html.7z'
if os.path.isfile(os.path.join(directory, frontpage_fname_enc)):
_HTML_data['frontpage_fname'] = frontpage_fname_enc
# footer part
lines = []
adr = praxis.branch.org_unit.address
if adr is not None:
lines.extend(adr.format())
for comm in praxis.branch.org_unit.comm_channels:
if comm['is_confidential'] is True:
continue
lines.append('%s: %s' % (
comm['l10n_comm_type'],
comm['url']
))
adr = ''
if len(lines) > 0:
adr = gmTools.html_escape_string('\n'.join(lines), replace_eol = True, keep_visual_eol = True)
_HTML_data['branch'] = gmTools.html_escape_string(praxis['branch'])
_HTML_data['praxis'] = gmTools.html_escape_string(praxis['praxis'])
_HTML_data['gm_ver'] = gmTools.html_escape_string(gmTools.coalesce(_cfg.get(option = 'client_version'), 'git HEAD'))
_HTML_data['adr'] = adr
# create file
index_fname = os.path.join(directory, 'index.html')
index_file = open(index_fname, mode = 'wt', encoding = 'utf8')
index_file.write(_INDEX_HTML_CONTENT % _HTML_data)
index_file.close()
return index_fname
#--------------------------------------------------------
def _create_frontpage_html(self, patient, praxis, directory, data, docs_list):
# <li><a href="documents/filename-1.ext">document 1 description</a></li>
_HTML_LIST_ITEM = ' <li><a href="%s">%s</a></li>'
# header part
_HTML_data = {
'html_title_header': _('Patient data for'),
'html_title_patient': gmTools.html_escape_string(patient.get_description_gender(with_nickname = False) + ', ' + _('born') + ' ' + patient.get_formatted_dob('%Y %B %d')),
'title': _('Patient data excerpt'),
'pat_name': gmTools.html_escape_string(patient.get_description_gender(with_nickname = False)),
'pat_dob': gmTools.html_escape_string(_('born') + ' ' + patient.get_formatted_dob('%Y %B %d')),
'mugshot_url': 'documents/no-such-file.png',
'mugshot_alt': _('no patient photograph available'),
'mugshot_title': '',
'docs_title': _('Documents'),
'browse_root': _('browse storage medium'),
'browse_docs': _('browse documents area'),
'doc_subdir': DOCUMENTS_SUBDIR,
'browse_dicomdir': '',
'run_dicom_viewer': '',
'date' : gmTools.html_escape_string(gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y %B %d'))
}
for key in data:
_HTML_data[key] = data[key]
# documents part
_HTML_docs_list = []
for doc in docs_list:
subdir = os.path.join(directory, DOCUMENTS_SUBDIR, doc[0])
if os.path.isdir(subdir):
_HTML_docs_list.append(_HTML_LIST_ITEM % (os.path.join(DOCUMENTS_SUBDIR, doc[0]), _('DIRECTORY: %s/%s/') % (DOCUMENTS_SUBDIR, doc[0])))
_HTML_docs_list.append(' <ul>')
for fname in os.listdir(subdir):
tmp = os.path.join(subdir, fname)
if os.path.isdir(tmp):
_HTML_docs_list.append(' <li><a href="%s">%s</a></li>' % (os.path.join(DOCUMENTS_SUBDIR, doc[0], fname), _('DIRECTORY: %s/%s/%s/') % (DOCUMENTS_SUBDIR, doc[0], fname)))
else:
_HTML_docs_list.append(' <li><a href="%s">%s</a></li>' % (os.path.join(DOCUMENTS_SUBDIR, doc[0], fname), fname))
_HTML_docs_list.append(' </ul>')
else:
_HTML_docs_list.append(_HTML_LIST_ITEM % (os.path.join(DOCUMENTS_SUBDIR, doc[0]), doc[1]))
_HTML_data['docs_list'] = u'\n '.join(_HTML_docs_list)
# footer part
lines = []
adr = praxis.branch.org_unit.address
if adr is not None:
lines.extend(adr.format())
for comm in praxis.branch.org_unit.comm_channels:
if comm['is_confidential'] is True:
continue
lines.append('%s: %s' % (
comm['l10n_comm_type'],
comm['url']
))
adr = ''
if len(lines) > 0:
adr = gmTools.html_escape_string('\n'.join(lines), replace_eol = True, keep_visual_eol = True)
_HTML_data['branch'] = gmTools.html_escape_string(praxis['branch'])
_HTML_data['praxis'] = gmTools.html_escape_string(praxis['praxis'])
_HTML_data['gm_ver'] = gmTools.html_escape_string(gmTools.coalesce(_cfg.get(option = 'client_version'), 'git HEAD'))
_HTML_data['adr'] = adr
# create file
frontpage_fname = os.path.join(directory, 'frontpage.html')
frontpage_file = open(frontpage_fname, mode = 'wt', encoding = 'utf8')
frontpage_file.write(_FRONTPAGE_HTML_CONTENT % _HTML_data)
frontpage_file.close()
return frontpage_fname
#--------------------------------------------------------
def _clone_dwv(self, target_dir=None):
_log.debug('cloning dwv')
# find DWV
dwv_src_dir = os.path.join(gmTools.gmPaths().local_base_dir, 'resources', 'dwv4export')
if not os.path.isdir(dwv_src_dir):
_log.debug('[%s] not found', dwv_src_dir)
dwv_src_dir = os.path.join(gmTools.gmPaths().system_app_data_dir, 'resources', 'dwv4export')
if not os.path.isdir(dwv_src_dir):
_log.debug('[%s] not found', dwv_src_dir)
return None
# clone it
if target_dir is None:
target_dir = gmTools.mk_sandbox_dir()
dwv_target_dir = os.path.join(target_dir, 'dwv')
gmTools.rmdir(dwv_target_dir)
try:
shutil.copytree(dwv_src_dir, dwv_target_dir)
except (shutil.Error, OSError):
_log.exception('cannot include DWV, skipping')
return None
return dwv_target_dir
#--------------------------------------------------------
def _create_readme(self, patient, directory):
_README_CONTENT = (
'This is a patient data excerpt created by the GNUmed Electronic Medical Record.\n'
'\n'
'Patient: %s\n'
'\n'
'Please display <frontpage.html> to browse patient data.\n'
'\n'
'Individual documents are stored in the subdirectory\n'
'\n'
' documents/\n'
'\n'
'\n'
'Data may need to be decrypted with either GNU Privacy\n'
'Guard or 7zip/WinZip.\n'
'\n'
'.asc:\n'
' https://gnupg.org\n'
'\n'
'.7z:\n'
' https://www.7-zip.org\n'
' https://www.winzip.com\n'
'\n'
'To obtain any needed keys you will have to get in touch with\n'
'the creator or the owner of this patient media excerpt.\n'
)
readme_fname = os.path.join(directory, 'README')
readme_file = open(readme_fname, mode = 'wt', encoding = 'utf8')
if patient is None:
pat_str = _('<protected>')
else:
pat_str = patient.get_description_gender(with_nickname = False) + ', ' + _('born') + ' ' + patient.get_formatted_dob('%Y %B %d')
readme_file.write(_README_CONTENT % pat_str)
readme_file.close()
return readme_fname
#--------------------------------------------------------
def _create_cd_inf(self, patient, directory):
_CD_INF_CONTENT = (
'[Patient Info]\r\n' # needs \r\n for Windows
'PatientName=%s, %s\r\n'
'Gender=%s\r\n'
'BirthDate=%s\r\n'
'CreationDate=%s\r\n'
'PID=%s\r\n'
'EMR=GNUmed\r\n'
'Version=%s\r\n'
'#StudyDate=\r\n'
'#VNRInfo=<body part>\r\n'
'\r\n'
'# name format: lastnames, firstnames\r\n'
'# date format: YYYY-MM-DD (ISO 8601)\r\n'
'# gender format: %s\r\n'
)
fname = os.path.join(directory, 'CD.INF')
cd_inf = open(fname, mode = 'wt', encoding = 'utf8')
cd_inf.write(_CD_INF_CONTENT % (
patient['lastnames'],
patient['firstnames'],
gmTools.coalesce(patient['gender'], '?'),
patient.get_formatted_dob('%Y-%m-%d'),
gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y-%m-%d'),
patient.ID,
_cfg.get(option = 'client_version'),
' / '.join([ '%s = %s (%s)' % (g['tag'], g['label'], g['l10n_label']) for g in patient.gender_list ])
))
cd_inf.close()
return fname
#--------------------------------------------------------
def _create_autorun_inf(self, patient, directory):
_AUTORUN_INF_CONTENT = ( # needs \r\n for Windows
'[AutoRun.Amd64]\r\n' # 64 bit
'label=%(label)s\r\n' # patient name/DOB
'shellexecute=index.html\r\n'
'action=%(action)s\r\n' # % _('Browse patient data')
'%(icon)s\r\n' # "icon=gnumed.ico" or ""
'UseAutoPlay=1\r\n'
'\r\n'
'[AutoRun]\r\n' # 32 bit
'label=%(label)s\r\n' # patient name/DOB
'shellexecute=index.html\r\n'
'action=%(action)s\r\n' # % _('Browse patient data')
'%(icon)s\r\n' # "icon=gnumed.ico" or ""
'UseAutoPlay=1\r\n'
'\r\n'
'[Content]\r\n'
'PictureFiles=yes\r\n'
'VideoFiles=yes\r\n'
'MusicFiles=no\r\n'
'\r\n'
'[IgnoreContentPaths]\r\n'
'\documents\r\n'
'\r\n'
'[unused]\r\n'
'open=requires explicit executable\r\n'
)
autorun_dict = {
'label': self._compute_autorun_inf_label(patient),
'action': _('Browse patient data'),
'icon': ''
}
media_icon_kwd = '$$gnumed_patient_media_export_icon'
media_icon_kwd_exp = gmKeywordExpansion.get_expansion (
keyword = media_icon_kwd,
textual_only = False,
binary_only = True
)
icon_tmp_fname = media_icon_kwd_exp.save_to_file (
target_mime = 'image/x-icon',
target_extension = '.ico',
ignore_conversion_problems = True
)
if icon_tmp_fname is None:
_log.error('cannot retrieve <%s>', media_icon_kwd)
else:
media_icon_fname = os.path.join(directory, 'gnumed.ico')
try:
shutil.copy2(icon_tmp_fname, media_icon_fname)
autorun_dict['icon'] = 'icon=gnumed.ico'
except Exception:
_log.exception('cannot move %s to %s', icon_tmp_fname, media_icon_fname)
autorun_fname = os.path.join(directory, 'AUTORUN.INF')
autorun_file = open(autorun_fname, mode = 'wt', encoding = 'cp1252', errors = 'replace')
autorun_file.write(_AUTORUN_INF_CONTENT % autorun_dict)
autorun_file.close()
return autorun_fname
#--------------------------------------------------------
def _compute_autorun_inf_label(self, patient):
if patient is None:
# if no patient provided - assume the target media
# is to be encrypted and thusly do not expose patient data,
# AUTORUN.INF itself will not be encrypted because
# Windows must be able to parse it
return _('GNUmed patient data excerpt')[:32]
LABEL_MAX_LEN = 32
dob = patient.get_formatted_dob(format = ' %Y%m%d', none_string = '', honor_estimation = False)
if dob == '':
gender_template = ' (%s)'
else:
gender_template = ' %s'
gender = gmTools.coalesce(patient['gender'], '', gender_template)
name_max_len = LABEL_MAX_LEN - len(gender) - len(dob) # they already include appropriate padding
name = patient.active_name
last = name['lastnames'].strip()
first = name['firstnames'].strip()
len_last = len(last)
len_first = len(first)
while (len_last + len_first + 1) > name_max_len:
if len_first > 6:
len_first -= 1
if first[len_first - 1] == ' ':
len_first -= 1
continue
len_last -= 1
if last[len_last - 1] == ' ':
len_last -= 1
last = last[:len_last].strip().upper()
first = first[:len_first].strip()
# max 32 chars, supposedly ASCII, but CP1252 likely works pretty well
label = (('%s %s%s%s' % (last, first, dob, gender)).strip())[:32]
return label
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def get_items(self, designation=None, order_by='pk_identity, list_position, designation, description'):
return get_export_items(order_by = order_by, pk_identity = self.__pk_identity, designation = designation)
items = property(get_items)
#--------------------------------------------------------
def get_printouts(self, order_by='list_position, designation, description'):
return get_print_jobs(order_by = order_by, pk_identity = self.__pk_identity)
printouts = property(get_printouts)
#===========================================================================
# passphrase escrow
#---------------------------------------------------------------------------
def store_passphrase_of_file_callback(filename:str=None, passphrase:str=None, comment:dict=None):
return store_passphrase_of_file (
filename = filename,
passphrase = passphrase,
hash_type = 'sha256',
comment = comment
)
#---------------------------------------------------------------------------
def store_passphrase_of_file(filename:str=None, passphrase:str=None, hash_type:str='md5', comment:dict=None) -> bool:
"""Call store_object_passphrase on a given file."""
