Get COPD and Asthma articles from database.

DrugDrugInteraction/DDIExtractionWithEffect3.py

@@ -0,0 +1,209 @@
+'''
+Created on 13 Sep 2016
+
+@author: mbaxkhm4
+
+Created at the University of Manchester, School of Computer Science
+Licence GNU/GPL 3.0
+'''
+import Cell
+import Annotation
+from QueryDBClass import QueryDBCalss
+from  Data.Table import Table
+from AnalyzePattern import GetMean,GetRange
+import re
+
+def getCellsByTableID(TableID,db):
+    rows = db.getTableCellsWithTableArticleData(TableID)
+    cells = []
+    for row in rows:
+        cell = Cell.Cell()
+        cell.idArticle = row[20]
+        cell.idPMC = row[24]
+        cell.idTable = row[13]
+        cell.tableOrder = row[14]
+        cell.pragmaticClass = row[22]
+        cell.idCell = row[0]
+        cell.cellID = row[1]
+        cell.cellType = row[2]
+        cell.rowN = row[4]
+        cell.columnN = row[5]
+        cell.Content = row[9]
+        cell.Header = row[10]
+        cell.Stub = row[11]
+        cell.Super_row = row[12]
+        cell.HeaderId = row[6]
+        cell.StubId = row[7]
+        cell.SuperRowId = row[8]
+        roles = db.getCellRole(cell.idCell)
+        for role in roles:
+            if role[0]==1:
+                cell.isHeader = True
+            if role[0]==2:
+                cell.isStub = True
+            if role[0]==3:
+                cell.isData = True
+            if role[0]==4:
+                cell.isSuperRow = True
+        annotations = db.getCellAnnotation(cell.idCell)
+        cell_annotations = []
+        if(annotations!= None):
+            for ann in annotations:
+                Annot = Annotation.Annotation()
+                Annot.annotationID = ann[0]
+                Annot.Content = ann[1]
+                Annot.Start = ann[2]
+                Annot.End = ann[3]
+                Annot.AnnotationCID = ann[4]
+                Annot.AnnotationDesc =ann[5]
+                Annot.AgentName = ann[6]
+                Annot.AgentType = ann[7]
+                Annot.AnnotationURL = ann[8]
+                cell_annotations.append(Annot)
+        cell.Annotations = cell_annotations
+        cells.append(cell)
+    return cells
+if __name__=="__main__":
+    queryclass = QueryDBCalss("localhost","root","","ddi_data", )
+    queryclass.CreateAdditionalDDITables()
+    cursor = queryclass.db.cursor()
+    #Get tables
+    sql = """SELECT idArticle,Title,SpecId,idTable,TableOrder,TableCaption,Section FROM ddi_data.article inner join
+     arttable on idArticle=Article_idArticle where Section='34073-7'"""
+    #Get cells and annotations that contain potential DDIs
+    #sql = """select annotation.Content,AnnotationDescription,Table_idTable,RowN,ColumnN,TableOrder,idArticle,Title,SpecId,
+    #AnnotationID from annotation inner join cell on cell.idCell=annotation.Cell_idCell inner join arttable on
+    #arttable.idTable=cell.Table_idTable inner join article on article.idArticle = arttable.Article_idArticle
+    #where Section='34073-7' and AnnotationDescription  IN ('Pharmacologic Substance (phsu)','Biologically Active Substance (bacs)',
+    #'Organic Chemical (orch)','Hazardous or Poisonous Substance (hops)','Carbohydrate (carb)','Element, Ion, or Isotope (elii)',
+    #'Nucleic Acid, Nucleoside, or Nucleotide (nnon)','Indicator, Reagent, or Diagnostic Aid (irda)',
+    #'Biomedical or Dental Material (bodm)', 'Inorganic Chemical (inch)','Hormone (horm)')
+    #"""
+    cursor.execute(sql)
+    results = cursor.fetchall()
+    columnOfDrugs = -1
+    isfirst = False
+    #Get all drug annotated content
+    for res in results:
+        idArticle = res[0]
+        Title = res[1]
+        SpecId = res[2]
+        idTable = res[3]
+        TableOrder = res[4]
+        TableCaption  = res [5]
+        Section = res[6]
+        PotentialDrugFromHeader = -1
+        PotentialEffectFromHeader = -1
+        PotentialDrugFromAnnotations = -1
+        cells = getCellsByTableID(idTable,queryclass)
+        most_annotated = {}
+        annotated_cells=[]
+        drugcolumns = []
+        effectcolums = []
+        spanningRows = []
+        pastCell = ''
+        numOfColumns = 0
+        NotCalcNumOfColumns = True
+        cellid = 0
+        drugset = -1
+        hasHeader = False
+        if cells[0].isHeader:
+            hasHeader = True
+
+        DrugColumnsSet = False
+        for cell in cells:
+            if drugset>-1 and cell.rowN>0:
+                DrugColumnsSet = True
+            if(cell.rowN==0 and NotCalcNumOfColumns):
+                numOfColumns = numOfColumns+1
+            if cell.rowN==1:
+                NotCalcNumOfColumns = False
+            if hasHeader:
+                if ("drug" in cell.Content.lower() or "interacting agent" in cell.Content.lower() or'coadministered' in  cell.Content.lower() or 'co-administered' in  cell.Content.lower()) and ('effect' not in cell.Content.lower() and 'dose' not in cell.Content.lower() and 'exposure' not in cell.Content.lower() and 'recommendation' not in cell.Content.lower()) and cell.isHeader and DrugColumnsSet==False:
