def system(self):
"""
Reference to `Doc` object for job's publishing control document
"""
if not hasattr(self, "_system"):
opts = dict(id=None, before=self.started)
if self.id:
query = Query("pub_proc", "pub_system")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
opts["id"] = row.pub_system
else:
name = self.__opts.get("system")
if name:
query = Query("document d", "d.id")
query.join("doc_type t", "t.id = d.doc_type")
query.where("t.name = 'PublishingSystem'")
query.where(query.Condition("d.title", name))
rows = query.execute(self.cursor).fetchall()
if len(rows) > 1:
raise Exception(f"multiple {name} docs")
if not rows:
message = "Publishing system {!r} not found"
raise Exception(message.format(name))
row = rows[0]
opts["id"] = row.id
opts["title"] = name
if opts["id"]:
self._system = Doc(self.session, **opts)
else:
self._system = None
return self._system
def subsystem(self):
"""
Reference to the `Job.Subsystem` object controlling this job
"""
if not hasattr(self, "_subsystem"):
self._subsystem = None
if self.system:
if self.system.root is None:
doc = self.system
args = doc.cdr_id, doc.version, doc.title
doc = "{}V{} ({})".format(*args)
message = "{} can't be parsed".format(doc)
raise Exception(message)
name = self.__opts.get("subsystem")
if not name and self.id:
query = Query("pub_proc", "pub_subset")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
name = row.pub_subset
if name:
path = "SystemSubset/SubsetName"
for node in self.system.root.findall(path):
if Doc.get_text(node) == name:
parent = node.getparent()
self._subsystem = Job.Subsystem(parent, name)
break
return self._subsystem
def _values_for_path(self):
"""
Find values located in document at specified path
Parameters:
DocId - required string indicating which document to look in
Path - required string for location of values to be returned
Pub - if present (regardless of value) look for values in
the latest publishable version of the document
Return:
XML document node with the following structure:
ReportBody
ReportName
Value*
@Loc
"""
doc_id = self.__opts.get("DocId")
if not doc_id:
raise Exception("Missing required 'DocId' parameter")
path = self.__opts.get("Path")
if not doc_id:
raise Exception("Missing required 'Path' parameter")
table = "query_term_pub" if "Pub" in self.__opts else "query_term"
query = Query(table, "value", "node_loc").order("node_loc")
query.where(query.Condition("doc_id", Doc(self.session, id=doc_id).id))
query.where(query.Condition("path", path))
body = self.__start_body()
for value, loc in query.execute(self.cursor).fetchall():
etree.SubElement(body, "Value", Loc=loc).text = value
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 _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 _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 parms(self):
"""
Dictionary of parameters for the job
Default values from the control document. Some may be overridden
for this job.
Have to strip unwanted space from the values; see
https://sourceforge.net/p/adodbapi/bugs/27/
"""
if not hasattr(self, "_parms"):
if self.id:
query = Query("pub_proc_parm", "parm_name", "parm_value")
query.where(query.Condition("pub_proc", self.id))
self._parms = {}
for name, value in query.execute(self.cursor).fetchall():
if value is not None:
value = value.strip() # bug in adodbapi
self._parms[name] = value
else:
if not self.subsystem:
raise Exception("Missing publishing subsystem")
requested = self.__opts.get("parms") or {}
defined = self.subsystem.parms.copy()
undefined = set(requested) - set(defined)
if undefined:
messages = "Paramater(s) {} undefined"
#raise Exception(messages.format(", ".join(undefined)))
raise Exception(messages.format(undefined))
defined.update(requested)
self.session.logger.info("job parms: %r", defined)
self._parms = defined
return self._parms
def docs(self):
"""
List of documents requested or published for this job
For a job which is being created, this will be populated from the
`docs` argument passed into the constructor. For a job which is
already in the database and which has been published, the list
will be pulled from the `pub_proc_doc` table. For a job which is
in the database, queued but not yet run, the list will have
the documents explicitly requested at job creation time, but will
not yet have the documents which will be picked up by the control
document's query logic for this job type.
It might seem redundant to create new Doc objects for an unsaved
job's documents, but in most cases the Doc objects passed to the
constructor will only have document IDs, and no version information.
We can't really get the date/time cutoff used to pick the right
version without creating a new object.