try:
f = open(filename, 'rb')
except Exception:
_log.exception('cannot open [%s]', filename)
return False
if comment is None:
comment = {}
comment['__filename__'] = filename
return store_object_passphrase (
obj = f,
passphrase = passphrase,
hash_type = hash_type,
comment = comment
)
#---------------------------------------------------------------------------
def store_object_passphrase(obj=None, passphrase:str=None, hash_type:str='md5', owner=None, comment:dict=None) -> bool:
"""Store in the database the (encrypted) passphrase for an object.
The passphrase is stored encrypted with the public key of
the owner as well as with any public key configured as a
passphrase trustee.
Args:
obj: an instance supporting the (binary) read protocol
passphrase: the passphrase to store
hash_type: the hash to use, defaults to 'md5'
owner: staff member to encrypt passphrase to (by public key), defaults to current provider
comment: a structured comment on the object
Returns:
True/False based on success
"""
assert obj, '<obj> must not be None'
assert passphrase, '<passphrase> must not be None'
if hash_type not in hashlib.algorithms_available:
_log.error('hash type [%s] not available amongst %s', hash_type, hashlib.algorithms_available)
return False
pubkey_files = []
if owner is None:
owner = gmStaff.gmCurrentProvider()
owner_key_file = owner.public_key_file
if owner_key_file:
pubkey_files.append(owner_key_file)
else:
_log.warning('no public key for owner [%s]', owner)
trustee_key_files = gmStaff.get_public_keys_of_passphrase_trustees(as_files = True)
if trustee_key_files:
pubkey_files.extend(trustee_key_files)
else:
_log.warning('there are no trustee public keys configured for passphrase escrow')
if not pubkey_files:
_log.error('cannot escrow passphrase, neither owner nor trustee public keys available')
return False
hashor = hashlib.new(hash_type, usedforsecurity = False)
chunk_size = 5 * 1024 * 1024
data = obj.read(chunk_size)
while data:
hashor.update(data)
data = obj.read(chunk_size)
hash_val = hashor.hexdigest()
encrypted_phrase = gmCrypto.encrypt_data_with_gpg (
data = passphrase,
recipient_key_files = pubkey_files,
comment = '[%s]::%s' % (hash_type, hash_val),
verbose = _cfg.get(option = 'debug')
)
SQL = """INSERT INTO gm.obj_export_passphrase (
hash_type, hash, phrase, description
) VALUES (
%(hash_type)s,
%(hash)s,
%(phrase)s,
%(desc)s
)"""
args = {
'hash_type': hash_type,
'hash': hash_val,
'phrase': encrypted_phrase,
'desc': comment
}
gmPG2.run_rw_queries(queries = [{'cmd': SQL, 'args': args}])
return True
#---------------------------------------------------------------------------
def save_file_passphrases_into_files() -> list[str]: # | None:
try:
hash_val = input('Please enter the file hash: ')
except KeyboardInterrupt:
return None
return save_object_passphrase_to_file(hash_val)
#---------------------------------------------------------------------------
def save_object_passphrase_to_file(hash:str=None) -> list[str]:
"""Save encrypted passphrases known for a hash into files.
Args:
hash: the hash to look up passphrases for
Returns
List of files containing encrypted passphrases, or None.
"""
SQL = 'SELECT * FROM gm.obj_export_passphrase WHERE hash = %(hash)s'
args = {'hash': hash}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}])
if not rows:
return None
phrase_files = []
for row in rows:
phrasefile_name = '%s-%s-passphrase.txt.asc' % (row['hash'], row['hash_type'])
with open(phrasefile_name, mode = 'wt', encoding = 'utf8') as phrasefile:
phrasefile.write('%s: %s\n' % (row['hash_type'], row['hash']))
if row['description']:
phrasefile.write('%s' % row['description'])
phrasefile.write('\n')
phrasefile.write('\n')
phrasefile.write(row['phrase'])
phrase_files.append(phrasefile_name)
return phrase_files
#============================================================
#============================================================
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
del _
from Gnumed.pycommon import gmI18N
gmI18N.activate_locale()
gmI18N.install_domain()
from Gnumed.business import gmPraxis
#---------------------------------------
def test_export_items():
# items = get_export_items()
# for item in items:
# print item.format()
import random
create_export_item(description = 'description %s' % random.random(), pk_identity = 12, pk_doc_obj = None, filename = 'dummy.dat')
items = get_export_items()
for item in items:
print(item.format())
item['pk_doc_obj'] = 1
item.save()
print(item)
#---------------------------------------
def test_export_area():
exp = cExportArea(12)
#print exp.export_with_meta_data()
#print exp.items
#exp.add_file(sys.argv[2])
#prax =
gmPraxis.gmCurrentPraxisBranch(branch = gmPraxis.cPraxisBranch(1))
#print(prax)
#print(prax.branch)
#try:
# pwd = sys.argv[2]
#except IndexError:
# pwd = None
#print(exp.export(passphrase = pwd))
#for item in exp.items:
# print(item)
# item['list_position'] = 4
# item.save()
# print(item)
# input()
print(exp.dump_items_to_disk())
#---------------------------------------
def test_label():
from Gnumed.business.gmPerson import cPatient
#from Gnumed.business.gmPersonSearch import ask_for_patient
#while ask_for_patient() is not None:
pat_min = 1
pat_max = 100
try:
pat_min = int(sys.argv[2])
pat_max = int(sys.argv[3])
except Exception:
pass
cPatient(aPK_obj = pat_min)
f = open('x-auto_inf_labels.txt', mode = 'w', encoding = 'utf8')
f.write('--------------------------------\n')
f.write('12345678901234567890123456789012\n')
f.write('--------------------------------\n')
for pat_id in range(pat_min, pat_max):
try:
exp_area = cExportArea(pat_id)
pat = cPatient(aPK_obj = pat_id)
except Exception:
continue
f.write(exp_area._compute_autorun_inf_label(pat) + '\n')
f.close()
return
#---------------------------------------
def test_store_passphrase_of_file():
gmStaff.set_current_provider_to_logged_on_user()
print('file:', sys.argv[2])
for h_t in [None, 'md5', 'sha256', 'ripemd160', 'invalid_hash_type']:
print(h_t, '-', store_passphrase_of_file(filename = sys.argv[2], passphrase='12345', hash_type = h_t))
#---------------------------------------
def test_save_object_passphrase_to_file():
print(save_object_passphrase_to_file(hash = sys.argv[2]))
#---------------------------------------
#test_export_items()
gmPG2.request_login_params(setup_pool = True)
#test_export_area()
#test_label()
test_store_passphrase_of_file()
#test_save_object_passphrase_to_file()
#============================================================
# CDROM "run.bat":
#
#@echo off
#
#if defined ProgramFiles(x86) (
# ::64-bit
# start /B x64\mdicom.exe /scan .
#) else (
# ::32-bit
# start /B win32\mdicom.exe /scan .
#)
#
#--------------------------------------------------Functions
def create_export_item(description=None, pk_identity=None, pk_doc_obj=None, filename=None)-
Expand source code
def create_export_item(description=None, pk_identity=None, pk_doc_obj=None, filename=None): args = { 'desc': description, 'pk_obj': pk_doc_obj, 'pk_pat': pk_identity, 'fname': filename } cmd = """ INSERT INTO clin.export_item ( description, fk_doc_obj, fk_identity, data, filename ) VALUES ( gm.nullify_empty_string(%(desc)s), %(pk_obj)s, %(pk_pat)s, (CASE WHEN %(pk_obj)s IS NULL THEN %(fname)s::bytea ELSE NULL::bytea END), (CASE WHEN %(pk_obj)s IS NULL THEN gm.nullify_empty_string(%(fname)s) ELSE NULL END) ) RETURNING pk """ rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False) return cExportItem(aPK_obj = rows[0]['pk']) def delete_export_item(pk_export_item=None)-
Expand source code
def delete_export_item(pk_export_item=None): args = {'pk': pk_export_item} cmd = "DELETE FROM clin.export_item WHERE pk = %(pk)s" gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True def get_export_items(order_by=None, pk_identity=None, designation=None, return_pks=False)-
Expand source code
def get_export_items(order_by=None, pk_identity=None, designation=None, return_pks=False): args = { 'pat': pk_identity, 'desig': gmTools.coalesce(designation, PRINT_JOB_DESIGNATION) } where_parts = [] if pk_identity is not None: where_parts.append('pk_identity = %(pat)s') # note that invalidly linked items will be # auto-healed when instantiated if designation is None: where_parts.append("designation IS DISTINCT FROM %(desig)s") else: where_parts.append('designation = %(desig)s') if order_by is None: order_by = 'pk_identity, list_position' order_by = ' ORDER BY %s' % order_by cmd = (_SQL_get_export_items % ' AND '.join(where_parts)) + order_by rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if return_pks: return [ r['pk_export_item'] for r in rows ] return [ cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) for r in rows ] def get_print_jobs(order_by=None, pk_identity=None)-
Expand source code
def get_print_jobs(order_by=None, pk_identity=None): return get_export_items(order_by = order_by, pk_identity = pk_identity, designation = PRINT_JOB_DESIGNATION) def save_file_passphrases_into_files() ‑> list[str]-
Expand source code
def save_file_passphrases_into_files() -> list[str]: # | None: try: hash_val = input('Please enter the file hash: ') except KeyboardInterrupt: return None return save_object_passphrase_to_file(hash_val) def save_object_passphrase_to_file(hash: str = None) ‑> list[str]-
Save encrypted passphrases known for a hash into files.
Args
hash- the hash to look up passphrases for
Returns List of files containing encrypted passphrases, or None.
Expand source code
def save_object_passphrase_to_file(hash:str=None) -> list[str]: """Save encrypted passphrases known for a hash into files. Args: hash: the hash to look up passphrases for Returns List of files containing encrypted passphrases, or None. """ SQL = 'SELECT * FROM gm.obj_export_passphrase WHERE hash = %(hash)s' args = {'hash': hash} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}]) if not rows: return None phrase_files = [] for row in rows: phrasefile_name = '%s-%s-passphrase.txt.asc' % (row['hash'], row['hash_type']) with open(phrasefile_name, mode = 'wt', encoding = 'utf8') as phrasefile: phrasefile.write('%s: %s\n' % (row['hash_type'], row['hash'])) if row['description']: phrasefile.write('%s' % row['description']) phrasefile.write('\n') phrasefile.write('\n') phrasefile.write(row['phrase']) phrase_files.append(phrasefile_name) return phrase_files def store_object_passphrase(obj=None, passphrase: str = None, hash_type: str = 'md5', owner=None, comment: dict = None) ‑> bool-
Store in the database the (encrypted) passphrase for an object.
