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Unstructured XML via non-tab deliminator?

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栀梦
栀梦 2020-12-15 13:43

We have a complex XML Structure and really a big one (>500 MB). the XSD of the structure is: This XSD

As we know this is a complex one. and because of size or non-t

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  • 栀梦
    2020-12-15 14:24

    The simplest approach here would be to use xsd your.xsd /c, add the generated your.cs to the project, and just use XmlSerializer against whatever type is the "root" type; it looks like this will be drugbanktype, so:

    var ser = new XmlSerializer(typeof(drugbanktype));
var obj = (drugbanktype)ser.Deserialize(reader);

    then just walk obj to find the things you need; presumably:

    foreach(var drug in obj.drug) {
  ...
}

    Note: the type names that xsd.exe spits out are apologetically awful; they simply mirror the xml structure from the xsd. You can change them if you like, but it gets awkward if you're ever going to update the xsd and need to re-generate the C#.

    When dealing with a huge amount of data, your best bet is to use XmlReader to skip through data you don't want, then use XmlSerializer and a sub-tree reader to read data you do want; this means you can process items one at a time without needing to deserialize everything into a single object model, which can cause memory issues. For example:

    class Program
{
    static void Main()
    {
        using (var reader = XmlReader.Create("my.xml"))
        {
            var ser = new XmlSerializer(typeof(Product));
            while(reader.Read())
            {
                if(reader.NodeType == XmlNodeType.Element 
                    && reader.Name == "product"
                    && reader.NamespaceURI == "http://www.drugbank.ca")
                {
                    using (var subReader = reader.ReadSubtree())
                    {
                        var obj = (Product)ser.Deserialize(subReader);
                        Console.WriteLine(obj.Name);
                    }
                }
            }
        }
    }
}
[XmlRoot("product", Namespace = "http://www.drugbank.ca")]
public class Product
{
    [XmlElement("name", Namespace = "http://www.drugbank.ca")]
    public string Name { get; set; }
}

    The while(reader.Read()) looks through all nodes sequentially; when we detect <product> (the if check), we use ReadSubtree to create a sub-reader scoped to that element, and deserialize just that element. Then we keep moving forwards.

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  • 醉梦人生
    2020-12-15 14:26

    Decided to create the SQL database the hard way. None of the tools worked well. I only crate a few of the tables. You can add more if needed.

    Step 1 Crate Database in SQL Server Management Studio using following query. Query may give errors if you run multiple times and database or table already exists.

    The run following c# project :

    using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using System.Data;
using System.Data.SqlClient;
using System.Xml;
using System.Xml.Linq;
using System.IO;

namespace DrubBank
{
    class Program
    {
        const string FILENAME = @"c:\temp\full database.xml";
        static void Main(string[] args)
        {
            new UploadXml(FILENAME);
        }
    }
    public class UploadXml
    {
        const string INSERT_DRUG =
            "INSERT INTO [DrugBank].[dbo].[Drugs] (" +
            "[Type],[Created],[Updated],[ID],[Name],[Description],[Case Number],[Unii],[State]," +
            "[Synthesis Reference],[Indication] ,[Pharmacodynamics] ,[Mechanism of Action], [Toxicity]," +
            "[Metabolism] , [Absorption] ,[Half Life], [Protein Binding]," +
            "[Route of Eelimination], [Volume of Distribution] ,[Clearance])" +
            " VALUES " +
            "(@Type, @Created, @Updated, @ID, @Name, @Description, @Case_Number, @Unii, @State," +
             "@Synthesis_Reference,@Indication ,@Pharmacodynamics ,@Mechanism_of_Action, @Toxicity," +
             "@Metabolism , @Absorption ,@Half_Life, @Protein_Binding," +
             "@Route_of_Elimination, @Volume_of_Distribution ,@Clearance)";

        const string INSERT_DRUG_LINK =
            "INSERT INTO [DrugBank].[dbo].[Links] (" +
            "[ID],[Title],[URL])" +
            " VALUES " +
            "(@ID,@Title, @URL)";

        const string INSERT_DRUG_ARTICLE =
            "INSERT INTO [DrugBank].[dbo].[Articles] (" +
            "[ID],[Pubmed ID],[Citation])" +
            " VALUES " +
            "(@ID,@Pubmed_ID, @Citation)";

        const string INSERT_DRUG_INTERACTION =
            "INSERT INTO [DrugBank].[dbo].[Interactions] (" +
            "[ID],[Interaction ID],[Description])" +
            " VALUES " +
            "(@ID,@Interaction_ID, @Description)";

        const string INSERT_DRUG_ID =
            "INSERT INTO [DrugBank].[dbo].[IDs] (" +
            "[ID],[ALT ID])" +
            " VALUES " +
            "(@ID, @ALT_ID)";

