sartography
/
protocol-builder-mock
mirror of https://github.com/sartography/protocol-builder-mock.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
protocol-builder-mock/pb/models.py

300 lines
15 KiB
Python
Raw Blame History

from marshmallow import fields
from sqlalchemy import func
from pb import db, ma
class Sponsor(db.Model):
SPONSOR_ID = db.Column(db.Integer, primary_key=True)
SP_NAME = db.Column(db.String, nullable=True)
SP_MAILING_ADDRESS = db.Column(db.String, nullable=True)
SP_PHONE = db.Column(db.String, nullable=True)
SP_FAX = db.Column(db.String, nullable=True)
SP_EMAIL = db.Column(db.String, nullable=True)
SP_HOMEPAGE = db.Column(db.String, nullable=True)
COMMONRULEAGENCY = db.Column(db.Boolean, nullable=True)
SP_TYPE = db.Column(db.String, nullable=True)
SP_TYPE_GROUP_NAME = db.Column(db.String, nullable=True)
@staticmethod
def all_types():
types = [
Sponsor(SP_TYPE="Federal", SP_TYPE_GROUP_NAME="Government"),
Sponsor(SP_TYPE="Foundation/Not for Profit", SP_TYPE_GROUP_NAME="Other External Funding"),
Sponsor(SP_TYPE="Incoming Sub Award", SP_TYPE_GROUP_NAME="Government"),
Sponsor(SP_TYPE="Industry", SP_TYPE_GROUP_NAME="Industry"),
Sponsor(SP_TYPE="Internal/Departmental/Gift", SP_TYPE_GROUP_NAME="Internal Funding"),
Sponsor(SP_TYPE="No Funding", SP_TYPE_GROUP_NAME="Internal Funding"),
Sponsor(SP_TYPE="Other Colleges and Universities", SP_TYPE_GROUP_NAME="Other External Funding"),
Sponsor(SP_TYPE="State", SP_TYPE_GROUP_NAME="Government"),
]
return types
@staticmethod
def get_type_group_name(type_code):
for t in Sponsor.all_types():
if t.SP_TYPE == type_code:
return t.SP_TYPE_GROUP_NAME
class SponsorSchema(ma.Schema):
class Meta:
fields = ("SPONSOR_ID", "SP_NAME", "SP_MAILING_ADDRESS",
"SP_PHONE", "SP_FAX", "SP_EMAIL", "SP_HOMEPAGE",
"COMMONRULEAGENCY", "SP_TYPE")
class StudySponsor(db.Model):
id = db.Column(db.Integer, primary_key=True)
SS_STUDY = db.Column(db.Integer, db.ForeignKey('study.STUDYID'))
SPONSOR_ID = db.Column(db.Integer, db.ForeignKey('sponsor.SPONSOR_ID'))
study = db.relationship("Study", back_populates="sponsors")
sponsor = db.relationship("Sponsor")
class StudySponsorSchema(ma.Schema):
class Meta:
fields = ("SS_STUDY", "SPONSOR_ID", "SP_NAME", "SP_TYPE", "SP_TYPE_GROUP_NAME", "COMMONRULEAGENCY")
SP_TYPE = fields.Function(lambda obj: obj.sponsor.SP_TYPE)
SP_NAME = fields.Function(lambda obj: obj.sponsor.SP_NAME)
SP_TYPE_GROUP_NAME = fields.Function(lambda obj: obj.sponsor.SP_TYPE_GROUP_NAME)
COMMONRULEAGENCY = fields.Function(lambda obj: obj.sponsor.COMMONRULEAGENCY)
class Study(db.Model):
STUDYID = db.Column(db.Integer, primary_key=True)
HSRNUMBER = db.Column(db.String())
TITLE = db.Column(db.Text(), nullable=False)
NETBADGEID = db.Column(db.String(), nullable=False)
DATE_MODIFIED = db.Column(db.DateTime(timezone=True), default=func.now())
Q_COMPLETE = db.relationship("IRBStatus", backref="study", lazy='dynamic')
irb_info = db.relationship("IRBInfo", backref="study", lazy='dynamic')
requirements = db.relationship("RequiredDocument", backref="study", lazy='dynamic')
investigators = db.relationship("Investigator", backref="study", lazy='dynamic')
study_details = db.relationship("StudyDetails", uselist=False, backref="study")
sponsors = db.relationship("StudySponsor", back_populates="study", cascade="all, delete, delete-orphan")
class StudySchema(ma.Schema):
class Meta:
# Fields to expose
fields = ("STUDYID", "HSRNUMBER", "TITLE", "NETBADGEID",