The passphrase is stored encrypted with the public key of the owner as well as with any public key configured as a passphrase trustee.
Args
obj- an instance supporting the (binary) read protocol
passphrase- the passphrase to store
hash_type- the hash to use, defaults to 'md5'
owner- staff member to encrypt passphrase to (by public key), defaults to current provider
comment- a structured comment on the object
Returns
True/False based on success
Expand source code
def store_object_passphrase(obj=None, passphrase:str=None, hash_type:str='md5', owner=None, comment:dict=None) -> bool: """Store in the database the (encrypted) passphrase for an object. The passphrase is stored encrypted with the public key of the owner as well as with any public key configured as a passphrase trustee. Args: obj: an instance supporting the (binary) read protocol passphrase: the passphrase to store hash_type: the hash to use, defaults to 'md5' owner: staff member to encrypt passphrase to (by public key), defaults to current provider comment: a structured comment on the object Returns: True/False based on success """ assert obj, '<obj> must not be None' assert passphrase, '<passphrase> must not be None' if hash_type not in hashlib.algorithms_available: _log.error('hash type [%s] not available amongst %s', hash_type, hashlib.algorithms_available) return False pubkey_files = [] if owner is None: owner = gmStaff.gmCurrentProvider() owner_key_file = owner.public_key_file if owner_key_file: pubkey_files.append(owner_key_file) else: _log.warning('no public key for owner [%s]', owner) trustee_key_files = gmStaff.get_public_keys_of_passphrase_trustees(as_files = True) if trustee_key_files: pubkey_files.extend(trustee_key_files) else: _log.warning('there are no trustee public keys configured for passphrase escrow') if not pubkey_files: _log.error('cannot escrow passphrase, neither owner nor trustee public keys available') return False hashor = hashlib.new(hash_type, usedforsecurity = False) chunk_size = 5 * 1024 * 1024 data = obj.read(chunk_size) while data: hashor.update(data) data = obj.read(chunk_size) hash_val = hashor.hexdigest() encrypted_phrase = gmCrypto.encrypt_data_with_gpg ( data = passphrase, recipient_key_files = pubkey_files, comment = '[%s]::%s' % (hash_type, hash_val), verbose = _cfg.get(option = 'debug') ) SQL = """INSERT INTO gm.obj_export_passphrase ( hash_type, hash, phrase, description ) VALUES ( %(hash_type)s, %(hash)s, %(phrase)s, %(desc)s )""" args = { 'hash_type': hash_type, 'hash': hash_val, 'phrase': encrypted_phrase, 'desc': comment } gmPG2.run_rw_queries(queries = [{'cmd': SQL, 'args': args}]) return True def store_passphrase_of_file(filename: str = None, passphrase: str = None, hash_type: str = 'md5', comment: dict = None) ‑> bool-
Call store_object_passphrase on a given file.
Expand source code
def store_passphrase_of_file(filename:str=None, passphrase:str=None, hash_type:str='md5', comment:dict=None) -> bool: """Call store_object_passphrase on a given file.""" try: f = open(filename, 'rb') except Exception: _log.exception('cannot open [%s]', filename) return False if comment is None: comment = {} comment['__filename__'] = filename return store_object_passphrase ( obj = f, passphrase = passphrase, hash_type = hash_type, comment = comment ) def store_passphrase_of_file_callback(filename: str = None, passphrase: str = None, comment: dict = None)-
Expand source code
def store_passphrase_of_file_callback(filename:str=None, passphrase:str=None, comment:dict=None): return store_passphrase_of_file ( filename = filename, passphrase = passphrase, hash_type = 'sha256', comment = comment )
Classes
class cExportArea (pk_identity)-
Expand source code
class cExportArea(object): def __init__(self, pk_identity): self.__pk_identity = pk_identity #-------------------------------------------------------- def add_form(self, form=None, designation=None): if len(form.final_output_filenames) == 0: return True items = [] for fname in form.final_output_filenames: item = self.add_file(filename = fname) if item is None: for prev_item in items: delete_export_item(pk_export_item = prev_item['pk_export_item']) return False items.append(item) item['description'] = _('form: %s %s (%s)') % (form.template['name_long'], form.template['external_version'], fname) item['designation'] = designation item.save() return True #-------------------------------------------------------- def add_forms(self, forms=None, designation=None): all_ok = True for form in forms: all_ok = all_ok and self.add_form(form = form, designation = designation) return all_ok #-------------------------------------------------------- def add_path(self, path, comment=None): """Add a DIR entry to the export area. This sort of entry points to a certain directory on a certain machine. The content of the the directory will be included in exports, the directory *itself* will not. For *that*, use a disposable top-level directory into which you put the directory to include as a subdirectory. """ assert (os.path.isdir(path)), '<path> must exist: %s' % path path_item_data = 'DIR::%s::%s/' % (platform.node(), path.rstrip('/')) _log.debug('attempting to add path item [%s]', path_item_data) item = self.path_item_exists(path_item_data) if item is not None: _log.debug('[%s] already in export area', path) return item if comment is None: comment = _('path [%s/] on computer "%s"') % ( path.rstrip('/'), platform.node() ) else: comment += _(' (on "%s")') % platform.node() item = create_export_item ( description = comment, pk_identity = self.__pk_identity, filename = path_item_data ) try: README = open(os.path.join(path, DIRENTRY_README_NAME), mode = 'wt', encoding = 'utf8') README.write('GNUmed DIRENTRY information\n') README.write('created: %s\n' % gmDateTime.pydt_now_here()) README.write('machine: %s\n' % platform.node()) README.write('path: %s\n' % path) README.close() except OSError: _log.exception('READONLY DIRENTRY [%s]', path) return item #-------------------------------------------------------- def path_item_exists(self, path_item_data): assert (path_item_data.startswith('DIR::')), 'invalid <path_item_data> [%s]' % path_item_data where_parts = [ 'pk_identity = %(pat)s', 'filename = %(fname)s', 'pk_doc_obj IS NULL' ] args = { 'pat': self.__pk_identity, 'fname': path_item_data } SQL = _SQL_get_export_items % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}], get_col_idx = True) if len(rows) == 0: return None r = rows[0] return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) #-------------------------------------------------------- def add_file(self, filename=None, hint=None): try: open(filename).close() except Exception: _log.exception('cannot open file <%s>', filename) return None file_md5 = gmTools.file2md5(filename = filename, return_hex = True) existing_item = self.md5_exists(md5 = file_md5, include_document_parts = False) if existing_item is not None: _log.debug('md5 match (%s): %s already in export area', file_md5, filename) return existing_item path, basename = os.path.split(filename) item = create_export_item ( description = '%s: %s (%s/)' % ( gmTools.coalesce(hint, _('file'), '%s'), basename, path ), pk_identity = self.__pk_identity, filename = filename ) if item.update_data_from_file(filename = filename): return item # failed to insert data, hence remove export item entry delete_export_item(pk_export_item = item['pk_export_item']) return None #-------------------------------------------------------- def add_files(self, filenames=None, hint=None): all_ok = True for fname in filenames: all_ok = all_ok and (self.add_file(filename = fname, hint = hint) is not None) return all_ok #-------------------------------------------------------- def add_documents(self, documents=None): for doc in documents: doc_tag = _('%s (%s)%s') % ( doc['l10n_type'], gmDateTime.pydt_strftime(doc['clin_when'], '%Y %b %d'), gmTools.coalesce(doc['comment'], '', ' "%s"') ) for obj in doc.parts: if self.document_part_item_exists(pk_part = obj['pk_obj']): continue f_ext = '' if obj['filename'] is not None: f_ext = os.path.splitext(obj['filename'])[1].strip('.').strip() if f_ext != '': f_ext = ' .' + f_ext.upper() obj_tag = _('part %s (%s%s)%s') % ( obj['seq_idx'], gmTools.size2str(obj['size']), f_ext, gmTools.coalesce(obj['obj_comment'], '', ' "%s"') ) create_export_item ( description = '%s - %s' % (doc_tag, obj_tag), pk_doc_obj = obj['pk_obj'] ) #-------------------------------------------------------- def document_part_item_exists(self, pk_part=None): cmd = "SELECT EXISTS (SELECT 1 FROM clin.export_item WHERE fk_doc_obj = %(pk_obj)s)" args = {'pk_obj': pk_part} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows[0][0] #-------------------------------------------------------- def md5_exists(self, md5=None, include_document_parts=False): where_parts = [ 'pk_identity = %(pat)s', 'md5_sum = %(md5)s' ] args = { 'pat': self.__pk_identity, 'md5': md5 } if not include_document_parts: where_parts.append('pk_doc_obj IS NULL') cmd = _SQL_get_export_items % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return None r = rows[0] return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) #-------------------------------------------------------- def remove_item(self, item): if item.is_valid_DIRENTRY: tag, node, local_fs_path = item['filename'].split('::', 2) gmTools.remove_file(os.path.join(local_fs_path, DIRENTRY_README_NAME)) elif item.is_DIRENTRY: return False return delete_export_item(pk_export_item = item['pk_export_item']) #-------------------------------------------------------- def dump_items_to_disk(self, base_dir:str=None, items:list=None, passphrase:str=None, convert2pdf:bool=False) -> str: """Dump export area items to disk. Args: base_dir: directory into which to dump the items, defaults to a new sandbox directory items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set convert2pdf: attempt to convert items into PDF before dumping them Returns: The base_dir into which items were dumped, or None. """ if items is None: items = self.items if len(items) == 0: return None if base_dir is None: base_dir = gmTools.mk_sandbox_dir() else: gmTools.mkdir(base_dir) _log.debug('dumping export items to: %s', base_dir) for item in items: saved_fname = item.save_to_file(directory = base_dir, passphrase = passphrase, convert2pdf = convert2pdf) if saved_fname is None: return None if passphrase: store_passphrase_of_file(filename = saved_fname, passphrase = passphrase, hash_type = 'sha256') return base_dir #-------------------------------------------------------- def dump_items_to_disk_as_zip(self, base_dir:str=None, items:list=None, passphrase:str=None) -> str: """Dump items to disk into a zip archive. Calls dump_items_to_disk(). Args: base_dir: directory into which to dump the items, defaults to a new sandbox directory items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set Returns: Zip archive name, or None. """ _log.debug('target dir: %s', base_dir) dump_dir = self.dump_items_to_disk(base_dir = base_dir, items = items) if dump_dir is None: _log.error('cannot dump export area items') return None if passphrase: zip_file = gmCrypto.create_encrypted_zip_archive_from_dir ( source_dir = dump_dir, comment = _('GNUmed Patient Media'), overwrite = True, passphrase = passphrase, verbose = _cfg.get(option = 'debug') ) if zip_file: store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256') else: _log.error('cannot zip+encrypt export area items dump') return zip_file zip_file = gmCrypto.create_zip_archive_from_dir ( dump_dir, comment = _('GNUmed Patient Media'), overwrite = True, verbose = _cfg.get(option = 'debug') ) if not zip_file: _log.error('cannot zip export area items dump') return zip_file #-------------------------------------------------------- def export(self, base_dir=None, items=None, passphrase=None): """Export items as structured patient media. Args: base_dir: directory into which to store the export, defaults to a new sandbox directory based on patient name items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set Returns: Base_dir name, else None or False on failure. """ if items is None: items = self.items if len(items) == 0: return None from Gnumed.business.gmPerson import cPatient pat = cPatient(aPK_obj = self.