"""
if not hasattr(self, "_docs"):
docs = []
if self.id:
query = Query("pub_proc_doc", "doc_id", "doc_version")
query.where(query.Condition("pub_proc", self.id))
for doc_id, version in query.execute(self.cursor).fetchall():
docs.append(Doc(self.session, id=doc_id, version=version))
else:
cutoff = self.parms.get("MaxDocUpdatedDate")
if not cutoff or cutoff == "JobStartDateTime":
cutoff = self.started
opts = dict(before=cutoff)
for requested in self.__opts.get("docs", []):
opts["id"] = requested.id
if self.force:
opts["version"] = "last"
elif requested.version:
if not (self.permissive or requested.publishable):
args = requested.cdr_id, requested.version
message = "{}V{} is not publishable".format(*args)
raise Exception(message)
opts["version"] = requested.version
else:
opts["version"] = "lastp"
try:
doc = Doc(self.session, **opts)
if not self.force and doc.active_status != "A":
raise Exception("{} is blocked".format(doc.id))
docs.append(doc)
except Exception as e:
raise Exception("{}: {}".format(requested.cdr_id, e))
self._docs = docs
return self._docs
def __init__(self):
"""Assemble the dictionary of all control value groups."""
groups = {}
query = Query("ctl", "grp", "name", "val", "comment")
query.where("inactivated IS NULL")
for row in query.execute().fetchall():
key = row.grp.lower()
group = groups.get(key)
if group is None:
group = groups[key] = self.Group(row.grp, key)
value = self.Value(row.name, row.val, row.comment)
group.values[value.key] = value
self.groups = groups
def build_tables(self):
"""Show the documents the user has locked."""
fields = "c.dt_out", "t.name", "d.id", "d.title"
query = Query("usr u", *fields).order(*fields[:3])
query.join("checkout c", "c.usr = u.id")
query.join("document d", "d.id = c.id")
query.join("doc_type t", "t.id = d.doc_type")
query.where("c.dt_in IS NULL")
query.where(query.Condition("u.id", self.user.id))
rows = []
for dt_out, doc_type, doc_id, title in query.execute(self.cursor):
doc_id = Reporter.Cell(doc_id, center=True)
rows.append([str(dt_out)[:19], doc_type, doc_id, title])
caption = f"Checked out by {self.user.fullname or self.user.name}"
return Reporter.Table(rows, caption=caption, columns=self.COLUMNS)
def output_dir(self):
"""
Destination location for the exported documents
"""
if not hasattr(self, "_output_dir"):
if self.id:
query = Query("pub_proc", "output_dir")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
self._output_dir = row.output_dir.replace("\\", "/")
else:
self._output_dir = None
return self._output_dir
def lockers(self):
"""Get sequence of id/name pairs for users with locked documents."""
if not hasattr(self, "_lockers"):
fields = "COUNT(*) AS n", "u.id", "u.name", "u.fullname"
query = Query("usr u", *fields)
query.join("checkout c", "c.usr = u.id")
query.join("document d", "d.id = c.id")
query.group(*fields[1:])
query.where("c.dt_in IS NULL")
users = []
for row in query.execute(self.cursor):
name = row.fullname or row.name
display = f"{name} ({row.n} locks)"
users.append((name.lower(), row.id, display))
self._lockers = [(uid, label) for key, uid, label in sorted(users)]
return self._lockers
def __find_pending_job(self):
"""
See if we've already got a job of this type in progress
Used to prevent having two or more of the same publishing job
type in flight at the same time.
Return:
True if there's already another job of this type in progress
"""
query = Query("pub_proc", "id").limit(1)
query.where(query.Condition("pub_system", self.system.id))
query.where(query.Condition("pub_subset", self.subsystem.name))
query.where("status NOT IN ('Success', 'Failure')")
row = query.execute(self.cursor).fetchone()
return row.id if row else None
def completed(self):
"""
Date/time when the job finished
"""
if not hasattr(self, "_completed"):
if self.id:
query = Query("pub_proc", "completed")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
self._completed = row.completed
else:
self._completed = None
if isinstance(self._completed, datetime.datetime):
self._completed = self._completed.replace(microsecond=0)
return self._completed
def no_output(self):
"""
Flag indicating that document output won't be written to disk
"""
if not hasattr(self, "_no_output"):
if "no_output" in self.__opts:
self._no_output = self.__opts["no_output"]
elif self.id:
query = Query("pub_proc", "no_output")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
self._no_output = row.no_output == "Y"
else:
self._no_output = False
return self._no_output
def started(self):
"""
When the job was created (so a bit of a misnomer)
"""
if not hasattr(self, "_started"):
if self.id:
query = Query("pub_proc", "started")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception("Job {} not found".format(self.id))
self._started = row.started
else:
self._started = datetime.datetime.now()
if isinstance(self._started, datetime.datetime):
self._started = self._started.replace(microsecond=0)
return self._started
def rule_id(self):
"""
Primary key of row in the `query_term_rule` table (or None)
See notes above about the custom rule mechanism, which AFAIK
has never been used.
