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ClinicalTrialsDataProcessing/scripts/drugtools/historical_nct_extractor.py

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from collections import namedtuple
from copy import copy
from datetime import datetime
from bs4 import BeautifulSoup
from drugtools.env_setup import ENV,postgres_conn
from tqdm import tqdm
#requires Python 3.10
#### GLOBALS
VERBOSE = True if ENV["VERBOSE"] == "True" else False
###CLASSES AND CONSTRUCTORS
TagDatePair = namedtuple("TagDatePair", ["tag","date"])
TagTextPair = namedtuple("TagTextPair", ["tag","text"])
#superclasses
class VersionData():
"""
This class holds two types of data:
- Data with a 1-to-1 relationship with the trial/version pair.
- Data with a child relationship with the trial/version pair.
This initializes with None attributes, and implements setter
methods to load them (just to double check types)
That way I can just pass around the VersionData instance
and add data as I go.
It will also implement the ability to load the data to the database
"""
def __init__(self,nct_id,version_id,submission_date):
#identifiers
self.nct_id = nct_id.strip()
self.version_id = version_id
self.submission_date = submission_date
#Study Status
self._primary_completion_date = None
self._primary_completion_date_category = None
self._start_date = None
self._start_date_category = None
self._completion_date = None
self._completion_date_category = None
self._overall_status = None
self._enrollment = None
self._enrollment_category = None
self._sponsor = None
#self._sponsor_category = None #I don't believe this is included in the raw data
self._responsible_party = None
#self._responsible_party_category = None #I don't believe this is included in the raw data
#self._collaborators = None #currently going to ignore as I've not fount it in AACT
def load_to_db(self,db_connection):
#load to initial table, then load any extra details into other tables
sql = """
INSERT INTO history.trial_snapshots
(
nct_id,
version,
submission_date,
primary_completion_date,
primary_completion_date_category,
start_date,
start_date_category,
completion_date,
completion_date_category,
overall_status,
enrollment,
enrollment_category,
sponsor,
responsible_party
)
VALUES
(
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s,
%s
)
"""
with db_connection.cursor() as db_cursor:
try:
db_cursor.execute(
sql,
(
self.nct_id,
self.version_id,
self.submission_date,
self._primary_completion_date,
self._primary_completion_date_category,
self._start_date,
self._start_date_category,
self._completion_date,
self._completion_date_category,
self._overall_status,
self._enrollment,
self._enrollment_category,
self._sponsor,
self._responsible_party
)
)
except Exception as err:
#catch any error, print the applicable information, and raise the error.
print(self)
raise err
db_connection.commit()
############ Functions
def extract_submission_dates(soup):
"""
Extract dates for each version
"""
table_rows = soup.findChildren("fieldset")[0].table.tbody.findChildren("tr")
version_date_dict = {}
for row in table_rows:
# if it is <td headers="VersionNumber">xx</td> then it contains what we need.
version_number = None
version_date = None
for td in row.findChildren("td"):
if ("headers" in td.attrs):
if (td.attrs["headers"][0]=="VersionNumber"):
version_number = int(td.text)
elif (td.attrs["headers"][0]=="VersionDate"):
version_date = datetime.strptime(td.text.strip() , "%B %d, %Y")
version_date_dict[version_number] = version_date
return version_date_dict
def optional_strip(possible_string):
if type(possible_string) == str:
return possible_string.strip()
else:
return possible_string
def extract_study_statuses(study_status_form, version_a,version_b):
"""
This extracts data from a study_status form and returns one or two
StudyStatusData objects,
"""
#get rows
rows = study_status_form.table.tbody.find_all("tr")
#iterate through rows,
for trow in rows:
#matching on rowLabels
match tr_to_td(trow):
case ["Primary Completion:" as row_label, old,new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
tagdate1 = extract_date_and_tag(old.text)
version_a._primary_completion_date = tagdate1.date
version_a._primary_completion_date_category = optional_strip(tagdate1.tag)
tagdate2 = extract_date_and_tag(new.text)
version_b._primary_completion_date = tagdate2.date
version_b._primary_completion_date_category = optional_strip(tagdate2.tag)
case ["Study Start:" as row_label, old, new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
tagdate1 = extract_date_and_tag(old.text)
version_a._start_date = tagdate1.date
version_a._start_date_category = optional_strip(tagdate1.tag)
tagdate2 = extract_date_and_tag(new.text)
version_b._start_date = tagdate2.date
version_b._start_date_category = optional_strip(tagdate2.tag)
case ["Study Completion:" as row_label, old,new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
tagdate1 = extract_date_and_tag(old.text)
version_a._completion_date = tagdate1.date
version_a._completion_date_category = optional_strip(tagdate1.tag)
tagdate2 = extract_date_and_tag(new.text)
version_b._completion_date = tagdate2.date
version_b._completion_date_category = optional_strip(tagdate2.tag)
case ["Overall Status:" as row_label, old,new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
#split out any notes such as "Suspended [reason for suspenstion ]"
version_a._overall_status = optional_strip(old.text.split("[")[0])
#split out any notes such as "Suspended [reason for suspenstion ]"
version_b._overall_status = optional_strip(new.text.split("[")[0])
#FIX: There is an issue with NCT00789633 where the overall status includes information as to why it was suspended.