        const string INSERT_DRUG_PRODUCT =
            "INSERT INTO [DrugBank].[dbo].[Products] (" +
            "[ID],[Name],[Labeller], [NDC ID], [NDC Product Code], [DPD ID]," +
            "[EMA Product Code],[EMA MA Number],[Started Marketing On], [Ended Marketing On], [Dosage Form]," +
            "[Strength],[Route],[FDA Application Number],[Generic],[Over the Counter],[Approved],[Country],[Source])" +
            " VALUES " +
            "(@ID,@Name,@Labeller, @NDC_ID, @NDC_Product_Code,@DPD_ID," +
            "@EMA_Product_Code,@EMA_MA_Number,@Started_Marketing_On, @Ended_Marketing_On, @Dosage_Form," +
            "@Strength,@Route,@FDA_Application_Number,@Generic,@Over_the_Counter,@Approved,@Country,@Source)";

        const string INSERT_DRUG_MIXTURE =
            "INSERT INTO [DrugBank].[dbo].[Mixtures] (" +
            "[ID], [Name] , [ingredients])" +
            " VALUES " +
            "(@ID, @Name, @ingredients)";

        const string INSERT_DRUG_PACKAGER =
             "INSERT INTO [DrugBank].[dbo].[Packagers] (" +
             "[ID], [Name], [URL])" +
             " VALUES " +
             "(@ID, @Name, @URL)";

        const string INSERT_DRUG_PRICE = 
             "INSERT INTO [DrugBank].[dbo].[Prices] (" +
             "[ID], [Description], [Cost], [Currency], [Unit])" +
             " VALUES " +
             "(@ID, @Description, @Cost, @Currency, @Unit)";

        const string INSERT_DRUG_CATEGORY =
            "INSERT INTO [DrugBank].[dbo].[Categories] (" +
            "[ID], [Category], [Mesh ID])" +
            " VALUES " +
            "(@ID, @Category, @Mesh_ID)";

        const string INSERT_DRUG_ORGANISM =
            "INSERT INTO [DrugBank].[dbo].[Organisms] (" +
            "[ID], [Organism])" +
            " VALUES " +
            "(@ID, @Organism)";

        const string INSERT_DRUG_PATENT =
            "INSERT INTO [DrugBank].[dbo].[Patents] (" +
            "[ID], [Number], [Country], [Approved], [Expires], [Pediatric Extension]) " +
            " VALUES " +
            "(@ID, @Number, @Country, @Approved, @Expires, @Pediatric_Extension) ";

        const string INSERT_DRUG_SEQUENCE =
            "INSERT INTO [DrugBank].[dbo].[Sequences] (" +
            "[ID], [Format], [Type], [Sequence])" +
            " VALUES " +
            "(@ID, @Format, @Type, @Sequence)";

        const string INSERT_DRUG_PROPERTY =
            "INSERT INTO [DrugBank].[dbo].[Properties] (" +
            "[ID], [Kind], [Value], [Source])" +
            " VALUES " +
            "(@ID, @Kind, @Value, @Source)";

        const string INSERT_DRUG_IDENTIFIER =
            "INSERT INTO [DrugBank].[dbo].[Identifiers] (" +
            "[ID], [Resource], [Identifier])" +
            " VALUES " +
            "(@ID, @Resource, @Identifier)";

        const string INSERT_DRUG_ENZYM =
            "INSERT INTO [DrugBank].[dbo].[Enzymes] (" +
            "[ID], [UniprotID])" +
            " VALUES " +
            "(@ID, @UniprotID)";

        SqlCommand productCmd = null;
        SqlCommand interactionCmd = null;
        SqlCommand articleCmd = null;
        SqlCommand linkCmd = null;
        SqlCommand drugCmd = null;
        SqlCommand idCmd = null;
        SqlCommand mixtureCmd = null;
        SqlCommand packagerCmd = null;
        SqlCommand priceCmd = null;
        SqlCommand categoryCmd = null;
        SqlCommand organismCmd = null;
        SqlCommand patentCmd = null;
        SqlCommand sequenceCmd = null;
        SqlCommand propertyCmd = null;
        SqlCommand identifierCmd = null;
        SqlCommand enzymCmd = null;

        public UploadXml(string filename)
        {
            string connStr = DrugBank.Properties.Settings.Default.DrugBankConnectionString;
            SqlConnection conn = new SqlConnection(connStr);
            conn.Open();

            drugCmd = new SqlCommand(INSERT_DRUG, conn);

            drugCmd.Parameters.Add("@Type", SqlDbType.VarChar, 20);
            drugCmd.Parameters.Add("@Created", SqlDbType.DateTime);
            drugCmd.Parameters.Add("@Updated", SqlDbType.DateTime);
            drugCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            drugCmd.Parameters.Add("@Name", SqlDbType.VarChar, 50);
            drugCmd.Parameters.Add("@Description", SqlDbType.VarChar);
            drugCmd.Parameters.Add("@Case_Number", SqlDbType.VarChar, 20);
            drugCmd.Parameters.Add("@Unii", SqlDbType.VarChar, 20);
            drugCmd.Parameters.Add("@State", SqlDbType.VarChar, 20);