__pk_identity) target_base_dir = base_dir if target_base_dir is None: target_base_dir = gmTools.mk_sandbox_dir(prefix = '%s-' % pat.subdir_name) gmTools.mkdir(target_base_dir) _log.debug('patient media base dir: %s', target_base_dir) if not gmTools.dir_is_empty(target_base_dir): _log.error('patient media base dir is not empty') return False from Gnumed.business.gmPraxis import gmCurrentPraxisBranch prax = gmCurrentPraxisBranch() html_data = {} # 1) assemble everything in a sandbox # - setup sandbox sandbox_dir = gmTools.mk_sandbox_dir() _log.debug('sandbox dir: %s', sandbox_dir) doc_dir = os.path.join(sandbox_dir, DOCUMENTS_SUBDIR) gmTools.mkdir(doc_dir) # - export mugshot mugshot = pat.document_folder.latest_mugshot if mugshot is not None: mugshot_fname = mugshot.save_to_file(directory = doc_dir) fname = os.path.split(mugshot_fname)[1] html_data['mugshot_url'] = os.path.join(DOCUMENTS_SUBDIR, fname) html_data['mugshot_alt'] =_('patient photograph from %s') % gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y') html_data['mugshot_title'] = gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y') # - export patient demographics as GDT/XML/VCF/MCF pat.export_as_gdt(filename = os.path.join(sandbox_dir, 'patient.gdt')) pat.export_as_xml_linuxmednews(filename = os.path.join(sandbox_dir, 'patient.xml')) pat.export_as_vcard(filename = os.path.join(sandbox_dir, 'patient.vcf')) pat.export_as_mecard(filename = os.path.join(sandbox_dir, u'patient.mcf')) # - create CD.INF self._create_cd_inf(pat, sandbox_dir) # - export items docs_list = [] for item in items: # if it is a dicomdir - put it into the root of the target media if item.is_DICOM_directory: _log.debug('exporting DICOMDIR DIRENTRY') # save into base dir item_fname = item.save_to_file(directory = sandbox_dir) # do not include into ./documents/ listing continue if item.is_valid_DIRENTRY: _log.debug('exporting DIRENTRY') # if there are files in the root dir: put it into a # subdir of ./documents/ where subdir is the leaf # of the item .filename if item.has_files_in_root: tag, node, local_fs_path = item['filename'].split('::', 2) subdir = local_fs_path.rstrip('/').split('/')[-1] subdir = os.path.join(doc_dir, subdir) gmTools.mkdir(subdir) item_fname = item.save_to_file(directory = subdir) # if it is subdirs only - put it into documents/ directly else: item_fname = item.save_to_file(directory = doc_dir) # include into ./documents/ listing fname = os.path.split(item_fname)[1] docs_list.append([fname, gmTools.html_escape_string(item['description'])]) continue if item.is_DIRENTRY: # DIRENTRY but not valid: skip continue # normal entry, doc obj links or data item item_fname = item.save_to_file(directory = doc_dir) fname = os.path.split(item_fname)[1] # collect items so we can later correlate items and descriptions # actually we should link to encrypted items, and to unencrypted ones docs_list.append([fname, gmTools.html_escape_string(item['description'])]) # - link to DICOMDIR if exists if 'DICOMDIR' in os.listdir(sandbox_dir): # in root path has_dicomdir = True html_data['browse_dicomdir'] = '<li><a href="./DICOMDIR">%s</a></li>' % _('show DICOMDIR file') else: has_dicomdir = False # - include DWV link if there is a DICOMDIR if has_dicomdir: # do not clone into media base to avoid encryption, # DWV will be cloned to there later on dwv_sandbox_dir = self._clone_dwv() if dwv_sandbox_dir is not None: html_data['run_dicom_viewer'] = '<li><a href="./dwv/viewers/mobile-local/index.html">%s</a></li>' % _('run Radiology Images (DICOM) Viewer') # - create frontpage.html frontpage_fname = self._create_frontpage_html(pat, prax, sandbox_dir, html_data, docs_list) # - start.html (just a convenience copy of frontpage.html) # (later overwritten, if encryption is requested) start_fname = os.path.join(sandbox_dir, 'start.html') try: shutil.copy2(frontpage_fname, start_fname) except Exception: _log.exception('cannot copy %s to %s', frontpage_fname, start_fname) # - index.html (just a convenience copy of frontpage.html) # (later overwritten if encryption is requested) index_fname = os.path.join(sandbox_dir, 'index.html') try: shutil.copy2(frontpage_fname, index_fname) except Exception: _log.exception('cannot copy %s to %s', frontpage_fname, index_fname) # 2) encrypt content of sandbox if passphrase is not None: encrypted = gmCrypto.encrypt_directory_content ( directory = sandbox_dir, receiver_key_ids = None, passphrase = passphrase, comment = None, verbose = _cfg.get(option = 'debug'), remove_unencrypted = True, store_passphrase_cb = store_passphrase_of_file_callback ) if not encrypted: _log.errror('cannot encrypt data in sandbox dir') return False # 3) add never-to-be-encrypted data # - AUTORUN.INF # - README if passphrase: self._create_autorun_inf(None, sandbox_dir) self._create_readme(None, sandbox_dir) else: self._create_autorun_inf(pat, sandbox_dir) self._create_readme(pat, sandbox_dir) # - praxis VCF/MCF shutil.move(prax.vcf, os.path.join(sandbox_dir, 'praxis.vcf')) prax.export_as_mecard(filename = os.path.join(sandbox_dir, u'praxis.mcf')) # - include DWV code if has_dicomdir: self._clone_dwv(target_dir = sandbox_dir) # - index.html as boilerplate for decryption if passphrase: index_fname = self._create_index_html(prax, sandbox_dir, html_data) # 4) move sandbox to target dir target_dir = gmTools.copy_tree_content(sandbox_dir, target_base_dir) if target_dir is None: _log.error('cannot fill target base dir') return False return target_dir #-------------------------------------------------------- def export_as_zip(self, base_dir=None, items=None, passphrase=None): _log.debug('target dir: %s', base_dir) export_dir = self.export(base_dir = base_dir, items = items) if export_dir is None: _log.debug('cannot export items') return None if passphrase: zip_file = gmCrypto.create_encrypted_zip_archive_from_dir ( export_dir, comment = _('GNUmed Patient Media'), overwrite = True, passphrase = passphrase, verbose = _cfg.get(option = 'debug') ) if zip_file: store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256') else: _log.debug('cannot create zip archive') return zip_file zip_file = gmCrypto.create_zip_archive_from_dir ( export_dir, comment = _('GNUmed Patient Media'), overwrite = True, verbose = _cfg.get(option = 'debug') ) if not zip_file: _log.debug('cannot create zip archive') return zip_file #-------------------------------------------------------- def _create_index_html(self, praxis, directory, data): # header part _HTML_data = { 'html_title_header': _('Patient data'), 'title': _('Patient data excerpt'), 'docs_title': _('Documents'), 'browse_root': _('browse storage medium'), 'browse_docs': _('browse documents area'), 'doc_subdir': DOCUMENTS_SUBDIR, 'date' : gmTools.html_escape_string(gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y %B %d')) } frontpage_fname_enc = 'frontpage.html.asc' if os.path.isfile(os.path.join(directory, frontpage_fname_enc)): _HTML_data['frontpage_fname'] = frontpage_fname_enc frontpage_fname_enc = 'frontpage.html.7z' if os.path.isfile(os.path.join(directory, frontpage_fname_enc)): _HTML_data['frontpage_fname'] = frontpage_fname_enc # footer part lines = [] adr = praxis.branch.org_unit.address if adr is not None: lines.extend(adr.format()) for comm in praxis.branch.org_unit.comm_channels: if comm['is_confidential'] is True: continue lines.append('%s: %s' % ( comm['l10n_comm_type'], comm['url'] )) adr = '' if len(lines) > 0: adr = gmTools.html_escape_string('\n'.join(lines), replace_eol = True, keep_visual_eol = True) _HTML_data['branch'] = gmTools.html_escape_string(praxis['branch']) _HTML_data['praxis'] = gmTools.html_escape_string(praxis['praxis']) _HTML_data['gm_ver'] = gmTools.html_escape_string(gmTools.coalesce(_cfg.get(option = 'client_version'), 'git HEAD')) _HTML_data['adr'] = adr # create file index_fname = os.path.join(directory, 'index.html') index_file = open(index_fname, mode = 'wt', encoding = 'utf8') index_file.write(_INDEX_HTML_CONTENT % _HTML_data) index_file.close() return index_fname #-------------------------------------------------------- def _create_frontpage_html(self, patient, praxis, directory, data, docs_list): # <li><a href="documents/filename-1.ext">document 1 description</a></li> _HTML_LIST_ITEM = ' <li><a href="%s">%s</a></li>' # header part _HTML_data = { 'html_title_header': _('Patient data for'), 'html_title_patient': gmTools.html_escape_string(patient.get_description_gender(with_nickname = False) + ', ' + _('born') + ' ' + patient.get_formatted_dob('%Y %B %d')), 'title': _('Patient data excerpt'), 'pat_name': gmTools.html_escape_string(patient.get_description_gender(with_nickname = False)), 'pat_dob': gmTools.html_escape_string(_('born') + ' ' + patient.get_formatted_dob('%Y %B %d')), 'mugshot_url': 'documents/no-such-file.png', 'mugshot_alt': _('no patient photograph available'), 'mugshot_title': '', 'docs_title': _('Documents'), 'browse_root': _('browse storage medium'), 'browse_docs': _('browse documents area'), 'doc_subdir': DOCUMENTS_SUBDIR, 'browse_dicomdir': '', 'run_dicom_viewer': '', 'date' : gmTools.html_escape_string(gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y %B %d')) } for key in data: _HTML_data[key] = data[key] # documents part _HTML_docs_list = [] for doc in docs_list: subdir = os.path.join(directory, DOCUMENTS_SUBDIR, doc[0]) if os.path.isdir(subdir): _HTML_docs_list.append(_HTML_LIST_ITEM % (os.path.join(DOCUMENTS_SUBDIR, doc[0]), _('DIRECTORY: %s/%s/') % (DOCUMENTS_SUBDIR, doc[0]))) _HTML_docs_list.append(' <ul>') for fname in os.listdir(subdir): tmp = os.path.join(subdir, fname) if os.path.isdir(tmp): _HTML_docs_list.append(' <li><a href="%s">%s</a></li>' % (os.path.join(DOCUMENTS_SUBDIR, doc[0], fname), _('DIRECTORY: %s/%s/%s/') % (DOCUMENTS_SUBDIR, doc[0], fname))) else: _HTML_docs_list.append(' <li><a href="%s">%s</a></li>' % (os.path.join(DOCUMENTS_SUBDIR, doc[0], fname), fname)) _HTML_docs_list.append(' </ul>') else: _HTML_docs_list.append(_HTML_LIST_ITEM % (os.path.join(DOCUMENTS_SUBDIR, doc[0]), doc[1])) _HTML_data['docs_list'] = u'\n '.join(_HTML_docs_list) # footer part lines = [] adr = praxis.branch.org_unit.address if adr is not None: lines.extend(adr.format()) for comm in praxis.branch.org_unit.comm_channels: if comm['is_confidential'] is True: continue lines.append('%s: %s' % ( comm['l10n_comm_type'], comm['url'] )) adr = '' if len(lines) > 0: adr = gmTools.html_escape_string('\n'.join(lines), replace_eol = True, keep_visual_eol = True) _HTML_data['branch'] = gmTools.html_escape_string(praxis['branch']) _HTML_data['praxis'] = gmTools.html_escape_string(praxis['praxis']) _HTML_data['gm_ver'] = gmTools.html_escape_string(gmTools.coalesce(_cfg.get(option = 'client_version'), 'git HEAD')) _HTML_data['adr'] = adr # create file frontpage_fname = os.path.join(directory, 'frontpage.html') frontpage_file = open(frontpage_fname, mode = 'wt', encoding = 'utf8') frontpage_file.write(_FRONTPAGE_HTML_CONTENT % _HTML_data) frontpage_file.close() return frontpage_fname #-------------------------------------------------------- def _clone_dwv(self, target_dir=None): _log.debug('cloning dwv') # find DWV dwv_src_dir = os.path.join(gmTools.gmPaths().local_base_dir, 'resources', 'dwv4export') if not os.path.isdir(dwv_src_dir): _log.debug('[%s] not found', dwv_src_dir) dwv_src_dir = os.path.join(gmTools.gmPaths().system_app_data_dir, 'resources', 'dwv4export') if not os.path.isdir(dwv_src_dir): _log.debug('[%s] not found', dwv_src_dir) return None # clone it if target_dir is None: target_dir = gmTools.mk_sandbox_dir() dwv_target_dir = os.path.join(target_dir, 'dwv') gmTools.rmdir(dwv_target_dir) try: shutil.copytree(dwv_src_dir, dwv_target_dir) except (shutil.Error, OSError): _log.exception('cannot include DWV, skipping') return None return dwv_target_dir #-------------------------------------------------------- def _create_readme(self, patient, directory): _README_CONTENT = ( 'This is a patient data excerpt created by the GNUmed Electronic Medical Record.\n' '\n' 'Patient: %s\n' '\n' 'Please display <frontpage.html> to browse patient data.\n' '\n' 'Individual documents are stored in the subdirectory\n' '\n' ' documents/\n' '\n' '\n' 'Data may need to be decrypted with either GNU Privacy\n' 'Guard or 7zip/WinZip.\n' '\n' '.asc:\n' ' https://gnupg.org\n' '\n' '.7z:\n' ' https://www.7-zip.org\n' ' https://www.winzip.com\n' '\n' 'To obtain any needed keys you will have to get in touch with\n' 'the creator or the owner of this patient media excerpt.\n' ) readme_fname = os.path.join(directory, 'README') readme_file = open(readme_fname, mode = 'wt', encoding = 'utf8') if patient is None: pat_str = _('<protected>') else: pat_str = patient.get_description_gender(with_nickname = False) + ', ' + _('born') + ' ' + patient.get_formatted_dob('%Y %B %d') readme_file.write(_README_CONTENT % pat_str) readme_file.close() return readme_fname #-------------------------------------------------------- def _create_cd_inf(self, patient, directory): _CD_INF_CONTENT = ( '[Patient Info]\r\n' # needs \r\n for Windows 'PatientName=%s, %s\r\n' 'Gender=%s\r\n' 'BirthDate=%s\r\n' 'CreationDate=%s\r\n' 'PID=%s\r\n' 'EMR=GNUmed\r\n' 'Version=%s\r\n' '#StudyDate=\r\n' '#VNRInfo=<body part>\r\n' '\r\n' '# name format: lastnames, firstnames\r\n' '# date format: YYYY-MM-DD (ISO 8601)\r\n' '# gender format: %s\r\n' ) fname = os.path.join(directory, 'CD.INF') cd_inf = open(fname, mode = 'wt', encoding = 'utf8') cd_inf.write(_CD_INF_CONTENT % ( patient['lastnames'], patient['firstnames'], gmTools.coalesce(patient['gender'], '?'), patient.get_formatted_dob('%Y-%m-%d'), gmDateTime.pydt_strftime(gmDateTime.pydt_now_here(), format = '%Y-%m-%d'), patient.ID, _cfg.get(option = 'client_version'), ' / '.join([ '%s = %s (%s)' % (g['tag'], g['label'], g['l10n_label']) for g in patient.gender_list ]) )) cd_inf.close() return fname #-------------------------------------------------------- def _create_autorun_inf(self, patient, directory): _AUTORUN_INF_CONTENT = ( # needs \r\n for Windows '[AutoRun.Amd64]\r\n' # 64 bit 'label=%(label)s\r\n' # patient name/DOB 'shellexecute=index.html\r\n' 'action=%(action)s\r\n' # % _('Browse patient data') '%(icon)s\r\n' # "icon=gnumed.ico" or "" 'UseAutoPlay=1\r\n' '\r\n' '[AutoRun]\r\n' # 32 bit 'label=%(label)s\r\n' # patient name/DOB 'shellexecute=index.html\r\n' 'action=%(action)s\r\n' # % _('Browse patient data') '%(icon)s\r\n' # "icon=gnumed.ico" or "" 'UseAutoPlay=1\r\n' '\r\n' '[Content]\r\n' 'PictureFiles=yes\r\n' 'VideoFiles=yes\r\n' 'MusicFiles=no\r\n' '\r\n' '[IgnoreContentPaths]\r\n' '\documents\r\n' '\r\n' '[unused]\r\n' 'open=requires explicit executable\r\n' ) autorun_dict = { 'label': self._compute_autorun_inf_label(patient), 'action': _('Browse patient data'), 'icon': '' } media_icon_kwd = '$$gnumed_patient_media_export_icon' media_icon_kwd_exp = gmKeywordExpansion.get_expansion ( keyword = media_icon_kwd, textual_only = False, binary_only = True ) icon_tmp_fname = media_icon_kwd_exp.save_to_file ( target_mime = 'image/x-icon', target_extension = '.ico', ignore_conversion_problems = True ) if icon_tmp_fname is None: _log.error('cannot retrieve <%s>', media_icon_kwd) else: media_icon_fname = os.path.join(directory, 'gnumed.ico') try: shutil.copy2(icon_tmp_fname, media_icon_fname) autorun_dict['icon'] = 'icon=gnumed.ico' except Exception: _log.exception('cannot move %s to %s', icon_tmp_fname, media_icon_fname) autorun_fname = os.path.join(directory, 'AUTORUN.INF') autorun_file = open(autorun_fname, mode = 'wt', encoding = 'cp1252', errors = 'replace') autorun_file.write(_AUTORUN_INF_CONTENT % autorun_dict) autorun_file.close() return autorun_fname #-------------------------------------------------------- def _compute_autorun_inf_label(self, patient): if patient is None: # if no patient provided - assume the target media # is to be encrypted and thusly do not expose patient data, # AUTORUN.INF itself will not be encrypted because # Windows must be able to parse it return _('GNUmed patient data excerpt')[:32] LABEL_MAX_LEN = 32 dob = patient.get_formatted_dob(format = ' %Y%m%d', none_string = '', honor_estimation = False) if dob == '': gender_template = ' (%s)' else: gender_template = ' %s' gender = gmTools.coalesce(patient['gender'], '', gender_template) name_max_len = LABEL_MAX_LEN - len(gender) - len(dob) # they already include appropriate padding name = patient.active_name last = name['lastnames'].strip() first = name['firstnames'].strip() len_last = len(last) len_first = len(first) while (len_last + len_first + 1) > name_max_len: if len_first > 6: len_first -= 1 if first[len_first - 1] == ' ': len_first -= 1 continue len_last -= 1 if last[len_last - 1] == ' ': len_last -= 1 last = last[:len_last].strip().upper() first = first[:len_first].strip() # max 32 chars, supposedly ASCII, but CP1252 likely works pretty well label = (('%s %s%s%s' % (last, first, dob, gender)).strip())[:32] return label #-------------------------------------------------------- # properties #-------------------------------------------------------- def get_items(self, designation=None, order_by='pk_identity, list_position, designation, description'): return get_export_items(order_by = order_by, pk_identity = self.__pk_identity, designation = designation) items = property(get_items) #-------------------------------------------------------- def get_printouts(self, order_by='list_position, designation, description'): return get_print_jobs(order_by = order_by, pk_identity = self.__pk_identity) printouts = property(get_printouts)Instance variables
var items-
Expand source code
def get_items(self, designation=None, order_by='pk_identity, list_position, designation, description'): return get_export_items(order_by = order_by, pk_identity = self.__pk_identity, designation = designation) var printouts-
Expand source code
def get_printouts(self, order_by='list_position, designation, description'): return get_print_jobs(order_by = order_by, pk_identity = self.__pk_identity)
Methods
def add_documents(self, documents=None)-
Expand source code
def add_documents(self, documents=None): for doc in documents: doc_tag = _('%s (%s)%s') % ( doc['l10n_type'], gmDateTime.pydt_strftime(doc['clin_when'], '%Y %b %d'), gmTools.coalesce(doc['comment'], '', ' "%s"') ) for obj in doc.parts: if self.document_part_item_exists(pk_part = obj['pk_obj']): continue f_ext = '' if obj['filename'] is not None: f_ext = os.path.splitext(obj['filename'])[1].strip('.').strip() if f_ext != '': f_ext = ' .' + f_ext.upper() obj_tag = _('part %s (%s%s)%s') % ( obj['seq_idx'], gmTools.size2str(obj['size']), f_ext, gmTools.coalesce(obj['obj_comment'], '', ' "%s"') ) create_export_item ( description = '%s - %s' % (doc_tag, obj_tag), pk_doc_obj = obj['pk_obj'] ) def add_file(self, filename=None, hint=None)-
Expand source code
def add_file(self, filename=None, hint=None): try: open(filename).close() except Exception: _log.exception('cannot open file <%s>', filename) return None file_md5 = gmTools.file2md5(filename = filename, return_hex = True) existing_item = self.md5_exists(md5 = file_md5, include_document_parts = False) if existing_item is not None: _log.debug('md5 match (%s): %s already in export area', file_md5, filename) return existing_item path, basename = os.path.split(filename) item = create_export_item ( description = '%s: %s (%s/)' % ( gmTools.coalesce(hint, _('file'), '%s'), basename, path ), pk_identity = self.__pk_identity, filename = filename ) if item.update_data_from_file(filename = filename): return item # failed to insert data, hence remove export item entry delete_export_item(pk_export_item = item['pk_export_item']) return None def add_files(self, filenames=None, hint=None)-
Expand source code
def add_files(self, filenames=None, hint=None): all_ok = True for fname in filenames: all_ok = all_ok and (self.add_file(filename = fname, hint = hint) is not None) return all_ok def add_form(self, form=None, designation=None)-
Expand source code
def add_form(self, form=None, designation=None): if len(form.final_output_filenames) == 0: return True items = [] for fname in form.final_output_filenames: item = self.add_file(filename = fname) if item is None: for prev_item in items: delete_export_item(pk_export_item = prev_item['pk_export_item']) return False items.append(item) item['description'] = _('form: %s %s (%s)') % (form.template['name_long'], form.template['external_version'], fname) item['designation'] = designation item.save() return True def add_forms(self, forms=None, designation=None)-
Expand source code
def add_forms(self, forms=None, designation=None): all_ok = True for form in forms: all_ok = all_ok and self.add_form(form = form, designation = designation) return all_ok def add_path(self, path, comment=None)-
Add a DIR entry to the export area.
This sort of entry points to a certain directory on a certain machine. The content of the the directory will be included in exports, the directory itself will not. For that, use a disposable top-level directory into which you put the directory to include as a subdirectory.