case _ as row_label:
print("row not matched: {}".format(row_label)) if VERBOSE else ""
def extract_study_design(study_status_form, version_a,version_b):
"""
This extracts data from a study_status form and returns one or two
StudyStatusData objects,
"""
#get rows
rows = study_status_form.table.tbody.find_all("tr")
#iterate through rows,
for trow in rows:
#matching on rowLabels
match tr_to_td(trow):
case ["Enrollment:" as row_label, old, new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
#Extract tag and text, add them to preallocated object
tagtext1 = extract_text_and_tag(old.text)
version_a._enrollment = tagtext1.text
version_a._enrollment_category = optional_strip(tagtext1.tag)
tagtext2 = extract_text_and_tag(new.text)
version_b._enrollment = tagtext2.text
version_b._enrollment_category = optional_strip(tagtext2.tag)
case _ as row_label:
print("row not matched: {}".format(row_label)) if VERBOSE else ""
def extract_sponsor_data(study_status_form, version_a,version_b):
"""
This extracts data from a study_status form and returns one or two
StudyStatusData objects,
"""
#get rows
rows = study_status_form.table.tbody.find_all("tr")
#iterate through rows,
for trow in rows:
#matching on rowLabels
match tr_to_td(trow):
case ["Sponsor:" as row_label, old, new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
version_a._sponsor = optional_strip(old.text)
version_b._sponsor = optional_strip(new.text)
case ["Responsible Party:" as row_label, old, new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
version_a._responsible_party = optional_strip(old.text)
version_b._responsible_party = optional_strip(new.text)
case ["Collaborators:" as row_label, old, new]:
print("row matched: {}".format(row_label)) if VERBOSE else ""
#TODO: find a trial with multiple collaborators and figure out how to identify/count them:w
# So far can't figure out where this is in AACT, so I'm going to ignore it.
pass
case _ as row_label:
print("row not matched: {}".format(row_label)) if VERBOSE else ""
def split_by_version(tag):
'''
OUTDATED: With the new format that separates old and new versions, I don't technically need this. It is a nice place to identify exact changes if those are every needed though and it removes the highlights cleanly.
'''
#clone elements and remove sub-tags that are not needed.
old = copy(tag)
for span in old.find_all(class_="add_hilite"):
span.extract()
new = copy(tag)
for span in new.find_all(class_="drop_hilite"):
span.extract()
return old,new
def extract_date_and_tag(text):
"""
Extracts a datetype according to the date format
and the estimate tag based on
"""
text = text.strip()
#handle various empty cases
if not text or text == '':
return TagDatePair(None, None)
date_split = text.split("[")
if len(date_split) > 1:
estimate_tag = date_split[1].split("]")[0].strip()
else:
estimate_tag = None
try:
date_object = datetime.strptime(date_split[0].strip(), date_MMMM_YYYY)
except ValueError as ve:
date_object = datetime.strptime(date_split[0].strip(), date_MMMM_DD_YYYY)
return TagDatePair(estimate_tag, date_object)
def extract_text_and_tag(text):
"""
Extracts a datetype according to the date format
and the estimate tag based on
"""
text = text.strip()
#handle various empty cases
if not text or text == '':
return TagTextPair(None, None)
date_split = text.split("[")
if len(date_split) > 1:
estimate_tag = date_split[1].split("]")[0].strip()
else:
estimate_tag = None
text_object = date_split[0].strip()
return TagTextPair(estimate_tag, text_object)
### FUNCTIONS
def tr_to_td(tr) -> tuple[str, str, str]:
"""
Takes an html data row of interest, extracts the record_name from the first <td>, and the data from the second <td>.
