creating initial app.py

app.py

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+from sqlalchemy import create_engine
+#from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import sessionmaker
+#import models
+DB_PASSWORD= "kc{!ET7g"
+DB_HOST ="10.230.50.66"
+DB_PORT = "1433"
+DB= "Reporting"
+# Construct the connection string
+SQL_DATABASE_URL = f'mssql+pymssql://Benedette:{DB_PASSWORD}@{DB_HOST}:{DB_PORT}/{DB}'
+# Create an engine instance
+engine = create_engine(
+    SQL_DATABASE_URL, connect_args={}, echo=True
+)
+SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+#linelist_factart_schema = models.t_Linelist_FACTART
+
+
+# Base = declarative_base()
+db = SessionLocal()
+# linelist_factart_schema
+
+# a wrapper around the SQLAlchemy engine to interact with a SQL database. 
+from llama_index.core import SQLDatabase
+# sql_database = SQLDatabase(engine)
+tables = ["Linelist_FACTART","LineListTransHTS", "LinelistPrep","LinelistHEI", "AggregateDSD","AggregateOTZEligibilityAndEnrollments","AggregateARTHistory"]
+sql_database = SQLDatabase(engine, include_tables=tables)
+sql_database
+
+import os
+os.environ["OPENAI_API_KEY"] 
+from llama_index.llms.openai import OpenAI
+llm = OpenAI(temperature=0, model="gpt-3.5-turbo")
+
+fact_linelist_str = (
+    "A client-level linelist that contains comprehensive data on all clients who have ever received treatment for HIV/AIDS, "
+    "encompassing various indicators and clinical parameters."
+    "Use this table to answer quetions related to active patients currently on treatment/txcurr, viral load results"
+    "Key attributes captured in this linelist include:"
+    "if input in the NUPI column is NULL then the client has no NUPI"
+    "Active patients is where ARTOutcomeDescription is Active."
+    "Clinical indicators like Last CD4 count, Last VL (Viral Load), and WHO Stage, aiding in the assessment of disease progression and treatment response."
+    "Demographic information, including Age at ART Start, Gender, Marital Status, and County/Sub-County, facilitating analysis of patient demographics."
+    "Medical history and co-morbidities, such as Diabetes and Hypertension status, providing context on underlying health conditions and associated risk factors."
+    "Facility-related data, such as Facility Name, Site Code,County, and Partner Name, enabling assessment of service delivery across different healthcare facilities and implementing partners."
+    "Pregnancy-related indicators, including Pregnant ART Start and Pregnant at Enrollment, supporting maternal and child health monitoring and intervention."
+    "clients are uniquley identified by concatenating PatientPKHash and Sitecode"
+    "LastVL is the most current VL for the client"
+    "LowViremia/suppressed is when a client viral load is less that 200 copies per ml,1= True 0 = False "
+    "HighViremia/unsuppressed is when a client viral load is more that 200 copies per ml,1= True 0 = False "
+    "HasValidVL is boolean value for if client has a valid VL"
+    "ISTxCurs indicates whether the patients are active on teatment where 1= True"
+    "Treatment Outcomes(ARTOutcomeDescription) is as at one point"
+    "This table can be used to answer queries such as:"
+    "What is the distribution of treatment outcomes among HIV/AIDS patients, such as Active, Transfer Out, and Loss to Follow-Up by county, partner,age?"
+    "What proportion of patients have achieved viral suppression, as indicated by their Last VL results by coounty?"
+    "What percentage of HIV/AIDS patients have co-morbid conditions such as diabetes or hypertension?"
+   
+)
+
+hts_linelist_str = (
+    "A client-level linelist containing comprehensive HIV testing data for all adult clients (> 18 years) who have undergone HIV testing."
+    "This dataset captures a wide range of information including demographic details, testing outcomes, testing history, and programmatic indicators."
+    "It serves as a valuable table for analyzing HIV testing patterns, testing outcomes, and testing strategies among adult populations."
+    "Please note that this dataset is not suitable for inquiries related to patients on treatment."
+    "use this table to answer any questions related to HIV testing"
+    "Additional details available include:"
+    "- Age at Testing (AgeAtTesting): Age of the client at the time of HIV testing."
+    "- Age Group (AgeGroup): Categorization of clients into 4-year age bands from 1 to 64 years."
+    "- Agency Name (AgencyName): Name of the funding body or organization supporting the testing program."
+    "- Client Self-Tested (ClientSelfTested): Indicates whether a client has ever performed self-testing for HIV."
+    "- Client Tested As (ClientTestedAs): Categorizes clients based on whether they were tested individually or as part of a couple."
+    "- County (County) and Sub-County (SubCounty): Geographic location of the testing facility."
+    "- Couple Discordant (CoupleDiscordant): Indicates whether a couple tested together was concordant or discordant for HIV."
+    "- Date of Birth (DOB): Date of birth of the client."
