Feat/Process Genome Data on ios

lib/zama/src/lib.rs

@@ -3,7 +3,9 @@ use std::os::raw::c_char;
 
 use tfhe::prelude::*;
 use tfhe::{ConfigBuilder, FheUint8, FheUint32, generate_keys, set_server_key};
-use bincode; // Make sure to add bincode to Cargo.toml
+use bincode;
+
+// use crate::genome_processing::{encode_genotype, get_genotype_encoding_map};
 
 #[unsafe(no_mangle)]
 pub extern "C" fn zama_run() -> *mut c_char {
@@ -71,7 +73,41 @@ pub extern "C" fn zama_get_client_key() -> *mut c_char {
     // Key generation
     let (client_key, server_keys) = generate_keys(config);
 
+    CString::new(serde_json::to_string(&client_key).unwrap())
+        .unwrap()
+        .into_raw()
+}
+
+
+#[unsafe(no_mangle)]
+pub extern "C" fn zama_get_server_key() -> *mut c_char {
+    // Basic configuration to use homomorphic integers
+    let config = ConfigBuilder::default().build();
+
+    // Key generation
+    let (client_key, server_keys) = generate_keys(config);
+
     CString::new(serde_json::to_string(&server_keys).unwrap())
         .unwrap()
         .into_raw()
 }
+
+// TODO: use a single function in getting the keys
+#[unsafe(no_mangle)]
+pub extern "C" fn zama_get_keys() -> *mut c_char {
+    let config = ConfigBuilder::default().build();
+
+    let (client_key, server_keys) = generate_keys(config);
+
+    // Serialize both keys into a JSON object
+    let keys = serde_json::json!({
+        "client_key": client_key,
+        "server_keys": server_keys,
+    });
+
+    // Serialize the entire JSON object to a string
+    let json_str = serde_json::to_string(&keys).unwrap();
+
+    // Convert to a CString and return a raw pointer
+    CString::new(json_str).unwrap().into_raw()
+}

monadic_ios/includes/lib_headers.h

@@ -5,9 +5,19 @@
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdlib.h>
+#include <stddef.h>
 
 char* zama_run();
 char* zama_get_client_key();
+char* zama_get_server_key();
+char* zama_get_keys();
+
+int32_t zama_process_genome_data(
+    const char* filename,
+    size_t num_lines,
+    const char* client_key_json,
+    const char* server_key_json
+);
 
 
 #endif

monadic_ios/monadic_ios.xcodeproj/project.pbxproj

@@ -7,8 +7,9 @@
 	objects = {
 
 /* Begin PBXBuildFile section */
-		CA445A852CFE803400BF9EFC /* libzama.a in Frameworks */ = {isa = PBXBuildFile; fileRef = CA445A842CFE802B00BF9EFC /* libzama.a */; };
+		CA42209D2D06772700AD2E5A /* libzama.a in Frameworks */ = {isa = PBXBuildFile; fileRef = CA42209C2D06771E00AD2E5A /* libzama.a */; };
 		CA445A8B2CFE855A00BF9EFC /* KeychainSwift in Frameworks */ = {isa = PBXBuildFile; productRef = CA445A8A2CFE855A00BF9EFC /* KeychainSwift */; };
+		CAB71F242D06C2E8004A4B4E /* libzama_poc.a in Frameworks */ = {isa = PBXBuildFile; fileRef = CAB71F232D06C2DE004A4B4E /* libzama_poc.a */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXContainerItemProxy section */
@@ -29,11 +30,12 @@
 /* End PBXContainerItemProxy section */
 