            drugCmd.Parameters.Add("@Synthesis_reference", SqlDbType.VarChar, 1024);
            drugCmd.Parameters.Add("@Indication", SqlDbType.VarChar);
            drugCmd.Parameters.Add("@Pharmacodynamics", SqlDbType.VarChar, 1024);
            drugCmd.Parameters.Add("@Mechanism_of_Action", SqlDbType.VarChar, 1024);
            drugCmd.Parameters.Add("@Toxicity", SqlDbType.VarChar, 1024);
            drugCmd.Parameters.Add("@Metabolism", SqlDbType.VarChar);
            drugCmd.Parameters.Add("@Absorption", SqlDbType.VarChar, 1024);
            drugCmd.Parameters.Add("@Half_Life", SqlDbType.VarChar, 256);
            drugCmd.Parameters.Add("@Protein_Binding", SqlDbType.VarChar, 64);
            drugCmd.Parameters.Add("@Route_of_Elimination", SqlDbType.VarChar);
            drugCmd.Parameters.Add("@Volume_of_Distribution", SqlDbType.VarChar);
            drugCmd.Parameters.Add("@Clearance", SqlDbType.VarChar);

            idCmd = new SqlCommand(INSERT_DRUG_ID, conn);
            idCmd.Parameters.Add("@ID", SqlDbType.VarChar, 256);
            idCmd.Parameters.Add("@ALT_ID", SqlDbType.VarChar, 20);

            articleCmd = new SqlCommand(INSERT_DRUG_ARTICLE, conn);

            articleCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            articleCmd.Parameters.Add("@Pubmed_ID", SqlDbType.VarChar, 256);
            articleCmd.Parameters.Add("@Citation", SqlDbType.VarChar, 20);

            linkCmd = new SqlCommand(INSERT_DRUG_LINK, conn);
            linkCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            linkCmd.Parameters.Add("@Title", SqlDbType.VarChar, 256);
            linkCmd.Parameters.Add("@URL", SqlDbType.VarChar, 64);

            interactionCmd = new SqlCommand(INSERT_DRUG_INTERACTION, conn);

            interactionCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            interactionCmd.Parameters.Add("@Interaction_ID", SqlDbType.VarChar, 20);
            interactionCmd.Parameters.Add("@Description", SqlDbType.VarChar, 256);

            productCmd = new SqlCommand(INSERT_DRUG_PRODUCT, conn);

            productCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@Name", SqlDbType.VarChar, 128);
            productCmd.Parameters.Add("@Labeller", SqlDbType.VarChar, 64);
            productCmd.Parameters.Add("@NDC_ID", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@NDC_Product_Code", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@DPD_ID", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@EMA_Product_Code", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@EMA_MA_Number", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@Started_Marketing_On", SqlDbType.DateTime2, 20);
            productCmd.Parameters.Add("@Ended_Marketing_On", SqlDbType.DateTime2, 20);
            productCmd.Parameters.Add("@Dosage_Form", SqlDbType.VarChar, 64);
            productCmd.Parameters.Add("@Strength", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@Route", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@FDA_Application_Number", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@Generic", SqlDbType.Bit);
            productCmd.Parameters.Add("@Over_the_Counter", SqlDbType.Bit);
            productCmd.Parameters.Add("@Approved", SqlDbType.Bit);
            productCmd.Parameters.Add("@Country", SqlDbType.VarChar, 20);
            productCmd.Parameters.Add("@Source", SqlDbType.VarChar, 20);


            mixtureCmd = new SqlCommand(INSERT_DRUG_MIXTURE, conn);

            mixtureCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            mixtureCmd.Parameters.Add("@Name", SqlDbType.VarChar, 64);
            mixtureCmd.Parameters.Add("@Ingredients", SqlDbType.VarChar, 64);

            packagerCmd = new SqlCommand(INSERT_DRUG_PACKAGER, conn);

            packagerCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            packagerCmd.Parameters.Add("@Name", SqlDbType.VarChar, 64);
            packagerCmd.Parameters.Add("@URL", SqlDbType.VarChar, 64);


            priceCmd = new SqlCommand(INSERT_DRUG_PRICE, conn);

            priceCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            priceCmd.Parameters.Add("@Description", SqlDbType.VarChar, 128);
            priceCmd.Parameters.Add("@Cost", SqlDbType.Decimal);
            priceCmd.Parameters.Add("@Currency", SqlDbType.VarChar,20);
            priceCmd.Parameters.Add("@Unit", SqlDbType.VarChar, 20);


            categoryCmd = new SqlCommand(INSERT_DRUG_CATEGORY, conn);

            categoryCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            categoryCmd.Parameters.Add("@Category", SqlDbType.VarChar, 128);
            categoryCmd.Parameters.Add("@Mesh_ID", SqlDbType.VarChar, 20);

            organismCmd = new SqlCommand(INSERT_DRUG_ORGANISM, conn);

            organismCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            organismCmd.Parameters.Add("@Organism", SqlDbType.VarChar, 128);

            patentCmd = new SqlCommand(INSERT_DRUG_PATENT, conn);

            patentCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            patentCmd.Parameters.Add("@Number", SqlDbType.VarChar, 20);
            patentCmd.Parameters.Add("@Country", SqlDbType.VarChar, 20);
            patentCmd.Parameters.Add("@Approved", SqlDbType.DateTime2);
            patentCmd.Parameters.Add("@Expires", SqlDbType.DateTime2);
            patentCmd.Parameters.Add("@Pediatric_Extension", SqlDbType.Bit);

            sequenceCmd = new SqlCommand(INSERT_DRUG_SEQUENCE, conn);

            sequenceCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            sequenceCmd.Parameters.Add("@Format", SqlDbType.VarChar, 20);
            sequenceCmd.Parameters.Add("@Sequence", SqlDbType.VarChar);
            sequenceCmd.Parameters.Add("@Type", SqlDbType.VarChar, 20);

            propertyCmd = new SqlCommand(INSERT_DRUG_PROPERTY, conn);

            propertyCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            propertyCmd.Parameters.Add("@Kind", SqlDbType.VarChar, 20);
            propertyCmd.Parameters.Add("@Value", SqlDbType.VarChar, 20);
            propertyCmd.Parameters.Add("@Source", SqlDbType.VarChar, 20);

            identifierCmd = new SqlCommand(INSERT_DRUG_IDENTIFIER, conn);

            identifierCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            identifierCmd.Parameters.Add("@Resource", SqlDbType.VarChar, 64);
            identifierCmd.Parameters.Add("@Identifier", SqlDbType.VarChar, 64);

            enzymCmd = new SqlCommand(INSERT_DRUG_ENZYM, conn);

            enzymCmd.Parameters.Add("@ID", SqlDbType.VarChar, 20);
            enzymCmd.Parameters.Add("@UniprotID", SqlDbType.VarChar, 20);

            XmlReader reader = XmlReader.Create(filename);
            while (!reader.EOF)
            {
                if (reader.Name != "drug")
                {
                    reader.ReadToFollowing("drug");
                }
                if (!reader.EOF)
                {
                    XElement drug = (XElement)XElement.ReadFrom(reader);
                    string primaryID = (string)drug.Elements().Where(x => (x.Name.LocalName == "drugbank-id") && (x.Attribute("primary") != null)).FirstOrDefault();

                    AddDrug(conn, drug, primaryID);
                    AddArticles(conn, drug, primaryID);
                    AddInteractions(conn, drug, primaryID);
                    AddProducts(conn, drug, primaryID);
                    AddMixtures(conn, drug, primaryID);
                    AddPackagers(conn, drug, primaryID);
                    AddPrices(conn, drug, primaryID);
                    AddCategories(conn, drug, primaryID);
                    AddOrganisms(conn, drug, primaryID);
                    AddPatents(conn, drug, primaryID);
                    AddSequences(conn, drug, primaryID);
                    AddProperties(conn, drug, primaryID);
                    AddIdentifiers(conn, drug, primaryID);
                    AddEnzymes(conn, drug, primaryID);
                }
            }

        }
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  • 没有蜡笔的小新
    2020-12-15 14:33

    Here is the SQL Script :

    Create Database DrugBank
;
GO

Use DrugBank
drop table Drugs
drop table IDs
drop table Articles
drop table Links
drop table Interactions
drop table Products
drop table Mixtures
drop table Packagers
drop table Prices
drop table Categories
drop table Organisms
drop table Patents
drop table Sequences
drop table Properties
drop table Identifiers
drop table Enzymes
;
GO

CREATE TABLE Drugs ( 
type varchar(20) NULL,
Created datetime NULL,
Updated datetime NULL,
ID varchar(20) primary key,
Name varchar(50) NULL,
Description varchar(max) NULL,
[Case Number] varchar(20) NULL,
Unii varchar(20) NULL,
State varchar(20) NULL,
[Synthesis Reference] varchar(1024) NULL,
Indication varchar(max) NULL,
Pharmacodynamics varchar(1024) NULL,
[Mechanism Of Action] varchar(1024) NULL,
Toxicity varchar(1024) NULL,
Metabolism varchar(max) NULL,
Absorption varchar(1024) NULL,
[Half Life] varchar(256) NULL,
[Protein Binding] varchar(64) NULL,
[Route of Eelimination] varchar(max) NULL,
[Volume of Distribution] varchar(max) NULL,
Clearance varchar(max) NULL
)



CREATE TABLE IDs
(
ID varchar(20),
[ALT ID] varchar(20)
)
CREATE TABLE Articles
(
ID varchar(20),
[Pubmed ID] varchar(20) NULL,
[Citation] varchar(1024) NULL
)
CREATE TABLE Links
(
ID varchar(20),
[Title] varchar(256) NULL,
[URL] varchar(64) NULL
)
CREATE TABLE Interactions
(
ID varchar(20),
[Interaction ID] varchar(20) NULL,
[Description] varchar(1024) NULL,

)
CREATE TABLE Products
(
[ID] varchar(20),
[Name] varchar(128) NULL,
[Labeller] varchar(64) NULL,
[NDC ID] varchar(20) NULL,
[NDC Product Code] varchar(20) NULL,
[DPD ID] varchar(20) NULL,
[EMA Product Code] varchar(20) NULL,
[EMA MA Number] varchar(20) NULL,
[Started Marketing On] date NULL,
[Ended Marketing On] date NULL,
[Dosage Form] varchar(64) NULL,
[Strength] varchar(20) NULL,
[Route] varchar(20) NULL,
[FDA Application Number] varchar(20) NULL,
[Generic] bit NULL,
[Over the Counter] bit NULL,
[Approved] bit NULL,
[Country] varchar(20) NULL,
[Source] varchar(20) NULL,