"DATE_MODIFIED")
class IRBInfo(db.Model):
SS_STUDY_ID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
UVA_STUDY_TRACKING = db.Column(db.String(), nullable=False, default='')
DATE_MODIFIED = db.Column(db.Date, nullable=True)
IRB_ADMINISTRATIVE_REVIEWER = db.Column(db.String(), nullable=False, default='')
AGENDA_DATE = db.Column(db.Date, nullable=True)
IRB_REVIEW_TYPE = db.Column(db.String(), nullable=False, default='')
IRBEVENT = db.Column(db.String(), nullable=False, default='')
IRB_STATUS = db.Column(db.String(), nullable=False, default='')
IRB_OF_RECORD = db.Column(db.String(), nullable=False, default='')
UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES = db.Column(db.Integer(), nullable=True)
STUDYIRBREVIEWERADMIN = db.Column(db.String(), nullable=False, default='')
class IRBInfoSchema(ma.Schema):
class Meta:
# Fields to expose
fields = ("UVA_STUDY_TRACKING", "DATE_MODIFIED", "IRB_ADMINISTRATIVE_REVIEWER",
"AGENDA_DATE", "IRB_REVIEW_TYPE", "IRBEVENT", "IRB_STATUS", "IRB_OF_RECORD",
"UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES", "STUDYIRBREVIEWERADMIN")
class Investigator(db.Model):
id = db.Column(db.Integer, primary_key=True)
STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'))
NETBADGEID = db.Column(db.String(), nullable=False)
INVESTIGATORTYPE = db.Column(db.String(), nullable=False)
INVESTIGATORTYPEFULL = db.Column(db.String(), nullable=False)
@staticmethod
def all_types():
types = [
Investigator(INVESTIGATORTYPE="PI", INVESTIGATORTYPEFULL="Primary Investigator"),
Investigator(INVESTIGATORTYPE="SI", INVESTIGATORTYPEFULL="Sub Investigator"),
Investigator(INVESTIGATORTYPE="DC", INVESTIGATORTYPEFULL="Department Contact"),
Investigator(INVESTIGATORTYPE="SC_I", INVESTIGATORTYPEFULL="Study Coordinator 1"),
Investigator(INVESTIGATORTYPE="SC_II", INVESTIGATORTYPEFULL="Study Coordinator 2"),
Investigator(INVESTIGATORTYPE="AS_C", INVESTIGATORTYPEFULL="Additional Study Coordinators"),
Investigator(INVESTIGATORTYPE="DEPT_CH", INVESTIGATORTYPEFULL="Department Chair"),
Investigator(INVESTIGATORTYPE="IRBC", INVESTIGATORTYPEFULL="IRB Coordinator"),
]
return types
def set_type(self, type_code):
self.INVESTIGATORTYPE = type_code
for t in self.all_types():
if t.INVESTIGATORTYPE == type_code:
self.INVESTIGATORTYPEFULL = t.INVESTIGATORTYPEFULL
class InvestigatorSchema(ma.Schema):
class Meta:
fields = ("NETBADGEID", "INVESTIGATORTYPE", "INVESTIGATORTYPEFULL")
class RequiredDocument(db.Model):
id = db.Column(db.Integer, primary_key=True)
AUXDOCID = db.Column(db.String(), nullable=False, default="")
AUXDOC = db.Column(db.String(), nullable=False, default="")
STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'))
@staticmethod
def all():
docs = [RequiredDocument(AUXDOCID=1, AUXDOC="Investigators Brochure"),
RequiredDocument(AUXDOCID=6, AUXDOC="Cancer Center's PRC Approval Form"),
RequiredDocument(AUXDOCID=8, AUXDOC="SOM CTO IND/IDE Review Letter"),
RequiredDocument(AUXDOCID=9, AUXDOC="HIRE Approval"),
RequiredDocument(AUXDOCID=10, AUXDOC="Cancer Center's PRC Approval Waiver"),
RequiredDocument(AUXDOCID=12, AUXDOC="Certificate of Confidentiality Application"),
RequiredDocument(AUXDOCID=14, AUXDOC="Institutional Biosafety Committee Approval"),
RequiredDocument(AUXDOCID=18, AUXDOC="SOM CTO Approval Letter - UVA PI Multisite Trial"),
RequiredDocument(AUXDOCID=20,
AUXDOC="IRB Approval or Letter of Approval from Administration: Study Conducted at non- UVA Facilities "),