 /* Begin PBXFileReference section */
-		CA445A842CFE802B00BF9EFC /* libzama.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libzama.a; path = libs/libzama.a; sourceTree = "<group>"; };
+		CA42209C2D06771E00AD2E5A /* libzama.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libzama.a; path = libs/libzama.a; sourceTree = "<group>"; };
 		CA98B90A2CF5E864006ABA9E /* monadic_ios.app */ = {isa = PBXFileReference; explicitFileType = wrapper.application; includeInIndex = 0; path = monadic_ios.app; sourceTree = BUILT_PRODUCTS_DIR; };
 		CA98B91A2CF5E866006ABA9E /* monadic_iosTests.xctest */ = {isa = PBXFileReference; explicitFileType = wrapper.cfbundle; includeInIndex = 0; path = monadic_iosTests.xctest; sourceTree = BUILT_PRODUCTS_DIR; };
 		CA98B9242CF5E866006ABA9E /* monadic_iosUITests.xctest */ = {isa = PBXFileReference; explicitFileType = wrapper.cfbundle; includeInIndex = 0; path = monadic_iosUITests.xctest; sourceTree = BUILT_PRODUCTS_DIR; };
 		CA98BA822CF876B8006ABA9E /* Bridging-Header.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = "Bridging-Header.h"; sourceTree = "<group>"; };
+		CAB71F232D06C2DE004A4B4E /* libzama_poc.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libzama_poc.a; path = libs/libzama_poc.a; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXFileSystemSynchronizedRootGroup section */
@@ -59,8 +61,9 @@
 			isa = PBXFrameworksBuildPhase;
 			buildActionMask = 2147483647;
 			files = (
+				CAB71F242D06C2E8004A4B4E /* libzama_poc.a in Frameworks */,
+				CA42209D2D06772700AD2E5A /* libzama.a in Frameworks */,
 				CA445A8B2CFE855A00BF9EFC /* KeychainSwift in Frameworks */,
-				CA445A852CFE803400BF9EFC /* libzama.a in Frameworks */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -106,7 +109,8 @@
 		CA98BA7D2CF87545006ABA9E /* Frameworks */ = {
 			isa = PBXGroup;
 			children = (
-				CA445A842CFE802B00BF9EFC /* libzama.a */,
+				CAB71F232D06C2DE004A4B4E /* libzama_poc.a */,
+				CA42209C2D06771E00AD2E5A /* libzama.a */,
 			);
 			name = Frameworks;
 			sourceTree = "<group>";
@@ -431,7 +435,10 @@
 					"$(inherited)",
 					"@executable_path/Frameworks",
 				);
-				LIBRARY_SEARCH_PATHS = "$(PROJECT_DIR)/libs";
+				LIBRARY_SEARCH_PATHS = (
+					"$(PROJECT_DIR)/libs",
+					"$(PROJECT_DIR)",
+				);
 				"LIBRARY_SEARCH_PATHS[arch=*]" = "$(PROJECT_DIR)/libs";
 				MARKETING_VERSION = 1.0;
 				PRODUCT_BUNDLE_IDENTIFIER = "com.aisha.monadic-ios";
@@ -463,7 +470,10 @@
 					"$(inherited)",
 					"@executable_path/Frameworks",
 				);
-				LIBRARY_SEARCH_PATHS = "$(PROJECT_DIR)/libs";
+				LIBRARY_SEARCH_PATHS = (
+					"$(PROJECT_DIR)/libs",
+					"$(PROJECT_DIR)",
+				);
 				"LIBRARY_SEARCH_PATHS[arch=*]" = "$(PROJECT_DIR)/libs";
 				MARKETING_VERSION = 1.0;
 				PRODUCT_BUNDLE_IDENTIFIER = "com.aisha.monadic-ios";

monadic_ios/monadic_ios/ContentView.swift

@@ -11,11 +11,18 @@ struct ContentView: View {
     @State private var statusText: String = ""
     @State private var clientKeyText: String = ""
 
+    // Define the number of lines
+    @State private var numLines = 20
+
+    @State private var presentImporter = false
+
+
     var body: some View {
         VStack {
+
             Text(statusText)
                 .padding()
-            
+
             Button("Run Zama Code") {
                 if let result = zama_run() {
                     let resultString = String(cString: result)
@@ -24,8 +31,27 @@ struct ContentView: View {
                 }
                 storeClientKey()
             }
-
-
+
+            Button("Upload Genome Data") {
+                presentImporter = true
+            }.fileImporter(isPresented: $presentImporter, allowedContentTypes: [.text]) { result in
+                uploadAndProcessGenomeData(result: result)
+            }
+            .padding()
+            .background(Color.blue)
+            .foregroundColor(.white)
+            .cornerRadius(8)
+
+            Button("Retrieve Server Key") {
+                guard let serverKey = retrieveServerKey() else {
+                    clientKeyText = "No server key found in keychain"
+                    return
+                }
+                let serverKeyLength = strlen(serverKey)
+                print("Length of server key: \(serverKeyLength)")
+            }
+
+
             Button("Retrieve Client Key") {
                 guard let clientKey = retrieveClientKey() else {
                     clientKeyText = "No client key found in keychain"
@@ -35,16 +61,35 @@ struct ContentView: View {
                 print("Length of client key: \(clientKeyLength)")
 