For the data, it just extracts the text.
The text itself then needs processed separately, based on what it should contain.
"""
#get list of cells
td_list = tr.find_all("td")
if len(td_list) == 3:
return td_list[0].text, td_list[1], td_list[2]
else:
return None, None, None
def get_forms(soup,version_a,version_b):
#extract all forms
for form in soup.body.find_all("form"):
#Match forms against ID types
if not "id" in form.attrs:
continue
#for each type of form (identified by the ID field)
# extract and add the data to the preallocated objects
match form.attrs["id"]:
case "form_StudyStatus":
extract_study_statuses(form,version_a,version_b)
case "form_SponsorCollaborators":
extract_sponsor_data(form, version_a, version_b)
case "form_Oversight":
pass
case "form_StudyDescription":
pass
case "form_Conditions":
pass
case "form_StudyDesign":
extract_study_design(form,version_a,version_b)
case "form_ArmsandInterventions":
pass
case "form_ProtocolOutcomeMeasures":
pass
case "form_Eligibility":
pass
case "form_ContactsLocations":
pass
case "form_IPDSharing":
pass
case "form_References":
pass
case "form_ParticipantFlow":
pass
case "form_BaselineCharacteristics":
pass
case "form_ROutcomeMeasures":
pass
case "form_AdverseEvents":
pass
case "form_LimitationsandCaveats":
pass
case "form_MoreInformation":
pass
case _ as form_name:
print("form not matched: {}".format(form_name)) if VERBOSE else ""
### CONSTANTS
date_MMMM_YYYY = "%B %Y"
date_MMMM_DD_YYYY = "%B %d, %Y"
def get_data_from_versions(nct_id,html, version_a_int, version_b_int):
soup = BeautifulSoup(html,"lxml")
version_date_dict = extract_submission_dates(soup)
#preallocate version data
version_a = VersionData(nct_id, version_a_int, version_date_dict.get(version_a_int))
version_b = VersionData(nct_id, version_b_int, version_date_dict.get(version_b_int))
#extract data from html and put it in the preallocated objects
get_forms(soup, version_a, version_b)
return version_a,version_b
def run():
with postgres_conn() as db_connection:
#pull the requests from the db
with db_connection.cursor() as curse:
sql = """
SELECT nct_id, version_a,version_b, html
FROM http.responses
WHERE response_code = 200
"""
curse.execute(sql)
for response in tqdm(curse.fetchall()):
nct_id, version_a, version_b, html = response
print(nct_id, version_a, version_b) if VERBOSE else ""
version1, version2 = get_data_from_versions(nct_id, html, version_a, version_b)
if version_b == version_a + 1:
version1.load_to_db(db_connection)
version2.load_to_db(db_connection)
else:
version2.load_to_db(db_connection)
if __name__ == "__main__":
run()
"""
Documentation:
TO add a new field to extraction-lib
1. Locate the field in the HTML
- form id (e.g. <form id="form_StudyStatus> gives the form id "form_StudyStatus)
- Table row's data label. This corresponds to the text of first column in the row and will
look something like
<td class="rowLabel" style="min-width: 210px;">Record Verification:</td>.
"Record Verification:" is the data label in the example above.
2. Identify what data you will be extracting
- type (date, text, int, etc)
- if it contains a category ([Actual] vs [Anticipated] etc)
3. Add data to:
- sql table: history.trial_snapshots
- the VersionData class
- the VersionData.load_to_db() function
4. Ensure the field matcher in `get_forms(*)` is matching on the form ID and has a function processing the form
5. Ensure the function processing the form has a match entry to proceess the row
- This should match on data label and then process the data by
- splitting into old and new versions
- Extracting the data for both old and new
- add the data to the passed VersionData objects
"""
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