Minor cleanup and bug fixes.
This commit is contained in:
Dan Funk
parent
473c724fe3
commit
43a9a66d63
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@ -1,2 +1,3 @@
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.idea
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__pycache__/
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__pycache__/
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app.db
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13
app.py
13
app.py
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@ -48,6 +48,7 @@ db = SQLAlchemy(app)
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migrate = Migrate(app, db)
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ma = Marshmallow(app)
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# Loads all the descriptions from the API so we can display them in the editor.
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description_map = {}
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with open(r'api.yml') as file:
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api_config = yaml.load(file, Loader=yaml.FullLoader)
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@ -55,7 +56,6 @@ with open(r'api.yml') as file:
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for schema in api_config['components']['schemas']:
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for field, values in api_config['components']['schemas'][schema]['properties'].items():
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description_map[field] = values['description']
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print(description_map)
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# **************************
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@ -117,7 +117,7 @@ def new_study():
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title=title,
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description_map=description_map)
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@app.route('/study/<study_id>}', methods=['GET', 'POST'])
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@app.route('/study/<study_id>', methods=['GET', 'POST'])
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def edit_study(study_id):
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study = db.session.query(Study).filter(Study.STUDYID == study_id).first()
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form = StudyForm(request.form, obj=study)
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@ -138,7 +138,7 @@ def edit_study(study_id):
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description_map={})
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@app.route('/investigator/<study_id>}', methods=['GET', 'POST'])
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@app.route('/investigator/<study_id>', methods=['GET', 'POST'])
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def new_investigator(study_id):
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form = InvestigatorForm(request.form)
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action = "/investigator/" + study_id
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@ -158,16 +158,17 @@ def new_investigator(study_id):
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description_map={})
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@app.route('/del_investigator/<inv_id>}', methods=['GET'])
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@app.route('/del_investigator/<inv_id>', methods=['GET'])
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def del_investigator(inv_id):
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db.session.query(Investigator).filter(Investigator.id == inv_id).delete()
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db.session.commit()
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return redirect('/')
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@app.route('/del_study/<study_id>}', methods=['GET'])
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@app.route('/del_study/<study_id>', methods=['GET'])
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def del_study(study_id):
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db.session.query(Study).filter(Study.STUDYID == study_id).delete()
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db.session.query(StudyDetails).filter(StudyDetails.STUDYID == study_id).delete()
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db.session.commit()
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return redirect('/')
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@ -187,7 +188,7 @@ def _update_study(study, form):
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db.session.add(study)
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db.session.commit()
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@app.route('/study_details/<study_id>}', methods=['GET', 'POST'])
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@app.route('/study_details/<study_id>', methods=['GET', 'POST'])
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def study_details(study_id):
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study_details = db.session.query(StudyDetails).filter(StudyDetails.STUDYID == study_id).first()
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if not study_details:
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@ -1,125 +0,0 @@
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"""empty message
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Revision ID: dde54f90dde2
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Revises: d3592c4e8a39
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Create Date: 2020-02-17 17:29:52.393203
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"""
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from alembic import op
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import sqlalchemy as sa
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# revision identifiers, used by Alembic.
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revision = 'dde54f90dde2'
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down_revision = 'd3592c4e8a39'
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.create_table('study',
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sa.Column('STUDYID', sa.Integer(), nullable=False),
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sa.Column('HSRNUMBER', sa.String(), nullable=True),
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sa.Column('TITLE', sa.String(length=80), nullable=False),
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sa.Column('NETBADGEID', sa.String(), nullable=False),
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sa.Column('Q_COMPLETE', sa.Boolean(), nullable=True),
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sa.Column('DATE_MODIFIED', sa.DateTime(timezone=True), nullable=True),
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sa.PrimaryKeyConstraint('STUDYID')
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)
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op.create_table('investigator',
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sa.Column('id', sa.Integer(), nullable=False),
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sa.Column('STUDYID', sa.Integer(), nullable=True),
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sa.Column('NETBADGEID', sa.String(), nullable=False),
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sa.Column('INVESTIGATORTYPE', sa.String(), nullable=False),
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sa.Column('INVESTIGATORTYPEFULL', sa.String(), nullable=False),
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sa.ForeignKeyConstraint(['STUDYID'], ['study.STUDYID'], ),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('required_document',
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sa.Column('id', sa.Integer(), nullable=False),
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sa.Column('AUXDOCID', sa.String(), nullable=False),
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sa.Column('AUXDOC', sa.String(), nullable=False),