)
CREATE TABLE Mixtures
(
[ID] varchar(20),
[Name] varchar(64),
[ingredients] varchar(64) NULL,
)
CREATE TABLE Packagers
(
[ID] varchar(20),
[Name] varchar(64),
[URL] varchar(64) NULL,
)
CREATE TABLE Prices
(
[ID] varchar(20),
[Description] varchar(128),
[Cost] decimal NULL,
[Currency] varchar(20),
[Unit] varchar(20),
)
CREATE TABLE Categories
(
[ID] varchar(20),
[Category] varchar(128),
[Mesh ID] varchar(20),
)
CREATE TABLE Organisms
(
[ID] varchar(20),
[Organism] varchar(128),
)
CREATE TABLE Patents
(
[ID] varchar(20),
[Number] varchar(20),
[Country] varchar(20),
[Approved] datetime2,
[Expires] datetime,
[Pediatric Extension] bit,
)
CREATE TABLE Sequences
(
[ID] varchar(20),
[Format] varchar(20),
[Type] varchar(20),
[Sequence] varchar(max),
)
CREATE TABLE Properties
(
[ID] varchar(20),
[Kind] varchar(64),
[Value] varchar(32),
[Source] varchar(128)
)
CREATE TABLE Identifiers
(
[ID] varchar(20),
[Resource] varchar(64),
[identifier] varchar(64)
)
CREATE TABLE Enzymes
(
[ID] varchar(20),
[UniprotID] varchar(20)
)
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  • 北海茫月
    2020-12-15 14:41

    Here is 2nd part of the code :

           public void AddDrug(SqlConnection conn, XElement drug, string primaryID)
        {
            string dType = ((string)drug.Attribute("type")).Trim();
            DateTime created = (DateTime)drug.Attribute("created");
            DateTime updated = (DateTime)drug.Attribute("updated");
            List<XElement> drugbank_ids = drug.Elements().Where(x => (x.Name.LocalName == "drugbank-id") && (x.Attribute("primary") != null)).ToList();

            string name = ((string)drug.Elements().Where(x => x.Name.LocalName == "name").FirstOrDefault()).Trim();
            foreach (string drugbank_id in drugbank_ids)
            {
                idCmd.Parameters["@ID"].Value = primaryID;
                idCmd.Parameters["@ALT_ID"].Value = drugbank_id;
                idCmd.ExecuteNonQuery();
            }

            string description = ((string)drug.Elements().Where(x => x.Name.LocalName == "description").FirstOrDefault()).Trim();
            int za = description.Length;
            string case_number = ((string)drug.Elements().Where(x => x.Name.LocalName == "cas-number").FirstOrDefault());
            int zb = case_number.Length;
            string unii = ((string)drug.Elements().Where(x => x.Name.LocalName == "unii").FirstOrDefault());
            int zc = unii.Length;
            string state = (drug.Elements().Where(x => x.Name.LocalName == "state").FirstOrDefault() == null) ? "" : ((string)drug.Elements().Where(x => x.Name.LocalName == "state").FirstOrDefault()).Trim();

            int zd = state.Length;
            string synthesis_reference = ((string)drug.Elements().Where(x => x.Name.LocalName == "synthesis-reference").FirstOrDefault());
            int ze = synthesis_reference.Length;
            string indication = ((string)drug.Elements().Where(x => x.Name.LocalName == "indication").FirstOrDefault());
            int zf = indication.Length;
            string pharmacodynamics = ((string)drug.Elements().Where(x => x.Name.LocalName == "pharmacodynamics").FirstOrDefault());
            int zg = pharmacodynamics.Length;
            string mechanism_of_action = ((string)drug.Elements().Where(x => x.Name.LocalName == "mechanism-of-action").FirstOrDefault());
            int zh = mechanism_of_action.Length;
            string toxicity = ((string)drug.Elements().Where(x => x.Name.LocalName == "toxicity").FirstOrDefault());
            int zi = toxicity.Length;
            string metabolism = ((string)drug.Elements().Where(x => x.Name.LocalName == "metabolism").FirstOrDefault());
            int zj = metabolism.Length;
            string absorption = ((string)drug.Elements().Where(x => x.Name.LocalName == "absorption").FirstOrDefault());
            int zk = absorption.Length;
            string half_life = ((string)drug.Elements().Where(x => x.Name.LocalName == "half-life").FirstOrDefault());
            int zl = half_life.Length;
            string protein_binding = ((string)drug.Elements().Where(x => x.Name.LocalName == "protein-binding").FirstOrDefault());
            int zm = protein_binding.Length;
            string route_of_elimination = ((string)drug.Elements().Where(x => x.Name.LocalName == "route-of-elimination").FirstOrDefault());
            int zn = route_of_elimination.Length;
            string volume_of_distribution = ((string)drug.Elements().Where(x => x.Name.LocalName == "volume-of-distribution").FirstOrDefault());
            int zo = volume_of_distribution.Length;
            string clearance = ((string)drug.Elements().Where(x => x.Name.LocalName == "clearance").FirstOrDefault());
            int zp = clearance.Length;

