将XML导入PostgreSQL数据库或转换XML->CSV->PostgreSQL

我有一个XML文件

<Cluster clsId="UNIPR_NIRI_PARDP" semType="geneProt"> <Entry entryId="UNIPR_NIRI_PARDP_1" baseForm="Protein nirI" type="PREFERRED">

<Variant WRITTENFORM="FMN-binding domain protein" type="orthographic"/> <Variant WRITTENFORM="FMN-binding domain-containing protein" type="orthographic"/> <Variant WRITTENFORM="unknown" type="orthographic"/> <Variant WRITTENFORM="FMN-binding" type="orthographic"/> <Variant WRITTENFORM="Pden_2486" type="orthographic"/> <Variant WRITTENFORM="nirI" type="orthographic"/> <SourceDC sourceName="BioThesaurus" sourceId="Q51699"/> <PosDC posName="POS" pos="N"/> <DC att="uniprot_ac" val="Q51699"/> <DC att="speciesNameNCBI" val="318586"/>

</Entry> </Cluster>

我需要将此内容导入postgresql。请在这方面帮助我，或者直接将XML转换为csv，或者将其转换为PostgreSQL

我需要有如下列的表

clsid、entryid、semType、baseForm、VARIANETWRITTENFORM、varianttype、dcatt、dcval

---

提前感谢。

首先，解析xml文件以获得包含所有所需信息的文件

例如，如果您只想有一个具有属性clsid、entryid、semType、baseForm、VarietWritenForm、varianttype、dcatt、dcval的表，那么您只需要一个文件，其中这些属性用一些字符分隔。文件中的每一行都对应于表中的每一行

接下来，在Postgresql中创建表模式。然后使用Postgresql的COPY命令，将所有数据从文件复制到表中

注意，如果您的xml文件很大，您应该使用基于事件的解析器。比如Java中的SAX和StAX

编辑 *注*：使用的库：stax2-api-3.1.1.jar、woodstox-core-asl-4.1.1jar 下面是代码，希望它能满足您的需要，如果没有，我相信它会让您开始：

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package test;

import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.net.MalformedURLException;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import java.util.ArrayList;
import org.codehaus.stax2.XMLInputFactory2;
import org.codehaus.stax2.XMLStreamReader2;

public class Main {

    /**
     * @param args the command line arguments
     */

    /*
     * dc(att), dc(val)
     */
    @SuppressWarnings("CallToThreadDumpStack")
    public static void main(String[] args) throws MalformedURLException, IOException, XMLStreamException {
        FileInputStream fstream = new FileInputStream(args[0]);
        Reader in = new InputStreamReader(fstream, "UTF-8");
        XMLInputFactory2 factory = (XMLInputFactory2) XMLInputFactory.newInstance();
        XMLStreamReader2 parser = (XMLStreamReader2) factory.createXMLStreamReader(in);

        FileOutputStream outStream = new FileOutputStream("/home/aseke/Desktop/out.txt");
        BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream, "UTF-8"));


        boolean isCluster = false;
        ArrayList<String> dc = new ArrayList<String>();
        ArrayList<String> variants = new ArrayList<String>();

        /* You actually do not need all of these variables, it's just for clarity */
        String clsID = null;
        String semType = null;
        String varWritten = null;
        String varType = null;
        String entryID = null;
        String baseForm = null;
        String dcAtt = null;
        String dcVal = null;
        String s = null;
        while (true) {
            int event = parser.next();
            if (event == XMLStreamConstants.END_DOCUMENT) {
                parser.close();
                break;
            }

            if (event == XMLStreamConstants.START_ELEMENT) {
                String tag = parser.getLocalName();

                if (tag.equals("Cluster")) {
                    isCluster = true;
                    clsID = parser.getAttributeValue(0);
                    semType = parser.getAttributeValue(1);
                } else if (tag.equals("Entry") && isCluster) {
                    entryID = parser.getAttributeValue(0);
                    baseForm = parser.getAttributeValue(1);
                } else if (tag.equals("Variant") && isCluster) {

