def _translated_summary(self):
"""
Find corresponding translation of English summary
Parameters:
EnglishSummary - required CDR ID for the document for which
we want to find the Spanish translation
Return:
XML document node with the following structure:
ReportBody
ReportName
TranslatedSummary
"""
english_id = self.__opts.get("EnglishSummary")
if not english_id:
raise Exception("Missing required 'EnglishSummary' parameter")
doc = Doc(self.session, id=english_id)
query = Query("query_term", "doc_id")
query.where("path = '/Summary/TranslationOf/@cdr:ref'")
query.where(query.Condition("int_val", doc.id))
row = query.execute(self.cursor).fetchone()
if not row:
message = "No translated summary found for {}".format(english_id)
raise Exception(message)
body = self.__start_body()
spanish_id = Doc.normalize_id(row.doc_id)
etree.SubElement(body, "TranslatedSummary").text = spanish_id
return body
def _glossary_term_names(self):
"""
Find GlossaryTermName documents linked to a GlossaryTermConcept doc
Parameters:
ConceptID - required CDR ID for the master concept document
Return:
XML document node with the following structure:
ReportBody
ReportName
GlossaryTermName*
@ref
"""
concept_id = self.__opts.get("ConceptId")
if not concept_id:
raise Exception("Missing required 'ConceptId' parameter")
path = "/GlossaryTermName/GlossaryTermConcept/@cdr:ref"
doc = Doc(self.session, id=concept_id)
query = Query("document d", "d.id", "d.title")
query.join("query_term n", "n.doc_id = d.id")
query.where(query.Condition("n.path", path))
query.where(query.Condition("n.int_val", doc.id))
body = self.__start_body()
for id, title in query.execute(self.cursor).fetchall():
cdr_id = Doc.normalize_id(id)
etree.SubElement(body, "GlossaryTermName", ref=cdr_id).text = title
return body
def _patient_summary(self):
"""
Find corresponding patient version for HP summary
Parameters:
HPSummary - required CDR ID for the Health Professional
for which we want to find the patient verion
Return:
XML document node with the following structure:
ReportBody
ReportName
PatientSummary
"""
hp_id = self.__opts.get("HPSummary")
if not hp_id:
raise Exception("Missing required 'HPSummary' parameter")
doc = Doc(self.session, id=hp_id)
query = Query("query_term", "doc_id")
query.where("path = '/Summary/PatientVersionOf/@cdr:ref'")
query.where(query.Condition("int_val", doc.id))
row = query.execute(self.cursor).fetchone()
if not row:
message = "No patient summary found for {}".format(hp_id)
raise Exception(message)
body = self.__start_body()
patient_id = Doc.normalize_id(row.doc_id)
etree.SubElement(body, "PatientSummary").text = patient_id
return body
def _genetics_syndromes(self):
"""
Find Term documents used to represent genetics syndromes
Parameters:
TitlePattern - optional string narrowing report to syndrome
names which match the pattern
Return:
XML document node with the following structure:
ReportBody
ReportName
ReportRow*
DocId
DocTitle
"""
pattern = self.__opts.get("TitlePattern")
query = Query("document d", "d.id", "d.title")
query.unique().order("d.title")
query.join("query_term t", "t.doc_id = d.id")
query.join("query_term s", "s.doc_id = t.doc_id",
"LEFT(s.node_loc, 8) = LEFT(t.node_loc, 8)")
query.where("t.path = '/Term/MenuInformation/MenuItem/MenuType'")
query.where("s.path = '/Term/MenuInformation/MenuItem/MenuStatus'")
query.where("s.value = 'Online'")
query.where("t.value = 'Genetics Professionals--GeneticSyndrome'")
if pattern:
query.where(query.Condition("d.title", pattern, "LIKE"))
body = self.__start_body()
for id, title in query.execute(self.cursor).fetchall():
wrapper = etree.SubElement(body, "ReportRow")
etree.SubElement(wrapper, "DocId").text = Doc.normalize_id(id)
etree.SubElement(wrapper, "DocTitle").text = title
return body
def _dated_actions(self):
"""
Find the to-do list for documents of a particular type
Parameters:
DocType - required string naming the document type for
which documents should be included
Return:
XML document node with the following structure:
ReportBody
ReportName
ReportRow*
DocId
DocTitle
"""
doctype = self.__opts.get("DocType")
if not doctype:
raise Exception("Missing required 'DocType' parameter")
path = "/{}/DatedAction/ActionDate".format(doctype)
query = Query("document d", "d.id", "d.title").unique()
query.join("query_term a", "a.doc_id = d.id")
query.where(query.Condition("a.path", path))
rows = query.execute(self.cursor).fetchall()