            drugCmd.Parameters["@Type"].Value = dType;
            drugCmd.Parameters["@Created"].Value = created;
            drugCmd.Parameters["@Updated"].Value = updated;
            drugCmd.Parameters["@ID"].Value = primaryID;
            drugCmd.Parameters["@Name"].Value = name;
            drugCmd.Parameters["@Description"].Value = description;
            drugCmd.Parameters["@Case_Number"].Value = case_number;
            drugCmd.Parameters["@Unii"].Value = unii;
            drugCmd.Parameters["@State"].Value = state;

            drugCmd.Parameters["@Synthesis_Reference"].Value = synthesis_reference;
            drugCmd.Parameters["@Indication"].Value = indication;
            drugCmd.Parameters["@Pharmacodynamics"].Value = pharmacodynamics;
            drugCmd.Parameters["@Mechanism_of_Action"].Value = mechanism_of_action;
            drugCmd.Parameters["@Toxicity"].Value = toxicity;
            drugCmd.Parameters["@Metabolism"].Value = metabolism;
            drugCmd.Parameters["@Absorption"].Value = absorption;
            drugCmd.Parameters["@Half_Life"].Value = half_life;
            drugCmd.Parameters["@Protein_Binding"].Value = protein_binding;
            drugCmd.Parameters["@Route_of_Elimination"].Value = route_of_elimination;
            drugCmd.Parameters["@Volume_of_Distribution"].Value = volume_of_distribution;
            drugCmd.Parameters["@Clearance"].Value = clearance;

            drugCmd.ExecuteNonQuery();

        }

        public void AddArticles(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement article in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("article")))
            {
                string pubmed_id = ((string)article.Elements().Where(XElement => XElement.Name.LocalName == "pubmed-id").FirstOrDefault());
                string citation = ((string)article.Elements().Where(XElement => XElement.Name.LocalName == "citation").FirstOrDefault());

                articleCmd.Parameters["@ID"].Value = id;
                articleCmd.Parameters["@Pubmed_ID"].Value = pubmed_id;
                articleCmd.Parameters["@Citation"].Value = citation;

                articleCmd.ExecuteNonQuery();

            }

            foreach (XElement article in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("link")))
            {
                string title = ((string)article.Elements().Where(XElement => XElement.Name.LocalName == "title").FirstOrDefault());
                string url = ((string)article.Elements().Where(XElement => XElement.Name.LocalName == "url").FirstOrDefault());

                linkCmd.Parameters["@ID"].Value = id;
                linkCmd.Parameters["@Title"].Value = title;
                linkCmd.Parameters["@URL"].Value = url;

                linkCmd.ExecuteNonQuery();
            }
        }
        public void AddInteractions(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement interaction in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("drug-interaction")))
            {
                string interactionID = ((string)interaction.Elements().Where(XElement => XElement.Name.LocalName == "drugbank-id").FirstOrDefault()).Trim();
                string description = ((string)interaction.Elements().Where(XElement => XElement.Name.LocalName == "description").FirstOrDefault());

                interactionCmd.Parameters["@ID"].Value = id;
                interactionCmd.Parameters["@Interaction_ID"].Value = interactionID;
                interactionCmd.Parameters["@Description"].Value = description;

                interactionCmd.ExecuteNonQuery();
            }

        }

        public void AddProducts(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement product in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("product")))
            {
                string name = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "name").FirstOrDefault()).Trim();
                string labeller = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "labeller").FirstOrDefault()).Trim();
                string ndc_id = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "ndc-id").FirstOrDefault());
                string ndc_product_code = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "ndc-product-code").FirstOrDefault());
                string dpd_id = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "dpd-id").FirstOrDefault());
                string ema_product_code = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "ema-product-code").FirstOrDefault());
                string ema_ma_number = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "ema-ma-number").FirstOrDefault());
                string started_marketing_onStr = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "started-marketing-on").FirstOrDefault());
                string ended_marketing_onStr = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "ended-marketing-on").FirstOrDefault());
                string dosage_form = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "dosage-form").FirstOrDefault());
                string strength = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "strength").FirstOrDefault());
                string route = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "route").FirstOrDefault());
                string fda_application_number = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "fda-application-number").FirstOrDefault());
                string genericStr = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "generic").FirstOrDefault());
                byte? generic = string.IsNullOrEmpty(genericStr) ? null : ((genericStr == "true") ? (byte?)1 : (byte?)0);
                string over_the_counterStr = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "over-the-counter").FirstOrDefault());
                byte? over_the_counter = string.IsNullOrEmpty(over_the_counterStr) ? null : ((over_the_counterStr == "true") ? (byte?)1 : (byte?)0);
                string approvedStr = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "approved").FirstOrDefault());
                byte? approved = string.IsNullOrEmpty(approvedStr) ? null : ((approvedStr == "true") ? (byte?)1 : (byte?)0);
                string country = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "country").FirstOrDefault());
                string source = ((string)product.Elements().Where(XElement => XElement.Name.LocalName == "source").FirstOrDefault());