Expand source code
def add_path(self, path, comment=None): """Add a DIR entry to the export area. This sort of entry points to a certain directory on a certain machine. The content of the the directory will be included in exports, the directory *itself* will not. For *that*, use a disposable top-level directory into which you put the directory to include as a subdirectory. """ assert (os.path.isdir(path)), '<path> must exist: %s' % path path_item_data = 'DIR::%s::%s/' % (platform.node(), path.rstrip('/')) _log.debug('attempting to add path item [%s]', path_item_data) item = self.path_item_exists(path_item_data) if item is not None: _log.debug('[%s] already in export area', path) return item if comment is None: comment = _('path [%s/] on computer "%s"') % ( path.rstrip('/'), platform.node() ) else: comment += _(' (on "%s")') % platform.node() item = create_export_item ( description = comment, pk_identity = self.__pk_identity, filename = path_item_data ) try: README = open(os.path.join(path, DIRENTRY_README_NAME), mode = 'wt', encoding = 'utf8') README.write('GNUmed DIRENTRY information\n') README.write('created: %s\n' % gmDateTime.pydt_now_here()) README.write('machine: %s\n' % platform.node()) README.write('path: %s\n' % path) README.close() except OSError: _log.exception('READONLY DIRENTRY [%s]', path) return item def document_part_item_exists(self, pk_part=None)-
Expand source code
def document_part_item_exists(self, pk_part=None): cmd = "SELECT EXISTS (SELECT 1 FROM clin.export_item WHERE fk_doc_obj = %(pk_obj)s)" args = {'pk_obj': pk_part} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows[0][0] def dump_items_to_disk(self, base_dir: str = None, items: list = None, passphrase: str = None, convert2pdf: bool = False) ‑> str-
Dump export area items to disk.
Args
base_dir- directory into which to dump the items, defaults to a new sandbox directory
items- which items to dump, defaults to all items
passphrase- used to symmetrically encrypt dumped files, if set
convert2pdf- attempt to convert items into PDF before dumping them
Returns
The base_dir into which items were dumped, or None.
Expand source code
def dump_items_to_disk(self, base_dir:str=None, items:list=None, passphrase:str=None, convert2pdf:bool=False) -> str: """Dump export area items to disk. Args: base_dir: directory into which to dump the items, defaults to a new sandbox directory items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set convert2pdf: attempt to convert items into PDF before dumping them Returns: The base_dir into which items were dumped, or None. """ if items is None: items = self.items if len(items) == 0: return None if base_dir is None: base_dir = gmTools.mk_sandbox_dir() else: gmTools.mkdir(base_dir) _log.debug('dumping export items to: %s', base_dir) for item in items: saved_fname = item.save_to_file(directory = base_dir, passphrase = passphrase, convert2pdf = convert2pdf) if saved_fname is None: return None if passphrase: store_passphrase_of_file(filename = saved_fname, passphrase = passphrase, hash_type = 'sha256') return base_dir def dump_items_to_disk_as_zip(self, base_dir: str = None, items: list = None, passphrase: str = None) ‑> str-
Dump items to disk into a zip archive.
Calls dump_items_to_disk().Args
base_dir- directory into which to dump the items, defaults to a new sandbox directory
items- which items to dump, defaults to all items
passphrase- used to symmetrically encrypt dumped files, if set
Returns
Zip archive name, or None.
Expand source code
def dump_items_to_disk_as_zip(self, base_dir:str=None, items:list=None, passphrase:str=None) -> str: """Dump items to disk into a zip archive. Calls dump_items_to_disk(). Args: base_dir: directory into which to dump the items, defaults to a new sandbox directory items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set Returns: Zip archive name, or None. """ _log.debug('target dir: %s', base_dir) dump_dir = self.dump_items_to_disk(base_dir = base_dir, items = items) if dump_dir is None: _log.error('cannot dump export area items') return None if passphrase: zip_file = gmCrypto.create_encrypted_zip_archive_from_dir ( source_dir = dump_dir, comment = _('GNUmed Patient Media'), overwrite = True, passphrase = passphrase, verbose = _cfg.get(option = 'debug') ) if zip_file: store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256') else: _log.error('cannot zip+encrypt export area items dump') return zip_file zip_file = gmCrypto.create_zip_archive_from_dir ( dump_dir, comment = _('GNUmed Patient Media'), overwrite = True, verbose = _cfg.get(option = 'debug') ) if not zip_file: _log.error('cannot zip export area items dump') return zip_file def export(self, base_dir=None, items=None, passphrase=None)-
Export items as structured patient media.
Args
base_dir- directory into which to store the export, defaults to a new sandbox directory based on patient name
items- which items to dump, defaults to all items
passphrase- used to symmetrically encrypt dumped files, if set
Returns
Base_dir name, else None or False on failure.
Expand source code
def export(self, base_dir=None, items=None, passphrase=None): """Export items as structured patient media. Args: base_dir: directory into which to store the export, defaults to a new sandbox directory based on patient name items: which items to dump, defaults to all items passphrase: used to symmetrically encrypt dumped files, if set Returns: Base_dir name, else None or False on failure. """ if items is None: items = self.items if len(items) == 0: return None from Gnumed.business.gmPerson import cPatient pat = cPatient(aPK_obj = self.__pk_identity) target_base_dir = base_dir if target_base_dir is None: target_base_dir = gmTools.mk_sandbox_dir(prefix = '%s-' % pat.subdir_name) gmTools.mkdir(target_base_dir) _log.debug('patient media base dir: %s', target_base_dir) if not gmTools.dir_is_empty(target_base_dir): _log.error('patient media base dir is not empty') return False from Gnumed.business.gmPraxis import gmCurrentPraxisBranch prax = gmCurrentPraxisBranch() html_data = {} # 1) assemble everything in a sandbox # - setup sandbox sandbox_dir = gmTools.mk_sandbox_dir() _log.debug('sandbox dir: %s', sandbox_dir) doc_dir = os.path.join(sandbox_dir, DOCUMENTS_SUBDIR) gmTools.mkdir(doc_dir) # - export mugshot mugshot = pat.document_folder.latest_mugshot if mugshot is not None: mugshot_fname = mugshot.save_to_file(directory = doc_dir) fname = os.path.split(mugshot_fname)[1] html_data['mugshot_url'] = os.path.join(DOCUMENTS_SUBDIR, fname) html_data['mugshot_alt'] =_('patient photograph from %s') % gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y') html_data['mugshot_title'] = gmDateTime.pydt_strftime(mugshot['date_generated'], '%B %Y') # - export patient demographics as GDT/XML/VCF/MCF pat.export_as_gdt(filename = os.path.join(sandbox_dir, 'patient.gdt')) pat.export_as_xml_linuxmednews(filename = os.path.join(sandbox_dir, 'patient.xml')) pat.export_as_vcard(filename = os.path.join(sandbox_dir, 'patient.vcf')) pat.export_as_mecard(filename = os.path.join(sandbox_dir, u'patient.mcf')) # - create CD.INF self._create_cd_inf(pat, sandbox_dir) # - export items docs_list = [] for item in items: # if it is a dicomdir - put it into the root of the target media if item.is_DICOM_directory: _log.debug('exporting DICOMDIR DIRENTRY') # save into base dir item_fname = item.save_to_file(directory = sandbox_dir) # do not include into ./documents/ listing continue if item.is_valid_DIRENTRY: _log.debug('exporting DIRENTRY') # if there are files in the root dir: put it into a # subdir of ./documents/ where subdir is the leaf # of the item .filename if item.has_files_in_root: tag, node, local_fs_path = item['filename'].split('::', 2) subdir = local_fs_path.rstrip('/').split('/')[-1] subdir = os.path.join(doc_dir, subdir) gmTools.mkdir(subdir) item_fname = item.save_to_file(directory = subdir) # if it is subdirs only - put it into documents/ directly else: item_fname = item.save_to_file(directory = doc_dir) # include into ./documents/ listing fname = os.path.split(item_fname)[1] docs_list.append([fname, gmTools.html_escape_string(item['description'])]) continue if item.is_DIRENTRY: # DIRENTRY but not valid: skip continue # normal entry, doc obj links or data item item_fname = item.save_to_file(directory = doc_dir) fname = os.path.split(item_fname)[1] # collect items so we can later correlate items and descriptions # actually we should link to encrypted items, and to unencrypted ones docs_list.append([fname, gmTools.html_escape_string(item['description'])]) # - link to DICOMDIR if exists if 'DICOMDIR' in os.listdir(sandbox_dir): # in root path has_dicomdir = True html_data['browse_dicomdir'] = '<li><a href="./DICOMDIR">%s</a></li>' % _('show DICOMDIR file') else: has_dicomdir = False # - include DWV link if there is a DICOMDIR if has_dicomdir: # do not clone into media base to avoid encryption, # DWV will be cloned to there later on dwv_sandbox_dir = self._clone_dwv() if dwv_sandbox_dir is not None: html_data['run_dicom_viewer'] = '<li><a href="./dwv/viewers/mobile-local/index.html">%s</a></li>' % _('run Radiology Images (DICOM) Viewer') # - create frontpage.html frontpage_fname = self._create_frontpage_html(pat, prax, sandbox_dir, html_data, docs_list) # - start.html (just a convenience copy of frontpage.html) # (later overwritten, if encryption is requested) start_fname = os.path.join(sandbox_dir, 'start.html') try: shutil.copy2(frontpage_fname, start_fname) except Exception: _log.exception('cannot copy %s to %s', frontpage_fname, start_fname) # - index.html (just a convenience copy of frontpage.html) # (later overwritten if encryption is requested) index_fname = os.path.join(sandbox_dir, 'index.html') try: shutil.copy2(frontpage_fname, index_fname) except Exception: _log.exception('cannot copy %s to %s', frontpage_fname, index_fname) # 2) encrypt content of sandbox if passphrase is not None: encrypted = gmCrypto.encrypt_directory_content ( directory = sandbox_dir, receiver_key_ids = None, passphrase = passphrase, comment = None, verbose = _cfg.get(option = 'debug'), remove_unencrypted = True, store_passphrase_cb = store_passphrase_of_file_callback ) if not encrypted: _log.errror('cannot encrypt data in sandbox dir') return False # 3) add never-to-be-encrypted data # - AUTORUN.INF # - README if passphrase: self._create_autorun_inf(None, sandbox_dir) self._create_readme(None, sandbox_dir) else: self._create_autorun_inf(pat, sandbox_dir) self._create_readme(pat, sandbox_dir) # - praxis VCF/MCF shutil.move(prax.vcf, os.path.join(sandbox_dir, 'praxis.vcf')) prax.export_as_mecard(filename = os.path.join(sandbox_dir, u'praxis.mcf')) # - include DWV code if has_dicomdir: self._clone_dwv(target_dir = sandbox_dir) # - index.html as boilerplate for decryption if passphrase: index_fname = self._create_index_html(prax, sandbox_dir, html_data) # 4) move sandbox to target dir target_dir = gmTools.copy_tree_content(sandbox_dir, target_base_dir) if target_dir is None: _log.error('cannot fill target base dir') return False return target_dir def export_as_zip(self, base_dir=None, items=None, passphrase=None)-
Expand source code
def export_as_zip(self, base_dir=None, items=None, passphrase=None): _log.debug('target dir: %s', base_dir) export_dir = self.export(base_dir = base_dir, items = items) if export_dir is None: _log.debug('cannot export items') return None if passphrase: zip_file = gmCrypto.create_encrypted_zip_archive_from_dir ( export_dir, comment = _('GNUmed Patient Media'), overwrite = True, passphrase = passphrase, verbose = _cfg.get(option = 'debug') ) if zip_file: store_passphrase_of_file(filename = zip_file, passphrase = passphrase, hash_type = 'sha256') else: _log.debug('cannot create zip archive') return zip_file zip_file = gmCrypto.create_zip_archive_from_dir ( export_dir, comment = _('GNUmed Patient Media'), overwrite = True, verbose = _cfg.get(option = 'debug') ) if not zip_file: _log.debug('cannot create zip archive') return zip_file def get_items(self, designation=None, order_by='pk_identity, list_position, designation, description')-
Expand source code
def get_items(self, designation=None, order_by='pk_identity, list_position, designation, description'): return get_export_items(order_by = order_by, pk_identity = self.__pk_identity, designation = designation) def get_printouts(self, order_by='list_position, designation, description')-