"""
if not hasattr(self, "_rule_id"):
if not self.rule:
self._rule_id = None
else:
query = Query("query_term_rule", "id")
query.where(query.Condition("name", self.rule))
row = query.execute(self.session.cursor).fetchone()
if not row:
raise Exception(f"Unknown query term rule: {self.rule}")
self._rule_id = row.id
return self._rule_id
def get_rules(cls, session):
"""
Find the available query term rules
Used by the user interface for managing search path definitions.
See notes above in the documentation for the `QueryTermDef` class
on the custom rule mechanism, which AFAIK has never been used.
Required positional argument:
session - reference to object for current login
Called by:
cdr.listQueryTermRules()
client XML wrapper command CdrListQueryTermRules
"""
session.log("QueryTermDef.get_rules()")
query = Query("query_term_rule", "name").order("name")
return [row.name for row in query.execute(session.cursor).fetchall()]
def email(self):
"""
String for the email address(es) to which processing notifications go
"""
if not hasattr(self, "_email"):
if "email" in self.__opts:
self._email = self.__opts["email"]
if isinstance(self._email, (list, tuple)):
self._email = ",".join(self._email)
elif self.id:
query = Query("pub_proc", "email")
query.where(query.Condition("id", self.id))
row = query.execute(self.cursor).fetchone()
if not row:
raise Exception(f"Job {self.id} not found")
self._email = row.email
else:
self._email = None
return self._email
def get_definitions(cls, session):
"""
Fetch the list of CDR query term definitions
Required positional argument:
session - reference to object for current login
Called by:
cdr.listQueryTermDefs()
client XML wrapper command CdrListQueryTermDefs
Return:
sequence of `QueryTermDef` objects
"""
session.log("QueryTermDef.get_definitions()")
query = Query("query_term_def d", "d.path", "r.name")
query.outer("query_term_rule r", "r.id = d.term_rule")
query.order("d.path", "r.name")
definitions = []
for row in query.execute(session.cursor).fetchall():
definitions.append(QueryTermDef(session, row.path, row.name))
return definitions
def _term_sets(self):
"""
Collect named sets of CDR terms
Parameters:
SetType - optional string restricting report to term sets
whose type name matches the pattern passed
(any wildcards in the pattern must be included,
the report code does not wrap the string in a
pair of wildcards); as of this writing, this
parameter is of limited use, as all of the
existing term sets have the set type of
"diagnosis macro"
Return:
XML document node with the following structure:
ReportBody
ReportName
TermSet*
Name
Members [string of CDR term IDs]
"""
query = Query("doc_version v", "v.id", "MAX(v.num) AS num")
query.join("query_term_pub t", "t.doc_id = v.id")
query.where("t.path = '/TermSet/TermSetType'")
query.where("v.publishable = 'Y'")
query.group("v.id")
pattern = self.__opts.get("SetType")
if pattern:
query.where(query.Condition("t.value", pattern, "LIKE"))
body = self.__start_body()
for id, num in query.execute(self.cursor).fetchall():
doc = Doc(self.session, id=id, version=num)
result = doc.filter("name:Get TermSet Name and Members")
body.append(result.result_tree.getroot())
return body
def add(self):
"""
Store the new query term definition
Called by:
cdr.addQueryTermDef()
client XML wrapper command CdrAddQueryTermDef
"""
self.session.log(f"QueryTermDef.add({self.path!r}, {self.rule!r})")
if not self.session.can_do("ADD QUERY TERM DEF"):
message = "User not authorized to add query term definitions"
raise Exception(message)
if not self.path:
raise Exception("Missing required path")
query = Query("query_term_def", "COUNT(*) AS n")
query.where(query.Condition("path", self.path))
if query.execute(self.session.cursor).fetchone().n > 0:
raise Exception("Duplicate query term definition")
names = "path, term_rule"
values = self.path, self.rule_id
insert = f"INSERT INTO query_term_def ({names}) VALUES (?, ?)"
self.session.cursor.execute(insert, values)
self.session.conn.commit()
#!/usr/bin/env python
"""Get one XML document from pub_proc_cg to stdout.
