text stringlengths 1 93.6k |
|---|
pidSeqMap = {}
|
for pid, admIdList in pidAdmMap.iteritems():
|
if len(admIdList) < 2: continue
|
sortedList = sorted([(admDateMap[admId], admDxMap[admId]) for admId in admIdList])
|
pidSeqMap[pid] = sortedList
|
print 'Building pids, dates, strSeqs'
|
pids = []
|
dates = []
|
seqs = []
|
for pid, visits in pidSeqMap.iteritems():
|
pids.append(pid)
|
seq = []
|
date = []
|
for visit in visits:
|
date.append(visit[0])
|
seq.append(visit[1])
|
dates.append(date)
|
seqs.append(seq)
|
print 'Converting strSeqs to intSeqs, and making types'
|
types = {}
|
newSeqs = []
|
for patient in seqs:
|
newPatient = []
|
for visit in patient:
|
newVisit = []
|
for code in visit:
|
if code in types:
|
newVisit.append(types[code])
|
else:
|
types[code] = len(types)
|
newVisit.append(types[code])
|
newPatient.append(newVisit)
|
newSeqs.append(newPatient)
|
pickle.dump(pids, open(outFile+'.pids', 'wb'), -1)
|
pickle.dump(dates, open(outFile+'.dates', 'wb'), -1)
|
pickle.dump(newSeqs, open(outFile+'.seqs', 'wb'), -1)
|
pickle.dump(types, open(outFile+'.types', 'wb'), -1)
|
# <FILESEP>
|
from dataclasses import dataclass
|
import html
|
from importlib import import_module
|
from operator import attrgetter
|
import re
|
from typing import List, Optional, TextIO, Type
|
from pydoc_markdown.interfaces import Context, SourceLinker
|
from pydoc_markdown.contrib.loaders.python import PythonLoader
|
from pydoc_markdown.contrib.renderers.markdown import (
|
MarkdownRenderer,
|
MarkdownReferenceResolver,
|
)
|
from pydoc_markdown.contrib.processors.google import GoogleProcessor
|
from pydoc_markdown.contrib.processors.filter import FilterProcessor
|
from pydoc_markdown.contrib.processors.crossref import CrossrefProcessor
|
from pydoc_markdown.util.docspec import ApiSuite
|
import docspec_python
|
import docspec
|
slugify = re.compile(r"[^a-zA-Z0-9_\-]")
|
dedup = re.compile(r"(-)\1+")
|
WHITELIST = ("__init__",)
|
class MayimRenderer(MarkdownRenderer):
|
def _render_recursive(
|
self, fp: TextIO, level: int, obj: docspec.ApiObject
|
):
|
self._render_object(fp, level, obj)
|
level += 1
|
members = sorted(getattr(obj, "members", []), key=attrgetter("name"))
|
for member in members:
|
self._render_recursive(fp, level, member)
|
def _render_object(self, fp: TextIO, level: int, obj: docspec.ApiObject):
|
if isinstance(obj, docspec.Indirection):
|
if obj.parent and obj.parent.name == "mayim":
|
self._render_root_level_object(fp, level, obj)
|
else:
|
super()._render_object(fp, level, obj)
|
if isinstance(obj, docspec.Class):
|
assert isinstance(obj.parent, docspec.Module)
|
module = import_module(obj.parent.name)
|
cls = getattr(module, obj.name)
|
resolver = MayimMarkdownReferenceResolver(global_=True)
|
parent_links = []
|
for base in cls.__mro__:
|
resolved = None
|
fullname = f"{base.__module__}.{base.__qualname__}"
|
if fullname.startswith("mayim") and base.__name__ != obj.name:
|
resolved = resolver.resolve_reference(
|
suite, obj, fullname, [docspec.Indirection]
|
)
|
if resolved:
|
module_name, member_name = self._resolve_name(
|
resolved
|
).rsplit(".", 1)
|
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