Expand source code
def get_printouts(self, order_by='list_position, designation, description'): return get_print_jobs(order_by = order_by, pk_identity = self.__pk_identity) def md5_exists(self, md5=None, include_document_parts=False)-
Expand source code
def md5_exists(self, md5=None, include_document_parts=False): where_parts = [ 'pk_identity = %(pat)s', 'md5_sum = %(md5)s' ] args = { 'pat': self.__pk_identity, 'md5': md5 } if not include_document_parts: where_parts.append('pk_doc_obj IS NULL') cmd = _SQL_get_export_items % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return None r = rows[0] return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) def path_item_exists(self, path_item_data)-
Expand source code
def path_item_exists(self, path_item_data): assert (path_item_data.startswith('DIR::')), 'invalid <path_item_data> [%s]' % path_item_data where_parts = [ 'pk_identity = %(pat)s', 'filename = %(fname)s', 'pk_doc_obj IS NULL' ] args = { 'pat': self.__pk_identity, 'fname': path_item_data } SQL = _SQL_get_export_items % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': SQL, 'args': args}], get_col_idx = True) if len(rows) == 0: return None r = rows[0] return cExportItem(row = {'data': r, 'idx': idx, 'pk_field': 'pk_export_item'}) def remove_item(self, item)-
Expand source code
def remove_item(self, item): if item.is_valid_DIRENTRY: tag, node, local_fs_path = item['filename'].split('::', 2) gmTools.remove_file(os.path.join(local_fs_path, DIRENTRY_README_NAME)) elif item.is_DIRENTRY: return False return delete_export_item(pk_export_item = item['pk_export_item'])
class cExportItem (aPK_obj=None, row=None, link_obj=None)-
Represents an item in the export area table
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- a simple value the primary key WHERE condition must be a simple column
- a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
row- must hold the fields
- idx: a dict mapping field names to position
- data: the field values in a list (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key field OR
- pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cExportItem(gmBusinessDBObject.cBusinessDBObject): """Represents an item in the export area table""" _cmd_fetch_payload = _SQL_get_export_items % "pk_export_item = %s" _cmds_store_payload = [ """UPDATE clin.export_item SET fk_identity = %(pk_identity)s, created_by = gm.nullify_empty_string(%(created_by)s), created_when = %(created_when)s, designation = gm.nullify_empty_string(%(designation)s), description = gm.nullify_empty_string(%(description)s), fk_doc_obj = %(pk_doc_obj)s, data = CASE WHEN %(pk_doc_obj)s IS NULL THEN coalesce(data, 'to be replaced by real data') ELSE NULL END, filename = CASE WHEN %(pk_doc_obj)s IS NULL THEN gm.nullify_empty_string(%(filename)s) ELSE NULL END WHERE pk = %(pk_export_item)s AND xmin = %(xmin_export_item)s """, "SELECT clin.export_item_set_list_position(%(pk_export_item)s, %(list_position)s)", _SQL_get_export_items % 'pk_export_item = %(pk_export_item)s' ] _updatable_fields = [ 'pk_identity', 'created_when', 'designation', 'description', 'pk_doc_obj', 'filename', 'list_position' ] #-------------------------------------------------------- def __init__(self, aPK_obj=None, row=None, link_obj=None): super(cExportItem, self).__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj) # force auto-healing if need be if self._payload[self._idx['pk_identity_raw_needs_update']]: _log.warning ( 'auto-healing export item [%s] from identity [%s] to [%s] because of document part [%s] seems necessary', self._payload[self._idx['pk_export_item']], self._payload[self._idx['pk_identity_raw']], self._payload[self._idx['pk_identity']], self._payload[self._idx['pk_doc_obj']] ) if self._payload[self._idx['pk_doc_obj']] is None: _log.error('however, .fk_doc_obj is NULL, which should not happen, leaving things alone for manual inspection') return # only flag ourselves as modified, do not actually # modify any values, better safe than sorry self._is_modified = True self.save() self.refetch_payload(ignore_changes = False, link_obj = link_obj) #-------------------------------------------------------- # def format(self): # return u'%s' % self #-------------------------------------------------------- def update_data(self, data=None): assert (data is not None), '<data> must not be <None>' if self.is_DIRENTRY or self.is_document_part: return False SQL = """ UPDATE clin.export_item SET data = %(data)s::bytea, fk_doc_obj = NULL WHERE pk = %(pk)s""" args = {'pk': self.pk_obj, 'data': data} gmPG2.run_rw_queries(queries = [{'cmd': SQL, 'args': args}], return_data = False, get_col_idx = False) # must update XMIN now ... self.refetch_payload() return True #-------------------------------------------------------- def update_data_from_file(self, filename=None, convert_document_part=False): if self.is_DIRENTRY: return False if self.is_document_part: if not convert_document_part: return False # sanity check if not (os.access(filename, os.R_OK) and os.path.isfile(filename)): _log.error('[%s] is not a readable file' % filename) return False cmd = """ UPDATE clin.export_item SET data = %(data)s::bytea, fk_doc_obj = NULL, filename = gm.nullify_empty_string(%(fname)s) WHERE pk = %(pk)s""" args = {'pk': self.pk_obj, 'fname': filename} if not gmPG2.file2bytea(query = cmd, filename = filename, args = args): return False # must update XMIN now ... self.refetch_payload() return True #-------------------------------------------------------- def save_to_file(self, aChunkSize:int=0, filename:str=None, directory:str=None, passphrase:str=None, convert2pdf:bool=False) -> str: """Save this entry to disk. Args: filename: The filename to save into, unless this is a DIRENTRY. directory: The directory to save the DIRENTRY _content into, if this is a DIRENTRY. passphrase: Encrypt file(s) with this passphrase, if not _None_. convert2pdf: Convert file(s) to PDF on the way out. Before encryption, that is. Returns: Directory for DIRENTRIES, or filename, or None on failure. """ if self.is_DIRENTRY and convert2pdf: # cannot convert dir entries to PDF return None # data linked from archive ? part_fname = self.__save_doc_obj ( filename = filename, directory = directory, passphrase = passphrase, convert2pdf = convert2pdf ) if part_fname is False: return None if part_fname is not None: return part_fname # valid DIRENTRY ? if self.is_valid_DIRENTRY: target_dir = self.__save_direntry ( directory, passphrase = passphrase ) if target_dir is False: return None if target_dir is not None: return target_dir # but still a DIRENTRY ? if self.is_DIRENTRY: # yes, but apparently not valid (anymore), say, # other machine or dir not found locally return None # normal item with data in export area table return self.__save_normal_item ( filename = filename, directory = directory, passphrase = passphrase, convert2pdf = convert2pdf ) #-------------------------------------------------------- def display_via_mime(self, chunksize=0, block=None): # document part if self._payload[self._idx['pk_doc_obj']] is not None: return self.document_part.display_via_mime(chunksize = chunksize, block = block) # DIR entry if self._payload[self._idx['filename']].startswith('DIR::'): # FIXME: error handling with malformed entries tag, node, path = self._payload[self._idx['filename']].split('::', 2) if node != platform.node(): msg = _( 'This item points to a directory on the computer named:\n' ' %s\n' 'You are, however, currently using another computer:\n' ' %s\n' 'Directory items can only be viewed/saved/exported\n' 'on the computer they are pointing to.' ) % (node, platform.node()) return False, msg success, msg = gmMimeLib.call_viewer_on_file(path, block = block) return success, msg # data -> save fname = self.save_to_file(aChunkSize = chunksize) if fname is None: return False, '' success, msg = gmMimeLib.call_viewer_on_file(fname, block = block) if not success: return False, msg return True, '' #-------------------------------------------------------- def get_useful_filename(self, patient=None, directory=None): patient_part = '' if patient is not None: patient_part = '-%s' % patient.subdir_name # preserve original filename extension if available suffix = '.dat' if self._payload[self._idx['filename']] is not None: tmp, suffix = os.path.splitext ( gmTools.fname_sanitize(self._payload[self._idx['filename']]).casefold() ) if suffix == '': suffix = '.dat' fname = gmTools.get_unique_filename ( prefix = '%s-gm-export_item%s-' % (self._payload[self._idx['list_position']], patient_part), suffix = suffix, tmp_dir = directory ) return fname #-------------------------------------------------------- # helpers #-------------------------------------------------------- def __save_normal_item(self, filename:str=None, directory:str=None, passphrase:str=None, convert2pdf:bool=False) -> str: _SQL = 'SELECT substring(data FROM %(start)s FOR %(size)s) FROM clin.export_item WHERE pk = %(pk)s' tmp_fname = gmTools.get_unique_filename() success = gmPG2.bytea2file ( data_query = {'cmd': _SQL, 'args': {'pk': self.pk_obj}}, filename = tmp_fname, data_size = self._payload[self._idx['size']] ) if not success: return None tmp_fname = gmMimeLib.adjust_extension_by_mimetype(tmp_fname) if convert2pdf: tmp_fname = gmMimeLib.convert_file(filename = tmp_fname, target_mime = 'application/pdf', target_extension = '.pdf') if filename is None: target_fname = self.get_useful_filename(directory = directory) else: target_fname = filename if passphrase is None: if not gmTools.rename_file(tmp_fname, target_fname, overwrite = True, allow_symlink = True): return None if filename is None: return gmMimeLib.adjust_extension_by_mimetype(target_fname) return target_fname enc_fname = gmCrypto.encrypt_file ( filename = tmp_fname, passphrase = passphrase, verbose = _cfg.get(option = 'debug'), remove_unencrypted = True, convert2pdf = False # already done, if desired ) removed = gmTools.remove_file(tmp_fname) if enc_fname is None: _log.error('cannot encrypt or, possibly, convert') return None if not removed: _log.error('cannot remove unencrypted file') gmTools.remove_file(enc_fname) return None return enc_fname #-------------------------------------------------------- def __save_doc_obj(self, filename=None, directory=None, passphrase=None, convert2pdf:bool=False): """Save doc object part into target. None: not a doc obj True: success False: failure (to save/convert/encrypt/remove unencrypted) """ if self._payload[self._idx['pk_doc_obj']] is None: return None part = self.document_part if filename is None: filename = part.get_useful_filename ( make_unique = False, directory = directory, include_gnumed_tag = False, date_before_type = True, name_first = False ) path, name = os.path.split(filename) filename = os.path.join(path, '%s-%s' % (self._payload[self._idx['list_position']], name)) if convert2pdf: target_mime = 'application/pdf' target_ext = '.pdf' else: target_mime = None target_ext = None part_fname = part.save_to_file ( filename = filename, target_mime = target_mime, target_extension = target_ext, ignore_conversion_problems = False ) if part_fname is None: _log.error('cannot save document part to file') return False if passphrase is None: return part_fname enc_filename = gmCrypto.encrypt_file ( filename = part_fname, passphrase = passphrase, verbose = _cfg.get(option = 'debug'), remove_unencrypted = True ) removed = gmTools.remove_file(part_fname) if enc_filename is None: _log.error('cannot encrypt') return False if removed: return enc_filename _log.error('cannot remove unencrypted file') gmTools.remove_file(enc_filename) return False #-------------------------------------------------------- def __save_direntry(self, directory=None, passphrase=None): """Move DIRENTRY source into target. None: not a DIRENTRY True: success False: failure """ # do not process malformed entries try: tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) except ValueError: _log.exception('malformed DIRENTRY: [%s]', self._payload[self._idx['filename']]) return False # source and target paths must not overlap if directory is None: directory = gmTools.mk_sandbox_dir(prefix = 'exp-') if directory.startswith(local_fs_path): _log.error('cannot dump DIRENTRY item [%s]: must not be subdirectory of target dir [%s]', self._payload[self._idx['filename']], directory) return False if local_fs_path.startswith(directory): _log.error('cannot dump DIRENTRY item [%s]: target dir [%s] must not be subdirectory of DIRENTRY', self._payload[self._idx['filename']], directory) return False _log.debug('dumping DIRENTRY item [%s] into [%s]', self._payload[self._idx['filename']], directory) sandbox_dir = gmTools.mk_sandbox_dir() _log.debug('sandbox: %s', sandbox_dir) tmp = gmTools.copy_tree_content(local_fs_path, sandbox_dir) if tmp is None: _log.error('cannot dump DIRENTRY item [%s] into [%s]: copy error', self._payload[self._idx['filename']], sandbox_dir) return False gmTools.remove_file(os.path.join(tmp, DIRENTRY_README_NAME)) if passphrase is not None: _log.debug('encrypting sandbox: %s', sandbox_dir) encrypted = gmCrypto.encrypt_directory_content ( directory = sandbox_dir, passphrase = passphrase, verbose = _cfg.get(option = 'debug'), remove_unencrypted = True ) if not encrypted: _log.error('cannot dump DIRENTRY item [%s]: encryption problem in [%s]', self._payload[self._idx['filename']], sandbox_dir) return False tmp = gmTools.copy_tree_content(sandbox_dir, directory) if tmp is None: _log.debug('cannot dump DIRENTRY item [%s] into [%s]: copy error', self._payload[self._idx['filename']], directory) return False return directory #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_is_doc_part(self): return self._payload[self._idx['pk_doc_obj']] is not None is_document_part = property(_get_is_doc_part) #-------------------------------------------------------- def _get_doc_part(self): if self._payload[self._idx['pk_doc_obj']] is None: return None return gmDocuments.cDocumentPart(aPK_obj = self._payload[self._idx['pk_doc_obj']]) document_part = property(_get_doc_part) #-------------------------------------------------------- def _get_is_print_job(self): return self._payload[self._idx['designation']] == PRINT_JOB_DESIGNATION def _set_is_print_job(self, is_print_job): desig = gmTools.bool2subst(is_print_job, PRINT_JOB_DESIGNATION, None, None) if self._payload[self._idx['designation']] == desig: return self['designation'] = desig self.save() is_print_job = property(_get_is_print_job, _set_is_print_job) #-------------------------------------------------------- def _is_DIRENTRY(self): """Check whether this item looks like a DIRENTRY.""" if self._payload[self._idx['filename']] is None: return False if not self._payload[self._idx['filename']].startswith('DIR::'): return False if len(self._payload[self._idx['filename']].split('::', 2)) != 3: return False return True is_DIRENTRY = property(_is_DIRENTRY) #-------------------------------------------------------- def _is_valid_DIRENTRY(self): """Check whether this item is a _valid_ DIRENTRY.""" if not self.is_DIRENTRY: return False # malformed ? try: tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) except ValueError: # should not happen because structure already checked in .is_DIRENTRY, # better safe than sorry _log.exception('DIRENTRY [%s]: malformed', self._payload[self._idx['filename']]) return False # this machine ? if node != platform.node(): _log.warning('DIRENTRY [%s]: not on this machine (%s)', self._payload[self._idx['filename']], platform.node()) return False # valid path ? if not os.path.isdir(local_fs_path): _log.warning('DIRENTRY [%s]: directory not found (old DIRENTRY ?)', self._payload[self._idx['filename']]) return False return True is_valid_DIRENTRY = property(_is_valid_DIRENTRY) #-------------------------------------------------------- def _is_DICOM_directory(self): """Check whether this item points to a DICOMDIR.""" if not self.is_valid_DIRENTRY: return False tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) found_DICOMDIR = False for fs_entry in os.listdir(local_fs_path): # found a subdir if os.path.isdir(os.path.join(local_fs_path, fs_entry)): # allow for any number of subdirs continue # found a file if fs_entry != 'DICOMDIR': # not named "DICOMDIR" -> not a DICOMDIR DIRENTRY return False # must be named DICOMDIR -> that's the only file allowed (and required) in ./ found_DICOMDIR = True return found_DICOMDIR is_DICOM_directory = property(_is_DICOM_directory) #-------------------------------------------------------- def _has_files_in_root(self): """True if there are files in the root directory.""" tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) for fs_entry in os.listdir(local_fs_path): if os.path.isfile(fs_entry): _log.debug('has files in top level: %s', local_fs_path) return True return False has_files_in_root = property(_has_files_in_root)Ancestors
Instance variables
var document_part-
Expand source code
def _get_doc_part(self): if self._payload[self._idx['pk_doc_obj']] is None: return None return gmDocuments.cDocumentPart(aPK_obj = self._payload[self._idx['pk_doc_obj']]) var has_files_in_root-
True if there are files in the root directory.
Expand source code
def _has_files_in_root(self): """True if there are files in the root directory.""" tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) for fs_entry in os.listdir(local_fs_path): if os.path.isfile(fs_entry): _log.debug('has files in top level: %s', local_fs_path) return True return False var is_DICOM_directory-
Check whether this item points to a DICOMDIR.
Expand source code
def _is_DICOM_directory(self): """Check whether this item points to a DICOMDIR.""" if not self.is_valid_DIRENTRY: return False tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) found_DICOMDIR = False for fs_entry in os.listdir(local_fs_path): # found a subdir if os.path.isdir(os.path.join(local_fs_path, fs_entry)): # allow for any number of subdirs continue # found a file if fs_entry != 'DICOMDIR': # not named "DICOMDIR" -> not a DICOMDIR DIRENTRY return False # must be named DICOMDIR -> that's the only file allowed (and required) in ./ found_DICOMDIR = True return found_DICOMDIR var is_DIRENTRY-
Check whether this item looks like a DIRENTRY.
Expand source code
def _is_DIRENTRY(self): """Check whether this item looks like a DIRENTRY.""" if self._payload[self._idx['filename']] is None: return False if not self._payload[self._idx['filename']].startswith('DIR::'): return False if len(self._payload[self._idx['filename']].split('::', 2)) != 3: return False return True var is_document_part-
Expand source code
def _get_is_doc_part(self): return self._payload[self._idx['pk_doc_obj']] is not None var is_print_job-
Expand source code
def _get_is_print_job(self): return self._payload[self._idx['designation']] == PRINT_JOB_DESIGNATION var is_valid_DIRENTRY-
Check whether this item is a valid DIRENTRY.
Expand source code
def _is_valid_DIRENTRY(self): """Check whether this item is a _valid_ DIRENTRY.""" if not self.is_DIRENTRY: return False # malformed ? try: tag, node, local_fs_path = self._payload[self._idx['filename']].split('::', 2) except ValueError: # should not happen because structure already checked in .is_DIRENTRY, # better safe than sorry _log.exception('DIRENTRY [%s]: malformed', self._payload[self._idx['filename']]) return False # this machine ? if node != platform.node(): _log.warning('DIRENTRY [%s]: not on this machine (%s)', self._payload[self._idx['filename']], platform.node()) return False # valid path ? if not os.path.isdir(local_fs_path): _log.warning('DIRENTRY [%s]: directory not found (old DIRENTRY ?)', self._payload[self._idx['filename']]) return False return True
Methods
def display_via_mime(self, chunksize=0, block=None)-
Expand source code
def display_via_mime(self, chunksize=0, block=None): # document part if self._payload[self._idx['pk_doc_obj']] is not None: return self.document_part.display_via_mime(chunksize = chunksize, block = block) # DIR entry if self._payload[self._idx['filename']].startswith('DIR::'): # FIXME: error handling with malformed entries tag, node, path = self._payload[self._idx['filename']].split('::', 2) if node != platform.node(): msg = _( 'This item points to a directory on the computer named:\n' ' %s\n' 'You are, however, currently using another computer:\n' ' %s\n' 'Directory items can only be viewed/saved/exported\n' 'on the computer they are pointing to.' ) % (node, platform.node()) return False, msg success, msg = gmMimeLib.call_viewer_on_file(path, block = block) return success, msg # data -> save fname = self.save_to_file(aChunkSize = chunksize) if fname is None: return False, '' success, msg = gmMimeLib.call_viewer_on_file(fname, block = block) if not success: return False, msg return True, '' def get_useful_filename(self, patient=None, directory=None)-
Expand source code
def get_useful_filename(self, patient=None, directory=None): patient_part = '' if patient is not None: patient_part = '-%s' % patient.subdir_name # preserve original filename extension if available suffix = '.dat' if self._payload[self._idx['filename']] is not None: tmp, suffix = os.path.splitext ( gmTools.fname_sanitize(self._payload[self._idx['filename']]).casefold() ) if suffix == '': suffix = '.dat' fname = gmTools.get_unique_filename ( prefix = '%s-gm-export_item%s-' % (self._payload[self._idx['list_position']], patient_part), suffix = suffix, tmp_dir = directory ) return fname def save_to_file(self, aChunkSize: int = 0, filename: str = None, directory: str = None, passphrase: str = None, convert2pdf: bool = False) ‑> str-
Save this entry to disk.
Args
filename- The filename to save into, unless this is a DIRENTRY.
directory- The directory to save the DIRENTRY _content into, if this is a DIRENTRY.
passphrase- Encrypt file(s) with this passphrase, if not None.
convert2pdf- Convert file(s) to PDF on the way out. Before encryption, that is.
Returns
Directory for DIRENTRIES, or filename, or None on failure.
Expand source code
def save_to_file(self, aChunkSize:int=0, filename:str=None, directory:str=None, passphrase:str=None, convert2pdf:bool=False) -> str: """Save this entry to disk. Args: filename: The filename to save into, unless this is a DIRENTRY. directory: The directory to save the DIRENTRY _content into, if this is a DIRENTRY. passphrase: Encrypt file(s) with this passphrase, if not _None_. convert2pdf: Convert file(s) to PDF on the way out. Before encryption, that is. Returns: Directory for DIRENTRIES, or filename, or None on failure. """ if self.is_DIRENTRY and convert2pdf: # cannot convert dir entries to PDF return None # data linked from archive ? part_fname = self.__save_doc_obj ( filename = filename, directory = directory, passphrase = passphrase, convert2pdf = convert2pdf ) if part_fname is False: return None if part_fname is not None: return part_fname # valid DIRENTRY ? if self.is_valid_DIRENTRY: target_dir = self.__save_direntry ( directory, passphrase = passphrase ) if target_dir is False: return None if target_dir is not None: return target_dir # but still a DIRENTRY ? if self.is_DIRENTRY: # yes, but apparently not valid (anymore), say, # other machine or dir not found locally return None # normal item with data in export area table return self.__save_normal_item ( filename = filename, directory = directory, passphrase = passphrase, convert2pdf = convert2pdf ) def update_data(self, data=None)-
Expand source code
def update_data(self, data=None): assert (data is not None), '<data> must not be <None>' if self.is_DIRENTRY or self.is_document_part: return False SQL = """ UPDATE clin.export_item SET data = %(data)s::bytea, fk_doc_obj = NULL WHERE pk = %(pk)s""" args = {'pk': self.pk_obj, 'data': data} gmPG2.run_rw_queries(queries = [{'cmd': SQL, 'args': args}], return_data = False, get_col_idx = False) # must update XMIN now ... self.refetch_payload() return True def update_data_from_file(self, filename=None, convert_document_part=False)-
Expand source code
def update_data_from_file(self, filename=None, convert_document_part=False): if self.is_DIRENTRY: return False if self.is_document_part: if not convert_document_part: return False # sanity check if not (os.access(filename, os.R_OK) and os.path.isfile(filename)): _log.error('[%s] is not a readable file' % filename) return False cmd = """ UPDATE clin.export_item SET data = %(data)s::bytea, fk_doc_obj = NULL, filename = gm.nullify_empty_string(%(fname)s) WHERE pk = %(pk)s""" args = {'pk': self.pk_obj, 'fname': filename} if not gmPG2.file2bytea(query = cmd, filename = filename, args = args): return False # must update XMIN now ... self.refetch_payload() return True
Inherited members