                 //                clientKeyText = clientKey
-                
+
                 clientKeyText = "Length of client key: \(clientKeyLength)"
-                
+
             }
         }
     }
+
+    func uploadAndProcessGenomeData(result: Result<URL, Error>) {
+        guard let url = try? result.get() else {
+            print("File upload failed:", result)
+            return
+        }
+
+        guard url.startAccessingSecurityScopedResource() else {
+            print("Failed to access file resource.")
+            return
+        }
+        defer { url.stopAccessingSecurityScopedResource() }
+
+        guard let filename = url.path.removingPercentEncoding else {
+            print("Filename is invalid.")
+            return
+        }
+
+        processGenomeData(filename: filename, numLines: numLines)
+    }
 }
 
 
-
 #Preview {
     ContentView()
 }

monadic_ios/monadic_ios/utils/zama.swift

@@ -10,17 +10,66 @@ import KeychainSwift
 
 let keychain = KeychainSwift()
 
+struct ClientKey {
+    var key: [UInt8]
+}
+
+struct ServerKey {
+    var key: [UInt8]
+}
+
 func storeClientKey() {
     guard let clientKey = zama_get_client_key() else {
         print("Failed to retrieve client key.")
         return
     }
     let clientKeyString = String(cString: clientKey)
 
+    guard let serverKey = zama_get_server_key() else {
+        print("Failed to retrieve server key.")
+        return
+    }
+    let serverKeyString = String(cString: serverKey)
+
+
     keychain.set(clientKeyString, forKey: "zamaClientKey")
+    keychain.set(serverKeyString, forKey: "zamaServerKey")
+
     print("Successfully stored client key.")
 }
 
 func retrieveClientKey() -> String? {
     return keychain.get("zamaClientKey")
 }
+func retrieveServerKey() -> String? {
+    return keychain.get("zamaServerKey")
+}
+
+
+func processGenomeData(filename: String, numLines: Int) {
+    // Retrieve keys from Keychain
+    guard let clientKey = retrieveClientKey(), let serverKey = retrieveServerKey() else {
+        print("Failed to retrieve keys from Keychain.")
+        return
+    }
+
+    // Convert keys to C strings
+    let clientKeyCString = (clientKey as NSString).utf8String
+    let serverKeyCString = (serverKey as NSString).utf8String
+
+
+    // Call zama_process_genome_data
+    let result = zama_process_genome_data(
+        filename,
+        numLines,
+        clientKeyCString,
+        serverKeyCString
+    )
+
+    if result == 0 {
+        print("Iteration completed successfully.")
+    } else {
+        print("Iteration failed.")
+    }
+}
+

zama-poc/Cargo.toml

@@ -11,14 +11,18 @@ bincode = "1.3.3"
 chrono = "0.4.38"
 env_logger = "0.11.3"
 log = "0.4.22"
-reqwest = { version = "0.11", features = ["json"] }
+reqwest = { version = "0.11", features = ["blocking", "json"] }
 rusqlite = { version = "0.26", features = ["bundled"] }
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 tfhe = { version = "0.7.1", features = [ "boolean", "shortint", "integer", "aarch64-unix" ] }
 tokio = { version = "1", features = ["full"] }
 tokio-stream = "0.1"
 
+[lib]
+crate-type = ["staticlib"]
+
+
 [[bin]]
 name = "main"
 path = "src/main.rs"
@@ -30,3 +34,4 @@ path = "src/server.rs"
 [[bin]]
 name = "client"
 path = "src/client.rs"
+

zama-poc/src/ffi/mod.rs

@@ -0,0 +1 @@
+pub mod processing;