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Update uploadToDatabase.py #17

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Update uploadToDatabase.py #17

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16 changes: 8 additions & 8 deletions uploadToDatabase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -554,7 +554,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
cursor = mydb.cursor()
#Import person table
f = open(outputPath + 'person.csv','r')
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO person(personIdentifier, dateAdded, dateUpdated, `precision`, recall, countSuggestedArticles, overallAccuracy, mode) VALUES(%s, %s, %s, %s, %s, %s, %s, %s)",
Expand All @@ -569,7 +569,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleAuthor table
f = open(outputPath + 'personArticleAuthor.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleAuthor(personIdentifier, pmid, authorFirstName, authorLastName, targetAuthor, `rank`) VALUES(%s, %s, %s, %s, %s, %s)",
Expand All @@ -584,7 +584,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleRelationship table
f = open(outputPath + 'personArticleRelationship.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleRelationship(personIdentifier, pmid, relationshipNameArticleFirstName, relationshipNameArticleLastName, relationshipNameIdentityFirstName, relationshipNameIdentityLastName, relationshipType, relationshipMatchType, relationshipMatchingScore, relationshipVerboseMatchModifierScore, relationshipMatchModifierMentor, relationshipMatchModifierMentorSeniorAuthor, relationshipMatchModifierManager, relationshipMatchModifierManagerSeniorAuthor) VALUES(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)",
Expand All @@ -599,7 +599,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleDepartment table
f = open(outputPath + 'personArticleDepartment.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleDepartment(personIdentifier, pmid, identityOrganizationalUnit, articleAffiliation, organizationalUnitType, organizationalUnitMatchingScore, organizationalUnitModifier, organizationalUnitModifierScore) VALUES(%s, %s, %s, %s, %s, %s, %s, %s)",
Expand All @@ -614,7 +614,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleScopusTargetAuthorAffiliation table
f = open(outputPath + 'personArticleScopusTargetAuthorAffiliation.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleScopusTargetAuthorAffiliation(personIdentifier, pmid, targetAuthorInstitutionalAffiliationSource, scopusTargetAuthorInstitutionalAffiliationIdentity, targetAuthorInstitutionalAffiliationArticleScopusLabel, targetAuthorInstitutionalAffiliationArticleScopusAffiliationId, targetAuthorInstitutionalAffiliationMatchType, targetAuthorInstitutionalAffiliationMatchTypeScore) VALUES(%s, %s, %s, %s, %s, %s, %s, %s)",
Expand All @@ -629,7 +629,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleScopusNonTargetAuthorAffiliation table
f = open(outputPath + 'personArticleScopusNonTargetAuthorAffiliation.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleScopusNonTargetAuthorAffiliation(personIdentifier, pmid, nonTargetAuthorInstitutionLabel, nonTargetAuthorInstitutionID, nonTargetAuthorInstitutionCount) VALUES(%s, %s, %s, %s, %s)",
Expand All @@ -644,7 +644,7 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#Import personArticleGrant table
f = open(outputPath + 'personArticleGrant.csv','r')
cursor = mydb.cursor()
csv_data = csv.reader(f)
csv_data = csv.reader(f, quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True)
for row in csv_data:
try:
cursor.execute("INSERT INTO personArticleGrant(personIdentifier, pmid, articleGrant, grantMatchScore, institutionGrant) VALUES(%s, %s, %s, %s, %s)",
Expand Down Expand Up @@ -675,4 +675,4 @@ def downloadDirectoryFroms3(bucketName,remoteDirectoryName):
#close the connection to the database.
mydb.commit()
cursor.close()
f.close()
f.close()