                    varWritten = parser.getAttributeValue(0);
                    varType = parser.getAttributeValue(1);

                    variants.add(varWritten + "~" + varType);
                } else if (tag.equals("DC") && isCluster) {
                    dcAtt = parser.getAttributeValue(0);
                    dcVal = parser.getAttributeValue(1);

                    dc.add(dcAtt + "~" + dcVal);
                }
            }

            if (event == XMLStreamConstants.END_ELEMENT && isCluster) {
                if (parser.getLocalName().equals("Cluster")) {
                    isCluster = false;
                    //clsid, entryid, semType, baseForm, variant(writtenform), variant(type), dc(att), dc(val)
                    // Use tabs as delimiter for Postgre COPY
                    String outStr = clsID + "/t" + entryID + "/t" + semType + "/t" + baseForm + "/t";

                    /* Add all variants */
                    for (String var : variants) {
                        String tmp[] = var.split("~");
                        varWritten = tmp[0];
                        varType = tmp[1];
                        outStr += varWritten + "/t" + varType + "/t";
                    }
                    /* Add al DCs */
                    for (String ss : dc) {
                        String[] tmp = ss.split("~");
                        dcAtt = tmp[0];
                        dcVal = tmp[1];
                        outStr += dcAtt + "/t" + dcVal + "/t";
                    }
                    // remove last tab "\t"
                    outStr = outStr.substring(0, outStr.length() - 2);
                    out.write(outStr);
                    variants.clear();
                    dc.clear();

                }
            }
        }

        // close all streams
        fstream.close();
        out.close();
        outStream.close();
    }
}

---

我在noko giri和OpenURI包的帮助下使用Ruby完成了这项工作。我的输入文件太大了。许多解析器都失败了，noko giri为此提供了帮助

我提供了三列答案，baseformvariantwrittenformdcval。此信息可能是问题的清晰信息

require 'nokogiri'
require 'open-uri'

doc = Nokogiri::XML(File.open("xai"))
ent = doc.xpath("//Entry")

value = String.new
ent.each do |e| 
    d = e.xpath("DC")   
    d.each do |f|       
        if f.attributes["att"].to_s =~ /uniprot_ac/
            value = f.attributes["val"].to_s
        end
    end
    f = e.xpath("Variant")  
    f.each do |g|
        puts "#{e.attributes["baseForm"].to_s}\t" + "#{g.attributes["WRITTENFORM"].to_s}\t" + "#{value}"
    end 
end

---

-首先，解析xml文件以获得包含所有所需信息的文件。建议我用一种简单的方法将xml文件解析成我所需要的所有文件。@Palani Kannan如果您使用java，我建议使用StAX解析器的woodstox实现。它使用起来非常简单。我相信你可以在网上找到一些例子。我是ruby用户。我用ruby做的。谢谢你的帮助。

UNIPR_NIRI_PARDP/tUNIPR_NIRI_PARDP_1/tgeneProt/tProtein nirI/tFMN-binding domain protein/torthographic/tFMN-binding domain-containing protein/torthographic/tunknown/torthographic/tFMN-binding/torthographic/tPden_2486/torthographic/tnirI/torthographic/tuniprot_ac/tQ51699/tspeciesNameNCBI/t318586

require 'nokogiri'
require 'open-uri'

doc = Nokogiri::XML(File.open("xai"))
ent = doc.xpath("//Entry")

value = String.new
ent.each do |e| 
    d = e.xpath("DC")   
    d.each do |f|       
        if f.attributes["att"].to_s =~ /uniprot_ac/
            value = f.attributes["val"].to_s
        end
    end
    f = e.xpath("Variant")  
    f.each do |g|
        puts "#{e.attributes["baseForm"].to_s}\t" + "#{g.attributes["WRITTENFORM"].to_s}\t" + "#{value}"
    end 
end