+    "- Enrollment Date (EnrollmentDate): Date when the client was enrolled into the CCC."
+    "- Entry Point (EntryPoint): Service point where the HIV test was conducted (e.g., VCT, OPD)."
+    "- Ever Tested for HIV (EverTestedForHiv): Indicates whether the client has ever been tested for HIV before."
+    "- Facility Name (FacilityName) and MFL Code (MFLCode): Name and code of the testing facility."
+    "- Final Test Result (FinalTestResult): Result of the HIV test for the encounter."
+    "- Gender (Gender) and Marital Status (MaritalStatus): Demographic characteristics of the client."
+    "- Linked (Linked): Boolean value indicating whether the client was successfully linked to follow-up services."
+    "- Months Since Last Test (MonthsSinceLastTest): Number of months since the client's last HIV test."
+    "- Test Date (TestDate): Date when the client was tested for HIV."
+    "- Test Strategy (TestStrategy): Strategy employed for HIV testing (e.g., Hospital Patient, Non-Patient)."
+    "- Test Type (TestType): Type of HIV test conducted during the encounter."
+    "- Tested (Tested): Boolean value indicating whether the client was tested for HIV."
+    "- Tested Before (TestedBefore): Indicates if the client has been tested for HIV within the last 12 months."
+    "- TB Screening (tbScreening): Outcome of TB screening conducted during the encounter."
+    "Positivity rate is number of positive tests from all the test conducted in a certain period"
+)
+
+prep_str = (
+    "A client-level line list containing comprehensive information on all clients enrolled in Pre-Exposure Prophylaxis (PrEP) programs."
+    "Additional information available includes:"
+    "- As of Date (AsofDate): End of the reporting month for the data."
+    "- Assessment Month (AssessmentMonth) and Assessment Year (AssessmentYear): Month and year when the client was assessed for PrEP enrollment."
+    "- Eligible for PrEP (EligiblePrep): Boolean value indicating whether the client is eligible for enrollment in PrEP based on risk category."
+    "- Latest HIV Risk Category (LatestHIVRiskCategory): Last recorded risk category from the HIV testing machine learning model."
+    "- Screened for PrEP (ScreenedPrep): Boolean value indicating whether the client was assessed for enrollment into PrEP."
+    "- PatientPKHash: Hashed value representing the unique client ID in the specific facility."
+    "Use this table to answer any prep related question,i.e from high risk clients how many were enrolled in Prep"
+)
+
+hei_str= ("A client level linelist that contains various indicators of HIV-exposed infants"
+          "this table should be used for any HEI related questions,Iincluding whether HEI is breastfeeding,tested at different timepoints, "
+          "outcome of Hei after they exit the HEI program"
+          "Additional information available includes:"
+          "-BF12mnths Indicates whether the HEI is breastfeeding at 12 months of age as of last cwc visit"
+          "-BF18mnths Indicates whether the HEI is breastfeeding at 18 months of age as of last cwc visit"
+          "-EBF6mnths Indicates whether the HEI is using Exclusive Replacement(ERF) feeding method at 6 months of age as of last cwc visit"
+          "-HEIExitCriteria the Exit reason for an exposed infant after 24months"
+          "-InitialPCRBtwn8wks_12mnthsIndicates whether the HEI's DNAPCR1 was done at age of between 8 weeks and 48 weeks"
+          "-TestedAt12months-Indicates whether the HEI's DNAPCR2 was done at age of 12 months of age")
+otzenroll_str=("An aggregate table that contains counts of TXCurr/number of active individuals between 10 and 19 years who are eligible for OTZ program, /enrolled in OTZ,"
+                "completed training modules and eligible for VL"
+               "Use this table for addressing any inquiries regarding OTZ and corresponding viral loads"
+               "AgeGroup: A 4-year age band from 1 to 64 years"
+                "CompletedToday_OTZ_Beyond: Has the client completed OTZ_Beyond today"
+                "CompletedToday_OTZ_Leadership: Has the client completed OTZ_Leadership today"
+                "CompletedToday_OTZ_MakingDecisions: Has the client completed OTZ_MakingDecisions today"
+                "CompletedToday_OTZ_Orientation: Has the client completed OTZ_Orientation today"
+                "CompletedToday_OTZ_Participation: Has the client completed OTZ_Participation today"
+                "CompletedToday_OTZ_SRH: Has the client completed OTZ_SRH today"
+                "CompletedToday_OTZ_Transition: Has the client completed OTZ_Transition today"
+                "CompletedToday_OTZ_TreatmentLiteracy: Has the client completed OTZ_TreatmentLiteracy today"
+                "CompletedTraining: Number of clients who have completed OTZ modules training"
+                "County: The County where the facility is located"
+                "EligibleVL: Is the client eligible for a viral load"
+                "Enrolled: Number of clients enrolled into OTZ program"
+                "FacilityName: The facility name as entered in KHMFL"
+                "FirstVL: The first ever documented viral load"
+                "Gender: Sex of the patient"
+                "HasValidVL: Does the client have a valid viral load"
+                "LastVL: This is the most current Viral load for the client -"
+                "LoadDate: Date when the dataset was ETL loaded"
+                "MFLCode: Master facility code as assigned in the KHMFL"
+                "ModulesPreviouslyCovered: Modules that the client has covered before this visit"
+                "OTZEnrollmentYearMonth: The year and the month the client was enrolled in OTZ program"
+                "PartnerName: The implementing partner mechanism"
+                "SubCounty: The Sub County where the facility is located"
+                "TransferInStatus: Did the client transfer in"
+                "ValidVLResult: The VL result that is within 12 months from the reporting period taking into account age group validity"
+                "ValidVLResultCategory: The viral load results categorizations as LDL, High-risk LLV, Low-risk LLV, and unsuppressed"
+                "patients_eligible: Number of clients eligible for enrollment into OTZ program")
+
+aggtxcurr_str= (
+    "An aggregate dataset containing counts of active number of patients/TxCurr for each facility at each month, disaggregated by various indicators."