If your document has non-ascii characters in it it may not work well
to try and pipe the output to a tool which expects ascii to be coming
from stdout. Consider instead using the --save option and loading the
encoded document directly into your tool.
"""
from argparse import ArgumentParser
from cdrapi.db import Query
parser = ArgumentParser()
parser.add_argument("id", type=int)
parser.add_argument("--tier")
parser.add_argument("--save", action="store_true")
opts = parser.parse_args()
query = Query("pub_proc_cg", "xml")
query.where(query.Condition("id", opts.id))
row = query.execute().fetchone()
if not row:
raise Exception(f"CDR{opts.id:d} not found in pub_proc_cg")
if opts.save:
with open(f"pub_proc_cg-{opts.id:d}.xml", "wb") as fp:
fp.write(row.xml.encode("utf-8"))
else:
print(row.xml)
def _menu_term_tree(self):
"""
Report on the menu term hierarchy
Parameters:
MenuType - required string restricting report to a single menu type
Return:
XML document node with the following structure:
ReportBody
ReportName
MenuItem*
TermId
TermName
MenuType
MenuStatus
DisplayName?
ParentId?
SortString
"""
menutype = self.__opts.get("MenuType", "%")
operand = "LIKE" if "%" in menutype else "="
fields = ("n.doc_id AS id", "n.value AS name", "t.value AS type",
"s.value AS status", "d.value AS display",
"p.int_val AS parent", "k.value AS sort_key")
i_path = "/Term/MenuInformation/MenuItem"
n_path = "/Term/PreferredName"
t_path = "{}/MenuType".format(i_path)
s_path = "{}/MenuStatus".format(i_path)
d_path = "{}/DisplayName".format(i_path)
p_path = "{}/MenuParent/@cdr:ref".format(i_path)
k_path = "{}/@SortOrder".format(i_path)
query = Query("query_term n", *fields).unique().order("n.doc_id")
query.join("query_term t", "t.doc_id = n.doc_id")
query.join("query_term s", "s.doc_id = t.doc_id",
"LEFT(s.node_loc, 8) = LEFT(t.node_loc, 8)")
query.outer("query_term d", "d.doc_id = t.doc_id",
"d.path = '{}'".format(d_path),
"LEFT(d.node_loc, 8) = LEFT(t.node_loc, 8)")
query.outer("query_term p", "p.doc_id = t.doc_id",
"p.path = '{}'".format(p_path),
"LEFT(p.node_loc, 8) = LEFT(t.node_loc, 8)")
query.outer("query_term k", "k.doc_id = t.doc_id",
"k.path = '{}'".format(k_path),
"LEFT(k.node_loc, 8) = LEFT(t.node_loc, 8)")
query.where("n.path = '{}'".format(n_path))
query.where("t.path = '{}'".format(t_path))
query.where("s.path = '{}'".format(s_path))
query.where(query.Condition("t.value", menutype, operand))
query.where(query.Condition("s.value", "Offline", "<>"))
body = self.__start_body()
for row in query.execute(self.cursor).fetchall():
sort_key = row.sort_key if row.sort_key is not None else row.name
wrapper = etree.SubElement(body, "MenuItem")
etree.SubElement(wrapper, "TermId").text = str(row.id)
etree.SubElement(wrapper, "TermName").text = row.name
etree.SubElement(wrapper, "MenuType").text = row.type
etree.SubElement(wrapper, "MenuStatus").text = row.status
if row.display is not None:
etree.SubElement(wrapper, "DisplayName").text = row.display
if row.parent is not None:
etree.SubElement(wrapper, "ParentId").text = str(row.parent)
etree.SubElement(wrapper, "SortString").text = sort_key
return body