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Merge branch 'main' into george-branch
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@danielfang97
danielfang97 authored Jul 8, 2023
2 parents 6e14726 + 52704f8 commit 9c4d118
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Showing 43 changed files with 951 additions and 385 deletions.
97 changes: 77 additions & 20 deletions backend/src/main/java/com/synbiohub/sbh3/controllers/AdminController.java
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Original file line number Diff line number Diff line change
@@ -1,16 +1,22 @@
package com.synbiohub.sbh3.controllers;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.synbiohub.sbh3.security.model.User;
import com.synbiohub.sbh3.services.AdminService;
import com.synbiohub.sbh3.services.SearchService;
import com.synbiohub.sbh3.services.UserService;
import com.synbiohub.sbh3.utils.ConfigUtil;
import jakarta.servlet.http.HttpServletRequest;
import lombok.AllArgsConstructor;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.web.bind.annotation.*;

import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

@RestController
Expand All @@ -20,12 +26,12 @@ public class AdminController {
private final AdminService adminService;
private final UserService userService;
private final SearchService searchService;


@GetMapping(value = "/admin/sparql")
@ResponseBody
public String runAdminSparqlQuery(@RequestParam String query) throws IOException {
Authentication auth = userService.checkAuthentication();
public String runAdminSparqlQuery(@RequestParam String query, HttpServletRequest request) throws Exception {
String inputToken = request.getHeader("X-authorization");
// Authentication auth = userService.checkAuthentication(inputToken);
Authentication auth = SecurityContextHolder.getContext().getAuthentication();
if (auth == null) {
return null;
}
Expand All @@ -34,14 +40,19 @@ public String runAdminSparqlQuery(@RequestParam String query) throws IOException

@GetMapping(value = "/admin")
@ResponseBody
public String status(@RequestParam Map<String,String> allParams, HttpServletRequest request) throws IOException {
return adminService.getStatus().toString();
public String status(@RequestParam Map<String,String> allParams, HttpServletRequest request) throws Exception {
return adminService.getStatus(request).toString();
}

/**
* This will just run a basic query on Virtuoso. If the result exists, return "Alive". Otherwise, return "Dead".
* @return
*/
@GetMapping(value = "/admin/virtuoso")
@ResponseBody
public String getVirtuosoStatus(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
public String getVirtuosoStatus() {
boolean vStatus = adminService.getDatabaseStatus();
return vStatus ? "Alive" : "Dead";
}

@GetMapping(value = "/admin/graphs")
Expand All @@ -54,8 +65,11 @@ public String getGraph(@RequestParam Map<String,String> allParams, HttpServletRe
@GetMapping(value = "/admin/log")
@ResponseBody
public String getLog(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
// prints the spring.log?
return null;
try {
return adminService.getLogs();
} catch (Exception e) {
return "Error reading spring.log file " + e.getMessage();
}
}

@GetMapping(value = "/admin/mail")
Expand All @@ -70,6 +84,7 @@ public String updateMailSettings(@RequestParam Map<String,String> allParams, Htt
return null;
}

//TODO: get admin plugins needs to be public, post admin plugins need to be admin only
@GetMapping(value = "/admin/plugins")
@ResponseBody
public String getPlugins(@RequestParam Map<String,String> allParams, HttpServletRequest request) throws IOException {
Expand All @@ -78,14 +93,38 @@ public String getPlugins(@RequestParam Map<String,String> allParams, HttpServlet

@PostMapping(value = "/admin/savePlugin")
@ResponseBody
public String savePlugin(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
public String savePlugin(@RequestParam Map<String,String> allParams, HttpServletRequest request) throws IOException {
if (!ConfigUtil.checkLocalJson("plugins")) {
ConfigUtil.set(ConfigUtil.getLocaljson(),"plugins", ConfigUtil.get("plugins"));
ConfigUtil.refreshLocalJson();
}
ObjectMapper mapper = new ObjectMapper();
if (allParams.get("id").equals("New")) {
int pluginArraySize = ConfigUtil.get("plugins").get(allParams.get("category")).size();
ArrayNode pluginArray = adminService.saveNewPlugin(allParams);
if (pluginArraySize != pluginArray.size()) {
mapper.writerWithDefaultPrettyPrinter().writeValue(new File("data/config.local.json"), ConfigUtil.getLocaljson());
return "Plugin (New, " + allParams.get("name") + ", " + allParams.get("url") + "/, " + allParams.get("category") + ") saved successfully";
} else {
return "Error saving new plugin: " + allParams.get("name");
}
} else {
adminService.updatePlugin(allParams);
return "Plugin " + allParams.get("name") + " updated.";
}
}

@PostMapping(value = "/admin/deletePlugin")
@ResponseBody
public String deletePlugin(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
try {
ObjectMapper mapper = new ObjectMapper();
adminService.deletePlugin(allParams.get("category"), allParams.get("id"));
mapper.writerWithDefaultPrettyPrinter().writeValue(new File("data/config.local.json"), ConfigUtil.getLocaljson());
return "Plugin ("+ allParams.get("id") + ", " + allParams.get("category") + ") deleted successfully";
} catch (IOException e) {
throw new RuntimeException(e);
}
}

@GetMapping(value = "/admin/registries")
Expand All @@ -109,8 +148,19 @@ public void deleteRegistry(@RequestBody String webOfRegistryName) {

@PostMapping(value = "/admin/setAdministratorEmail")
@ResponseBody
public String setAdminEmail(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
public String setAdminEmail(String newEmail) throws Exception {
User adminUser = userService.getUserProfile();
try {
if (adminUser.getIsAdmin()) {
Map<String, String> params = new HashMap<>();
params.put("email", newEmail);
userService.updateUserProfile(params);
return "Updated administrator email";
}
} catch (Exception e) {
return "Unable to update administrator email " + e.getMessage();
}
return "Unable to update administrator email, but no error was thrown";
}

@PostMapping(value = "/admin/retrieveFromWebOfRegistries")
Expand All @@ -122,14 +172,14 @@ public String updateRegistries(@RequestParam Map<String,String> allParams, HttpS
@PostMapping(value = "/admin/federate")
@ResponseBody
public String sendFederateRequest(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
return "This is send Federate Request. It is not yet implemented.";
}

@GetMapping(value = "/admin/remotes")
@ResponseBody
public String getRemotes(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
public String getRemotes() throws IOException {
// TODO: need to check format of remotes
return null;
return ConfigUtil.get("remotes").toString();
}

@PostMapping(value = "/admin/saveRemote") //benchling and ice remotes have different params
Expand Down Expand Up @@ -162,12 +212,19 @@ public String updateExplorerConfig(@RequestParam Map<String,String> allParams, H
return null;
}

/**
* I am not sure what this should be. It is a post request, but right now, all it's doing is getting the status
* @return
*/
// TODO: check if this method should be returning SBOL Explorer status
@PostMapping(value = "/admin/explorerUpdateIndex")
@ResponseBody
public String updateExplorerIndex(@RequestParam Map<String,String> allParams, HttpServletRequest request) {
return null;
public String updateExplorerIndex() throws IOException {
boolean SBOLExplorerStatus = adminService.getSBOLExplorerStatus();
return SBOLExplorerStatus ? "SBOLExplorer is not enabled" : "SBOLExplorer is enabled";
}

//TODO: get admin theme needs to be public, post admin theme needs to be admin only
@GetMapping(value = "/admin/theme")
@ResponseBody
public String getTheme() throws IOException {
Expand Down
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