                productCmd.Parameters["@ID"].Value = id;
                productCmd.Parameters["@Name"].Value = name;
                productCmd.Parameters["@Labeller"].Value = labeller;
                productCmd.Parameters["@NDC_ID"].Value = ndc_id;
                productCmd.Parameters["@NDC_Product_Code"].Value = ndc_product_code;
                productCmd.Parameters["@DPD_ID"].Value = dpd_id;
                productCmd.Parameters["@EMA_Product_Code"].Value = ema_product_code;
                productCmd.Parameters["@EMA_MA_Number"].Value = ema_ma_number;
                if (!string.IsNullOrEmpty(started_marketing_onStr))
                {
                    productCmd.Parameters["@Started_Marketing_On"].Value = DateTime.Parse(started_marketing_onStr);
                }
                else
                {
                    productCmd.Parameters["@Started_Marketing_On"].Value = new DateTime();
                }
                if (!string.IsNullOrEmpty(ended_marketing_onStr))
                {
                    productCmd.Parameters["@Ended_Marketing_On"].Value = DateTime.Parse(ended_marketing_onStr);
                }
                else
                {
                    productCmd.Parameters["@Ended_Marketing_On"].Value = new DateTime();
                }
                productCmd.Parameters["@Dosage_Form"].Value = dosage_form;
                productCmd.Parameters["@Strength"].Value = strength;
                productCmd.Parameters["@Route"].Value = route;
                productCmd.Parameters["@FDA_Application_Number"].Value = fda_application_number;
                productCmd.Parameters["@Generic"].Value = generic;
                productCmd.Parameters["@Over_the_Counter"].Value = over_the_counter;
                productCmd.Parameters["@Approved"].Value = approved;
                productCmd.Parameters["@Country"].Value = country;
                productCmd.Parameters["@Source"].Value = source;

                productCmd.ExecuteNonQuery();
            }
        }
        public void AddMixtures(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement mixture in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("mixture")))
            {
                string name = ((string)mixture.Elements().Where(XElement => XElement.Name.LocalName == "name").FirstOrDefault()).Trim();
                string ingredient = ((string)mixture.Elements().Where(XElement => XElement.Name.LocalName == "ingredients").FirstOrDefault()).Trim();

                mixtureCmd.Parameters["@ID"].Value = id;
                mixtureCmd.Parameters["@Name"].Value = name;
                mixtureCmd.Parameters["@Ingredients"].Value = ingredient;

                mixtureCmd.ExecuteNonQuery();

            }
        }
        public void AddPackagers(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement packager in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("packager")))
            {
                string name = ((string)packager.Elements().Where(XElement => XElement.Name.LocalName == "name").FirstOrDefault()).Trim();
                string url = ((string)packager.Elements().Where(XElement => XElement.Name.LocalName == "url").FirstOrDefault()).Trim();

                packagerCmd.Parameters["@ID"].Value = id;
                packagerCmd.Parameters["@Name"].Value = name;
                packagerCmd.Parameters["@URL"].Value = url;

                packagerCmd.ExecuteNonQuery();

            }
        }
        public void AddPrices(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement price in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("price")))
            {
                string description = ((string)price.Elements().Where(XElement => XElement.Name.LocalName == "description").FirstOrDefault()).Trim();
                XElement xCost = (price.Elements().Where(XElement => XElement.Name.LocalName == "cost").FirstOrDefault());
                string cost = ((string)xCost).Trim();
                string currency = (string)xCost.Attribute("currency");
                string unit = ((string)price.Elements().Where(XElement => XElement.Name.LocalName == "unit").FirstOrDefault()).Trim();

                priceCmd.Parameters["@ID"].Value = id;
                priceCmd.Parameters["@Description"].Value = description;
                priceCmd.Parameters["@Cost"].Value = cost;
                priceCmd.Parameters["@Currency"].Value = currency;
                priceCmd.Parameters["@Unit"].Value = unit;

                priceCmd.ExecuteNonQuery();

            }
        }
        public void AddCategories(SqlConnection conn, XElement drug, string id)
        {
            XElement categories = drug.Descendants().Where(XElement => XElement.Name.LocalName == ("categories")).FirstOrDefault();
            foreach (XElement xCategory in categories.Elements().Where(XElement => XElement.Name.LocalName == ("category")))
            {
                string category = ((string)xCategory.Elements().Where(XElement => XElement.Name.LocalName == "category").FirstOrDefault()).Trim();
                string meshID = ((string)xCategory.Elements().Where(XElement => XElement.Name.LocalName == "mesh-id").FirstOrDefault()).Trim();

                categoryCmd.Parameters["@ID"].Value = id;
                categoryCmd.Parameters["@Category"].Value = category;
                categoryCmd.Parameters["@Mesh_ID"].Value = meshID;

                categoryCmd.ExecuteNonQuery();
            }
        }
        public void AddOrganisms(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement xOrganism in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("affected-organism")))
            {
                string organism = ((string)xOrganism).Trim();

                organismCmd.Parameters["@ID"].Value = id;
                organismCmd.Parameters["@Organism"].Value = organism;

                organismCmd.ExecuteNonQuery();