+    "Query this table To identify increase/decrease the total number of active patients at overtime" 
+    "Number of acive patients or treatment is calculated at end of the month "
+    "AsofDateKey:the End of month reporting date (format = yyyy-mm-dd), use this date to extract number of active client as at that month "
+    "DATIMAgeGroup:	The DATIM Age disaggregations"
+    #"NumofPatients	The total number of active patients/TXcurr"
+    "isTxCurr:	The total number of active patients/TXcurr"
+)
+
+from llama_index.core.objects import (
+    SQLTableNodeMapping,
+    ObjectIndex,
+    SQLTableSchema,
+)
+
+from llama_index.core import VectorStoreIndex
+#store the table schema in an index 
+table_node_mapping = SQLTableNodeMapping(sql_database)
+
+#store schema information for each table.
+table_schema_objs = [
+    (SQLTableSchema(table_name="Linelist_FACTART", context_str=fact_linelist_str)),
+    (SQLTableSchema(table_name="LineListTransHTS", context_str=hts_linelist_str)),
+    (SQLTableSchema(table_name="LineListPrep", context_str=prep_str)),
+    (SQLTableSchema(table_name="LinelistHEI", context_str=hei_str)),
+    (SQLTableSchema(table_name="AggregateOTZEligibilityAndEnrollments", context_str=otzenroll_str)),
+    #(SQLTableSchema(table_name="AggregateDSD", context_str=dsd_str)),
+    (SQLTableSchema(table_name="AggregateARTHistory", context_str=aggtxcurr_str)),
+]  
+
+obj_index = ObjectIndex.from_objects(
+    table_schema_objs, # A list of table schema objects
+    table_node_mapping, # An object responsible for mapping tables to nodes.
+    VectorStoreIndex, # for vector-based searching or indexing.
+)
+
+from llama_index.core.indices.struct_store import SQLTableRetrieverQueryEngine
+
+query_engine = SQLTableRetrieverQueryEngine(
+    sql_database,
+    obj_index.as_retriever(similarity_top_k=2),
+)
+
+
+preamble = ("Given an input question, first create a syntactically correct"
+"query to run, then look at the results of the query and return the answer"
+"You can order the results by a relevant column to return the most"
+"interesting examples in the database."
+"Pay attention to use only the column names that you can see in the schema"
+"description. Be careful to not query for columns that do not exist."
+"Pay attention to which column is in which table. Also, qualify column names"
+"with the table name when needed.")
+
+prompt_intro = (" Here is the prompt: ")
+
+
+import gradio as gr
+def texttosql(question: str, conversation_history: list[str]):
+	    
+	    
+            context = " ".join([item["user"] + " " + item["chatbot"] for item in conversation_history])
+            response = query_engine.query(preamble +
+                                        "the user previously asked and received the following: " +
+                                        context +
+                                        prompt_intro +
+                                        question)
+        
+            conversation_history.append({"user": question, "chatbot": response.response})   
+        
+            
+            
+            return response.response,response.metadata["sql_query"] ,response.metadata["result"] , conversation_history
+        
+inputs = [gr.Textbox(lines=10, label="Question"),
+                gr.State(value=[])]
+outputs = [
+            gr.Textbox(label="Chatbot Response", type="text"),
+            gr.Textbox(label="sql_query", autoscroll = False, type="text"),
+            gr.Textbox(label="Metadata_result", autoscroll = False, type="text"),
+            # gr.Textbox(label="Source 3", max_lines = 10, autoscroll = False, type="text"),
+            gr.State()
+        ]
+        
+gr.Interface(fn=texttosql, inputs=inputs, outputs=outputs, title="txttosql Chatbot", 
+                    description="Enter a question and see the processed outputs in collapsible boxes.").launch()