RequiredDocument(AUXDOCID=21, AUXDOC="New Medical Device Form"),
RequiredDocument(AUXDOCID=22, AUXDOC="SOM CTO Review regarding need for IDE"),
RequiredDocument(AUXDOCID=23, AUXDOC="SOM CTO Review regarding need for IND"),
RequiredDocument(AUXDOCID=25, AUXDOC="Scientific Pre-review Documentation"),
RequiredDocument(AUXDOCID=26, AUXDOC="IBC Number"),
RequiredDocument(AUXDOCID=32, AUXDOC="IDS - Investigational Drug Service Approval"),
RequiredDocument(AUXDOCID=36, AUXDOC="RDRC Approval "),
RequiredDocument(AUXDOCID=40, AUXDOC="SBS/IRB Approval-FERPA"),
RequiredDocument(AUXDOCID=41, AUXDOC="HIRE Standard Radiation Language"),
RequiredDocument(AUXDOCID=42, AUXDOC="COI Management Plan "),
RequiredDocument(AUXDOCID=43, AUXDOC="SOM CTO Approval Letter-Non UVA, Non Industry PI MultiSite Study"),
RequiredDocument(AUXDOCID=44, AUXDOC="GRIME Approval"),
RequiredDocument(AUXDOCID=45, AUXDOC="GMEC Approval"),
RequiredDocument(AUXDOCID=46, AUXDOC="IRB Reliance Agreement Request Form- IRB-HSR is IRB of Record"),
RequiredDocument(AUXDOCID=47, AUXDOC="Non UVA IRB Approval - Initial and Last Continuation"),
RequiredDocument(AUXDOCID=48, AUXDOC="MR Physicist Approval- Use of Gadolinium"),
RequiredDocument(AUXDOCID=49, AUXDOC="SOM CTO Approval- Non- UVA Academia PI of IDE"),
RequiredDocument(AUXDOCID=51, AUXDOC="IDS Waiver"),
RequiredDocument(AUXDOCID=52, AUXDOC="Package Inserts"),
RequiredDocument(AUXDOCID=53, AUXDOC="IRB Reliance Agreement Request Form- IRB-HSR Not IRB of Record"),
RequiredDocument(AUXDOCID=54, AUXDOC="ESCRO Approval"),
RequiredDocument(AUXDOCID=57, AUXDOC="Laser Safety Officer Approval")]
return docs
class RequiredDocumentSchema(ma.Schema):
class Meta:
fields = ("AUXDOCID", "AUXDOC")
class IRBStatus(db.Model):
STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
STATUS = db.Column(db.String(), nullable=False, default="")
DETAIL = db.Column(db.String(), nullable=False, default="")
@staticmethod
def all():
status = [IRBStatus(STATUS="Error", DETAIL="Study ID does not exist."),
IRBStatus(STATUS="Error", DETAIL="General study errors. UVA Study Tracking Number is missing or not formatted correctly."),
IRBStatus(STATUS="No Error", DETAIL="Passed validation.")]
return status
class IRBStatusSchema(ma.Schema):
class Meta:
fields = ("STATUS", "DETAIL")
class StudyDetails(db.Model):
STUDYID = db.Column(db.Integer, db.ForeignKey('study.STUDYID'), primary_key=True)
IS_IND = db.Column(db.Integer, nullable=True)
IND_1 = db.Column(db.String, nullable=True)
IND_2 = db.Column(db.String, nullable=True)
IND_3 = db.Column(db.String, nullable=True)
IS_UVA_IND = db.Column(db.Integer, nullable=True)
IS_IDE = db.Column(db.Integer, nullable=True)
IS_UVA_IDE = db.Column(db.Integer, nullable=True)
IDE = db.Column(db.String, nullable=True)
IS_CHART_REVIEW = db.Column(db.Integer, nullable=True)
IS_RADIATION = db.Column(db.Integer, nullable=True)
GCRC_NUMBER = db.Column(db.String, nullable=True)
IS_GCRC = db.Column(db.Integer, nullable=True)
IS_PRC_DSMP = db.Column(db.Integer, nullable=True)
IS_PRC = db.Column(db.Integer, nullable=True)
PRC_NUMBER = db.Column(db.String, nullable=True)
IS_IBC = db.Column(db.Integer, nullable=True)
IBC_NUMBER = db.Column(db.String, nullable=True)
SPONSORS_PROTOCOL_REVISION_DATE = db.Column(db.Date, nullable=True)
IS_SPONSOR_MONITORING = db.Column(db.Integer, nullable=True)
IS_AUX = db.Column(db.Integer, nullable=True)