            }
        }
        public void AddPatents(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement patent in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("patent")))
            {
                string number = ((string)patent.Elements().Where(XElement => XElement.Name.LocalName == "number").FirstOrDefault()).Trim();
                string country = ((string)patent.Elements().Where(XElement => XElement.Name.LocalName == "country").FirstOrDefault()).Trim();
                DateTime approved = (DateTime)patent.Elements().Where(XElement => XElement.Name.LocalName == "approved").FirstOrDefault();
                DateTime expires = (DateTime)patent.Elements().Where(XElement => XElement.Name.LocalName == "expires").FirstOrDefault();
                string pediatric_extensionStr = ((string)patent.Elements().Where(XElement => XElement.Name.LocalName == "pediatric-extension").FirstOrDefault());
                byte? pediatric_extension = string.IsNullOrEmpty(pediatric_extensionStr) ? null : ((pediatric_extensionStr == "true") ? (byte?)1 : (byte?)0);

                patentCmd.Parameters["@ID"].Value = id;
                patentCmd.Parameters["@Number"].Value = number;
                patentCmd.Parameters["@Country"].Value = country;
                patentCmd.Parameters["@Approved"].Value = approved;
                patentCmd.Parameters["@Expires"].Value = expires;
                patentCmd.Parameters["@Pediatric_Extension"].Value = pediatric_extension;

                patentCmd.ExecuteNonQuery();

            }
        }
        public void AddSequences(SqlConnection conn, XElement drug, string id)
        {
            string format = "";
            string sequence = "";

            foreach (XElement xSequence in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("sequence")))
            {
                format = (string)xSequence.Attribute("format");
                sequence = ((string)xSequence).Trim();

                sequenceCmd.Parameters["@ID"].Value = id;
                sequenceCmd.Parameters["@Format"].Value = format == null ? "" : format;
                sequenceCmd.Parameters["@Type"].Value = "sequence";
                sequenceCmd.Parameters["@Sequence"].Value =sequence;

                sequenceCmd.ExecuteNonQuery(); 
            }

            XElement amino_acid_sequence = drug.Descendants().Where(XElement => XElement.Name.LocalName == ("amino-acid-sequence")).FirstOrDefault();
            if (amino_acid_sequence != null)
            {
                format = (string)amino_acid_sequence.Attribute("format");
                sequence = ((string)amino_acid_sequence).Trim();

                sequenceCmd.Parameters["@ID"].Value = id;
                sequenceCmd.Parameters["@Format"].Value = format;
                sequenceCmd.Parameters["@Type"].Value = "amino-acid-sequence";
                sequenceCmd.Parameters["@Sequence"].Value = sequence;

                sequenceCmd.ExecuteNonQuery();
            }

            XElement gene_sequence = drug.Descendants().Where(XElement => XElement.Name.LocalName == ("gene-sequence")).FirstOrDefault();
            if (gene_sequence != null)
            {
                format = (string)gene_sequence.Attribute("format");
                sequence = ((string)gene_sequence).Trim();

                sequenceCmd.Parameters["@ID"].Value = id;
                sequenceCmd.Parameters["@Format"].Value = format;
                sequenceCmd.Parameters["@Type"].Value = "gene_sequence";
                sequenceCmd.Parameters["@Sequence"].Value = sequence;

                sequenceCmd.ExecuteNonQuery();
            }

        }
        public void AddProperties(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement property in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("property")))
            {
                string kind = ((string)property.Elements().Where(XElement => XElement.Name.LocalName == "kind").FirstOrDefault()).Trim();
                string value = ((string)property.Elements().Where(XElement => XElement.Name.LocalName == "value").FirstOrDefault()).Trim();
                string source = ((string)property.Elements().Where(XElement => XElement.Name.LocalName == "source").FirstOrDefault()).Trim();

                propertyCmd.Parameters["@ID"].Value = id;
                propertyCmd.Parameters["@Kind"].Value = kind;
                propertyCmd.Parameters["@Value"].Value = value;
                propertyCmd.Parameters["@Source"].Value = source;

                propertyCmd.ExecuteNonQuery();
            }
        }
        public void AddIdentifiers(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement xIdentifier in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("external-identifier")))
            {
                string resource = ((string)xIdentifier.Elements().Where(XElement => XElement.Name.LocalName == "resource").FirstOrDefault()).Trim();
                string identifier = ((string)xIdentifier.Elements().Where(XElement => XElement.Name.LocalName == "identifier").FirstOrDefault()).Trim();

                identifierCmd.Parameters["@ID"].Value = id;
                identifierCmd.Parameters["@Resource"].Value = resource;
                identifierCmd.Parameters["@Identifier"].Value = identifier;

                identifierCmd.ExecuteNonQuery();

            }
        }
        public void AddEnzymes(SqlConnection conn, XElement drug, string id)
        {
            foreach (XElement enzyme in drug.Descendants().Where(XElement => XElement.Name.LocalName == ("uniprot-id")))
            {
                string uniprot_id = (string)enzyme;

                enzymCmd.Parameters["@ID"].Value = id;
                enzymCmd.Parameters["@UniprotID"].Value = uniprot_id;

                enzymCmd.ExecuteNonQuery();

            }
        }

    }
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  • 感动是毒
    2020-12-15 14:48

    Just to add an alternative version, 

    while (reader.Read())
{
    if (reader.NodeType == XmlNodeType.Element &&  reader.Name == "product")
    {                   
        var productElement = XElement.ReadFrom(reader);

        // use element
        string productName = productElement.Element("name").Value;
    }
}

    The XElement class is from System.Xml.Linq , I find it the easiest way to deal with XML (without full deserialization to a class).

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