body = self.__start_body()
for id, title in rows:
wrapper = etree.SubElement(body, "ReportRow")
etree.SubElement(wrapper, "DocId").text = Doc.normalize_id(id)
etree.SubElement(wrapper, "DocTitle").text = title
result = Doc(self.session, id=id).filter("name:Dated Actions")
wrapper.append(result.result_tree.getroot())
return body
def _board_member(self):
"""
Find corresponding person document linked from board member document
Parameters:
PersonID - required CDR ID for the Person document for which
we want to find the corresponding PDQBoardMemeberInfo
document
Return:
XML document node with the following structure:
ReportBody
ReportName
BoardMember
"""
person_id = self.__opts.get("PersonId")
if not person_id:
raise Exception("Missing required 'PersonId' parameter")
doc = Doc(self.session, id=person_id)
query = Query("query_term", "doc_id")
query.where("path = '/PDQBoardMemberInfo/BoardMemberName/@cdr:ref'")
query.where(query.Condition("int_val", doc.id))
row = query.execute(self.cursor).fetchone()
if not row:
message = "No board member found for {}".format(person_id)
raise Exception(message)
body = self.__start_body()
member_id = Doc.normalize_id(row.doc_id)
etree.SubElement(body, "BoardMember").text = member_id
return body
def _inactive_checked_out_documents(self):
"""
Report on locked documents which haven't seen any action recently
Parameters:
InactivityLength - required string for how long a document
can be active before showing up on the report
in the form YYYY-MM-DD
Return:
XML document node with the following structure:
ReportBody
ReportName
ReportRow*
DocId
DocType
CheckedOutTo
WhenCheckedOut
LastActivity
ActionType
ActionWhen
"""
deltas = self.__opts.get("InactivityLength")
if not deltas:
raise Exception("Missing required 'InactivityLength' parameter")
try:
years, months, days = [int(digits) for digits in deltas.split("-")]
except:
message = "InactivityLength parameter must be in YYYY-MM-DD format"
raise Exception(message)
delta = relativedelta(years=years, months=months, days=days)
cutoff = (datetime.now() - delta).replace(microsecond=0)
subquery = Query("audit_trail", "MAX(dt)")
subquery.where("document = a.document")
fields = "d.id", "t.name", "c.dt_out", "u.name", "w.name", "a.dt"
query = Query("document d", *fields)
query.join("doc_type t", "t.id = d.doc_type")
query.join("checkout c", "c.id = d.id")
query.join("open_usr u", "u.id = c.usr")
query.join("audit_trail a", "a.document = d.id")
query.join("action w", "w.id = a.action")
query.where("c.dt_in IS NULL")
query.where(query.Condition("c.dt_out", cutoff, "<"))
query.where(query.Condition("a.dt", cutoff, "<"))
query.where(query.Condition("a.dt", subquery))
rows = query.order("c.id").execute(self.cursor).fetchall()
body = self.__start_body()
for id, doctype, locked, locker, what, when in rows:
wrapper = etree.SubElement(body, "ReportRow")
etree.SubElement(wrapper, "DocId").text = Doc.normalize_id(id)
etree.SubElement(wrapper, "DocType").text = doctype
etree.SubElement(wrapper, "CheckedOutTo").text = locker
etree.SubElement(wrapper, "WhenCheckedOut").text = str(locked)
last_activity = etree.SubElement(wrapper, "LastActivity")
etree.SubElement(last_activity, "ActionType").text = what
etree.SubElement(last_activity, "ActionWhen").text = str(when)
return body
def _locked_documents(self):
"""
Report on documents locked by specified user
Parameters:
UserId - required string identifying a user account;
this is the value often referred to as the 'name'
rather than the integer primary key for the row
in the usr table
Return:
XML document node with the following structure:
ReportBody
ReportName
ReportRow*
DocId
DocType
WhenCheckedOut
"""
user_name = self.__opts.get("UserId")
if not user_name:
raise Exception("Missing required 'UserId' parameter")
query = Query("document d", "d.id", "t.name", "c.dt_out")
query.join("doc_type t", "t.id = d.doc_type")
query.join("checkout c", "c.id = d.id")
query.join("open_usr u", "u.id = c.usr")
query.where("c.dt_in IS NULL")
query.where(query.Condition("u.name", user_name))
rows = query.order("c.id").execute(self.cursor).fetchall()
body = self.__start_body()
for id, doctype, locked in rows:
wrapper = etree.SubElement(body, "ReportRow")
etree.SubElement(wrapper, "DocId").text = Doc.normalize_id(id)
etree.SubElement(wrapper, "DocType").text = doctype
etree.SubElement(wrapper, "WhenCheckedOut").text = str(locked)
return body