+                    drugcolumns.append(cell.columnN)
+                    drugset = cell.rowN
+                if "effect" in cell.Content.lower() and cell.isHeader and DrugColumnsSet==False:
+                    effectcolums.append(cell.columnN)
+            else:
+                if ("drug" in cell.Content.lower() or 'coadministered' in  cell.Content.lower() or 'co-administered' in  cell.Content.lower()) and ('effect' not in cell.Content.lower() and 'dose' not in cell.Content.lower() and 'exposure'  not in cell.Content.lower() and 'recommendation' not in cell.Content.lower()) and cell.rowN<3 and DrugColumnsSet==False:
+                    drugcolumns.append(cell.columnN)
+                    drugeffectset = cell.rowN
+                if "effect" in cell.Content.lower() and cell.rowN<3 and DrugColumnsSet==False:
+                    effectcolums.append(cell.columnN)
+            if cell.columnN==0 and NotCalcNumOfColumns==False:
+                isSpanning = True
+                for i in range(0,numOfColumns-1):
+                    if(cellid+i+1<len(cells) and cells[cellid+i].Content.lower()!=cells[cellid+i+1].Content.lower()):
+                        j=cellid
+                        numCellsInRow=0
+                        numCellsZero = 0
+                        while(cellid+i+1<len(cells) and j<len(cells) and cells[j].rowN==cells[cellid+i].rowN):
+                            if cells[j]=='':
+                                numCellsZero=numCellsZero+1
+                            numCellsInRow = numCellsInRow+1
+                            j=j+1
+                        if numCellsInRow>0 and (numCellsZero*1.0)/(numCellsInRow*1.0)<0.5:
+                            isSpanning = False
+                if isSpanning:
+                    spanningRows.append(cell.rowN)
+            cellid = cellid+1
+
+        drugcolumns = set(drugcolumns)
+        effectcolums = set(effectcolums)
+        spanningRows = set(spanningRows)
+        isGroup = -1
+        for i in range(0,len(cells)):
+            extract = ''
+            effect = ''
+            if cells[i].rowN in spanningRows or cells[i].rowN==0 or cells[i].rowN==drugset:
+                continue
+            if cells[i].columnN in drugcolumns:
+                extract = cells[i].Content
+                if extract=='':
+                    continue
+                for k in range(0,5):
+                    if i+k<len(cells) and cells[i+k].columnN in effectcolums:
+                        if cells[k+i].Content == "":
+                            continue
+                        effect = cells[k+i].Content
+            # Get drug name from the table based on SetID
+                sql1 = """Select * from structuredproductlabelmetadata where SetId = '"""+SpecId+"'"
+                cursor.execute(sql1)
+                results2 = cursor.fetchall()
+                for res1 in results2:
+                    drugname = res1[3]
+                    if extract.strip() =="" or extract.strip()==" ":
+                        continue
+                    print drugname+' '+extract+' '+effect
+                drugs = extract.split(":")
+                if len(drugs)>1:
+                    ex1 = drugs[0]
+                    ex2 = drugs[1]
+                    cursor = queryclass.db.cursor()
+                    sql = "INSERT into ddiinfo (documentId, SpecId,idTable,TableName,Drug1,Drug2,Effect,CueRule,isGroup) values (%s,%s,%s,%s,%s,%s,%s,%s,%s)"
+                    cursor.execute(sql, (
+                    idArticle, SpecId, idTable, TableOrder, drugname, ex1, effect, "DDI Method 3", 1))
+                    queryclass.db.commit()
+                    extract = ''
+                    isGroup = -1
+                    onedrugs = re.split(";|,|\n",ex2)
+                    for onedrug in onedrugs:
+                        cursor = queryclass.db.cursor()
+                        sql = "INSERT into ddiinfo (documentId, SpecId,idTable,TableName,Drug1,Drug2,Effect,CueRule,isGroup) values (%s,%s,%s,%s,%s,%s,%s,%s,%s)"
+                        cursor.execute(sql, (
+                            idArticle, SpecId, idTable, TableOrder, drugname, onedrug, effect, "DDI Method 3", -1))
+                        queryclass.db.commit()
+                        isGroup = -1
+                else:
+                    onedrugs = re.split(";|,|\n", extract)
+                    for onedrug in onedrugs:
+                        cursor = queryclass.db.cursor()
+                        sql = "INSERT into ddiinfo (documentId, SpecId,idTable,TableName,Drug1,Drug2,Effect,CueRule,isGroup) values (%s,%s,%s,%s,%s,%s,%s,%s,%s)"
+                        cursor.execute(sql, (
+                            idArticle, SpecId, idTable, TableOrder, drugname, onedrug, effect, "DDI Method 3", -1))
+                        queryclass.db.commit()
+                        isGroup = -1
+                effect=''
+                extract = ''
+
+    print "Done"