IS_SPONSOR = db.Column(db.Integer, nullable=True)
IS_GRANT = db.Column(db.Integer, nullable=True)
IS_COMMITTEE_CONFLICT = db.Column(db.Integer, nullable=True)
DSMB = db.Column(db.String, nullable=True)
DSMB_FREQUENCY = db.Column(db.Integer, nullable=True)
IS_DB = db.Column(db.Integer, nullable=True)
IS_UVA_DB = db.Column(db.Integer, nullable=True)
IS_CENTRAL_REG_DB = db.Column(db.Integer, nullable=True)
IS_CONSENT_WAIVER = db.Column(db.Integer, nullable=True)
IS_HGT = db.Column(db.Integer, nullable=True)
IS_GENE_TRANSFER = db.Column(db.Integer, nullable=True)
IS_TISSUE_BANKING = db.Column(db.Integer, nullable=True)
IS_SURROGATE_CONSENT = db.Column(db.Integer, nullable=True)
IS_ADULT_PARTICIPANT = db.Column(db.Integer, nullable=True)
IS_MINOR_PARTICIPANT = db.Column(db.Integer, nullable=True)
IS_MINOR = db.Column(db.Integer, nullable=True)
IS_BIOMEDICAL = db.Column(db.Integer, nullable=True)
IS_QUALITATIVE = db.Column(db.Integer, nullable=True)
IS_PI_SCHOOL = db.Column(db.Integer, nullable=True)
IS_PRISONERS_POP = db.Column(db.Integer, nullable=True)
IS_PREGNANT_POP = db.Column(db.Integer, nullable=True)
IS_FETUS_POP = db.Column(db.Integer, nullable=True)
IS_MENTAL_IMPAIRMENT_POP = db.Column(db.Integer, nullable=True)
IS_ELDERLY_POP = db.Column(db.Integer, nullable=True)
IS_OTHER_VULNERABLE_POP = db.Column(db.Integer, nullable=True)
OTHER_VULNERABLE_DESC = db.Column(db.String, nullable=True)
IS_MULTI_SITE = db.Column(db.Integer, nullable=True)
IS_UVA_LOCATION = db.Column(db.Integer, nullable=True)
NON_UVA_LOCATION = db.Column(db.String, nullable=True)
MULTI_SITE_LOCATIONS = db.Column(db.String, nullable=True)
IS_OUTSIDE_CONTRACT = db.Column(db.Integer, nullable=True)
IS_UVA_PI_MULTI = db.Column(db.Integer, nullable=True)
IS_NOT_PRC_WAIVER = db.Column(db.Integer, nullable=True)
IS_CANCER_PATIENT = db.Column(db.Integer, nullable=True)
UPLOAD_COMPLETE = db.Column(db.Integer, nullable=True)
IS_FUNDING_SOURCE = db.Column(db.Integer, nullable=True)
IS_PI_INITIATED = db.Column(db.Integer, nullable=True)
IS_ENGAGED_RESEARCH = db.Column(db.Integer, nullable=True)
IS_APPROVED_DEVICE = db.Column(db.Integer, nullable=True)
IS_FINANCIAL_CONFLICT = db.Column(db.Integer, nullable=True)
IS_NOT_CONSENT_WAIVER = db.Column(db.Integer, nullable=True)
IS_FOR_CANCER_CENTER = db.Column(db.Integer, nullable=True)
IS_REVIEW_BY_CENTRAL_IRB = db.Column(db.Integer, nullable=True)
IRBREVIEWERADMIN = db.Column(db.String, nullable=True)
IS_SPONSOR_TRACKING = db.Column(db.Integer, nullable=True)
SPONSOR_TRACKING = db.Column(db.Integer, nullable=True)
IS_DSMB = db.Column(db.Integer, nullable=True)
IS_COMPLETE_NON_IRB_REGULATORY = db.Column(db.Integer, nullable=True)
IS_INSIDE_CONTRACT = db.Column(db.Integer, nullable=True)
IS_CODED_RESEARCH = db.Column(db.Integer, nullable=True)
IS_OUTSIDE_SPONSOR = db.Column(db.Integer, nullable=True)
IS_UVA_COLLABANALYSIS = db.Column(db.Integer, nullable=True)
REVIEW_TYPE = db.Column(db.Integer, nullable=True)
REVIEWTYPENAME = db.Column(db.String, nullable=True)
class StudyDetailsSchema(ma.SQLAlchemyAutoSchema):
class Meta:
model = StudyDetails
load_instance = True
include_relationships = False
class SelectedUser(db.Model):
user_id = db.Column(db.String(), primary_key=True)
selected_user = db.Column(db.String(), nullable=True)
class SelectedUserSchema(ma.Schema):
class Meta:
fields = ("user_id", "selected_user")
Reference in New Issue View Git Blame Copy Permalink