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sa.Column('STUDYID', sa.Integer(), nullable=True),
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sa.ForeignKeyConstraint(['STUDYID'], ['study.STUDYID'], ),
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sa.PrimaryKeyConstraint('id')
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)
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op.create_table('study_details',
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sa.Column('STUDYID', sa.Integer(), nullable=False),
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sa.Column('IS_IND', sa.Integer(), nullable=True),
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sa.Column('IND_1', sa.String(), nullable=True),
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sa.Column('IND_2', sa.String(), nullable=True),
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sa.Column('IND_3', sa.String(), nullable=True),
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sa.Column('IS_UVA_IND', sa.Integer(), nullable=True),
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sa.Column('IS_IDE', sa.Integer(), nullable=True),
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sa.Column('IS_UVA_IDE', sa.Integer(), nullable=True),
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sa.Column('IDE', sa.String(), nullable=True),
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sa.Column('IS_CHART_REVIEW', sa.Integer(), nullable=True),
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sa.Column('IS_RADIATION', sa.Integer(), nullable=True),
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sa.Column('GCRC_NUMBER', sa.String(), nullable=True),
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sa.Column('IS_GCRC', sa.Integer(), nullable=True),
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sa.Column('IS_PRC_DSMP', sa.Integer(), nullable=True),
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sa.Column('IS_PRC', sa.Integer(), nullable=True),
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sa.Column('PRC_NUMBER', sa.String(), nullable=True),
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sa.Column('IS_IBC', sa.Integer(), nullable=True),
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sa.Column('IBC_NUMBER', sa.String(), nullable=True),
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sa.Column('SPONSORS_PROTOCOL_REVISION_DATE', sa.Integer(), nullable=True),
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sa.Column('IS_SPONSOR_MONITORING', sa.Integer(), nullable=True),
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sa.Column('IS_AUX', sa.Integer(), nullable=True),
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sa.Column('IS_SPONSOR', sa.Integer(), nullable=True),
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sa.Column('IS_GRANT', sa.Integer(), nullable=True),
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sa.Column('IS_COMMITTEE_CONFLICT', sa.Integer(), nullable=True),
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sa.Column('DSMB', sa.Integer(), nullable=True),
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sa.Column('DSMB_FREQUENCY', sa.Integer(), nullable=True),
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sa.Column('IS_DB', sa.Integer(), nullable=True),
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sa.Column('IS_UVA_DB', sa.Integer(), nullable=True),
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sa.Column('IS_CENTRAL_REG_DB', sa.Integer(), nullable=True),
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sa.Column('IS_CONSENT_WAIVER', sa.Integer(), nullable=True),
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sa.Column('IS_HGT', sa.Integer(), nullable=True),
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sa.Column('IS_GENE_TRANSFER', sa.Integer(), nullable=True),
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sa.Column('IS_TISSUE_BANKING', sa.Integer(), nullable=True),
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sa.Column('IS_SURROGATE_CONSENT', sa.Integer(), nullable=True),
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sa.Column('IS_ADULT_PARTICIPANT', sa.Integer(), nullable=True),
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sa.Column('IS_MINOR_PARTICIPANT', sa.Integer(), nullable=True),
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sa.Column('IS_MINOR', sa.Integer(), nullable=True),
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sa.Column('IS_BIOMEDICAL', sa.Integer(), nullable=True),
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sa.Column('IS_QUALITATIVE', sa.Integer(), nullable=True),
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sa.Column('IS_PI_SCHOOL', sa.Integer(), nullable=True),
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sa.Column('IS_PRISONERS_POP', sa.Integer(), nullable=True),
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sa.Column('IS_PREGNANT_POP', sa.Integer(), nullable=True),
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sa.Column('IS_FETUS_POP', sa.Integer(), nullable=True),
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sa.Column('IS_MENTAL_IMPAIRMENT_POP', sa.Integer(), nullable=True),
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sa.Column('IS_ELDERLY_POP', sa.Integer(), nullable=True),
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sa.Column('IS_OTHER_VULNERABLE_POP', sa.Integer(), nullable=True),
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sa.Column('OTHER_VULNERABLE_DESC', sa.String(), nullable=True),
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sa.Column('IS_MULTI_SITE', sa.Integer(), nullable=True),
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sa.Column('IS_UVA_LOCATION', sa.Integer(), nullable=True),
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sa.Column('NON_UVA_LOCATION', sa.String(), nullable=True),
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sa.Column('MULTI_SITE_LOCATIONS', sa.String(), nullable=True),
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sa.Column('IS_OUTSIDE_CONTRACT', sa.Integer(), nullable=True),
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sa.Column('IS_UVA_PI_MULTI', sa.Integer(), nullable=True),
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sa.Column('IS_NOT_PRC_WAIVER', sa.Integer(), nullable=True),
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sa.Column('IS_CANCER_PATIENT', sa.Integer(), nullable=True),
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sa.Column('UPLOAD_COMPLETE', sa.Integer(), nullable=True),
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sa.Column('IS_FUNDING_SOURCE', sa.Integer(), nullable=True),
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sa.Column('IS_PI_INITIATED', sa.Integer(), nullable=True),
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sa.Column('IS_ENGAGED_RESEARCH', sa.Integer(), nullable=True),
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sa.Column('IS_APPROVED_DEVICE', sa.Integer(), nullable=True),
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sa.Column('IS_FINANCIAL_CONFLICT', sa.Integer(), nullable=True),
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sa.Column('IS_NOT_CONSENT_WAIVER', sa.Integer(), nullable=True),
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sa.Column('IS_FOR_CANCER_CENTER', sa.Integer(), nullable=True),
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sa.Column('IS_REVIEW_BY_CENTRAL_IRB', sa.Integer(), nullable=True),
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sa.Column('IRBREVIEWERADMIN', sa.String(), nullable=True),
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sa.ForeignKeyConstraint(['STUDYID'], ['study.STUDYID'], ),
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sa.PrimaryKeyConstraint('STUDYID')
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)
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_table('study_details')
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op.drop_table('required_document')
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op.drop_table('investigator')
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op.drop_table('study')
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# ### end Alembic commands ###
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