Proteomics repository retriever

mzLib/Test/TestPrideProjectRetriever.cs

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+using NUnit.Framework;
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using UsefulProteomicsDatabases;
+using NUnit.Framework;
+
+namespace Test
+{
+    [TestFixture]
+    [System.Diagnostics.CodeAnalysis.ExcludeFromCodeCoverage]
+    public class TestPrideProjectRetriever
+    {
+        [Test]
+        public void TestProjectRetrieve()
+        {
+            string projectAccession = "PXD048176";
+            string outputFullFilePath = @"E:\junk\junk.txt";
+
+            //UP000008595 is Uukuniemi virus (strain S23) (Uuk) which only has 4 proteins
+            string returnedFilePath = PrideRetriever.RetrieveMassSpecProject("", outputFullFilePath);
+
+            Assert.AreEqual(outputFullFilePath, returnedFilePath);
+        }
+        [Test]
+        public void TestRetrieveProjectFileByName()
+        {
+            string projectAccession = "PXD048176";
+            string filename = "d_atg1_d_atg11_proteome_data_analysis.7z";
+            string outputDirectory = @"E:\junk";
+
+            //UP000008595 is Uukuniemi virus (strain S23) (Uuk) which only has 4 proteins
+            string returnedFilePath = PrideRetriever.RetrieveProjectFileByFilename(projectAccession,filename, outputDirectory);
+
+            Assert.AreEqual(outputDirectory, returnedFilePath);
+        }
+        [Test]
+        public void TestRetrieveProjectFileListByProjectAccession()
+        {
+            string projectAccession = "PXD048176";
+            string outputDirectory = @"E:\junk";
+
+            //UP000008595 is Uukuniemi virus (strain S23) (Uuk) which only has 4 proteins
+            string returnedFilePath = PrideRetriever.RetrieveProjectFileListByProjectAccession(projectAccession,  outputDirectory);
+
+            Assert.AreEqual(outputDirectory, returnedFilePath);
+        }
+        [Test]
+        public void TestPrideFtp()
+        {
+            PrideRetriever.PrideFtp();
+        }
+
+        [Test]
+        public void TestSimpleWebClientDownload()
+        {
+            string uri = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD048176/d_atg1_d_atg11_proteome_data_analysis.7z";
+            string fullFilePath = @"E:\junk\PXD048176\d_atg1_d_atg11_proteome_data_analysis.7z";
+            PrideRetriever.SimpleWebClientDownload(uri,fullFilePath);
+        }
+
+        [Test]
+        public void DownloadUniProtProteomes()
+        {
+            var j = ProteinDbRetriever.DownloadAvailableUniProtProteomes(@"E:\junk");
+        }
+    }
+}

mzLib/UsefulProteomicsDatabases/PrideRetriever.cs

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+using Easy.Common;
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Net;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace UsefulProteomicsDatabases
+{
+    public class PrideRetriever
+    {
+        private string b = "https://www.ebi.ac.uk/pride/ws/archive/v2/status/PXD048177";
+
+
+        public static string RetrieveMassSpecProject(string PrideProjectAccession, string outputFullFilePath)
+        {
+            string htmlQueryString = "https://www.ebi.ac.uk/pride/ws/archive/v2/status/" + PrideProjectAccession;
+
+            if (htmlQueryString.Length > 0)
+            {
+                Loaders.DownloadContent(htmlQueryString, outputFullFilePath);
+                return outputFullFilePath;
+            }
+
+            return "";
+        }
+        public static string RetrieveProjectFileByFilename(string prideProjectAccession, string prideFilename, string outputFileDirectory)
+        {
+            string htmlQueryString =
+                "https://www.ebi.ac.uk/pride/ws/archive/v2/files/fileByName?fileName=" + prideFilename + "&projectAccession=" + prideProjectAccession;
+
+            if (htmlQueryString.Length > 0)
+            {
+                Loaders.DownloadContent(htmlQueryString, Path.Join(outputFileDirectory,prideFilename));
+                return outputFileDirectory;
+            }
+
+            return "";
+        }
+        public static string RetrieveProjectFileListByProjectAccession(string prideProjectAccession, string outputFileDirectory)
+        {
+            string htmlQueryString =
+                "https://www.ebi.ac.uk/pride/private/ws/archive/v2/" + "projects/" + prideProjectAccession + "/files";
+
+            if (htmlQueryString.Length > 0)
+            {
+                Loaders.DownloadContent(htmlQueryString, Path.Join(outputFileDirectory, prideProjectAccession + ".json"));
+                return outputFileDirectory;
+            }
+
+            return "";
+        }
+        public static void PrideFtp()
+        {
+            // Get the object used to communicate with the server.
+            FtpWebRequest request = (FtpWebRequest)WebRequest.Create("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD048176/d_atg1_d_atg11_proteome_data_analysis.7z");
+            request.Method = WebRequestMethods.Ftp.DownloadFile;
+
+            // This example assumes the FTP site uses anonymous logon.
+            request.Credentials = new NetworkCredential("anonymous", "anonymous");
+
+            request.KeepAlive = true;
+            request.UsePassive = true;
+            request.UseBinary = true;
+
+            //// Read the file from the server & write to destination                
+            //using (FtpWebResponse response = (FtpWebResponse)request.GetResponse()) // Error here
+            //using (Stream responseStream = response.GetResponseStream())
+            //using (StreamReader reader = new StreamReader(responseStream))
+            //using (StreamWriter destination = new StreamWriter(destinationFile))
+            //{
+            //    destination.Write(reader.ReadToEnd());
+            //    destination.Flush();
+            //}
+
+        }
+
+        public static void SimpleWebClientDownload(string url, string fullFilePath)
+        {
+            WebClient client = new WebClient();
+            client.Credentials = new NetworkCredential("anonymous", "anonymous");
+            client.DownloadFile(
+                url, fullFilePath);
+        }
+    }
+}