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  • Phytophthoraregistrering-VIPSUTV-735
  • UpdateGrovfor
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  • VIPS/VIPSLogic
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  • Phytophthoraregistrering-VIPSUTV-735
  • UpdateGrovfor
  • VIPSInSchweiz
  • addIsPrivateToPOI-VIPSUTV-767
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  • develop
  • feature/time-series
  • feature/time-series-in-vipsweb
  • feature/upgrade-openlayers
  • feature/vipsutv-1047-timeseries
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34 results
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Dockerfile
View file @ aa5eda39
......@@ -4,7 +4,7 @@
# the first stage of our build will use a maven 3.6 parent image
FROM maven:3.6-openjdk-11 AS MAVEN_BUILD
FROM maven:3.8-openjdk-11 AS MAVEN_BUILD
# We need VIPSCommon too, so the source code must be available in the parent folder
COPY ./VIPSCommon ./VIPSCommon
......
pom.xml
View file @ aa5eda39
......@@ -5,7 +5,7 @@
<groupId>no.nibio.vips.</groupId>
<artifactId>VIPSLogic</artifactId>
<packaging>war</packaging>
<version>2023.1</version>
<version>2024.1</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
......@@ -62,12 +62,12 @@
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>10.4.1</version>
<version>10.5.0</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-database-postgresql</artifactId>
<version>10.1.0</version>
<version>10.4.1</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
......@@ -93,6 +93,11 @@
<version>4.7.9.Final</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.geotools</groupId>
<artifactId>gt-api</artifactId>
<version>30.1</version>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
......@@ -109,7 +114,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
......@@ -187,24 +192,24 @@
<dependency>
<groupId>org.locationtech.jts</groupId>
<artifactId>jts-core</artifactId>
<version>1.18.2</version>
<version>1.19.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.wololo</groupId>
<artifactId>jts2geojson</artifactId>
<version>0.16.1</version>
<version>0.18.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.2</version>
<version>1.10.0</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>no.nibio.vips</groupId>
<artifactId>VIPSCommon</artifactId>
<version>2.0.1</version>
<version>2.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>javax</groupId>
......@@ -230,21 +235,6 @@
<artifactId>cron4j</artifactId>
<version>2.2.5</version>
</dependency>
<!--dependency>
<groupId>org.openid4java</groupId>
<artifactId>openid4java</artifactId>
<version>0.9.8</version>
</dependency-->
<dependency>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
<version>1.19.1</version>
</dependency>
<!--dependency>
<groupId>edu.vt.middleware</groupId>
<artifactId>vt-password</artifactId>
<version>3.1.2</version>
</dependency-->
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
......@@ -258,7 +248,7 @@
<dependency>
<groupId>javax.measure</groupId>
<artifactId>unit-api</artifactId>
<version>1.0</version>
<version>2.2</version>
</dependency>
<dependency>
<groupId>com.webcohesion.enunciate</groupId>
......@@ -273,7 +263,7 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.36</version>
<version>2.0.11</version>
<scope>provided</scope>
</dependency>
</dependencies>
......@@ -282,7 +272,7 @@
<plugins>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.2.0</version>
<version>3.6.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
......@@ -321,7 +311,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.2.3</version>
<version>3.2.5</version>
<configuration>
<argLine>-Xmx6048m</argLine>
</configuration>
......
selenium/tests/test_selenium.py
View file @ aa5eda39
......@@ -7,7 +7,12 @@ from selenium.webdriver.support import expected_conditions as EC
# https://github.com/SeleniumHQ/seleniumhq.github.io/blob/trunk/examples/python/README.md
# BROWSER = 'chrome'
BROWSER = "firefox"
# BROWSER = "firefox"
BROWSER = "edge"
HOST_URL = "http://vipslogic-local.no"
#HOST_URL = "https://logic.testvips.nibio.no"
#HOST_URL = "https://logic.vips.nibio.no"
@pytest.fixture
......@@ -20,10 +25,15 @@ def browser():
firefox_options = webdriver.FirefoxOptions()
firefox_options.headless = False
driver = webdriver.Firefox(options=firefox_options)
elif BROWSER == "edge":
edge_options = webdriver.EdgeOptions()
edge_options.headless = False
driver = webdriver.Edge(options=edge_options)
else:
raise Exception("Browser must be set to either chrome or firefox")
raise Exception("Browser must be set to chrome, firefox or edge")
driver.get("http://vipslogic/index.html")
#driver.get("http://vipslogic/index.html")
driver.get(f"{HOST_URL}/index.html")
assert driver.title == "Please log in"
driver.implicitly_wait(0.5)
......@@ -45,7 +55,7 @@ def test_admin_organisms(browser):
link = WebDriverWait(browser, 15).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Organisms"]'))
)
assert link.get_attribute("href") == "http://vipslogic/organism"
assert link.get_attribute("href") == f"{HOST_URL}/organism"
link.click()
assert browser.title == "Organisms"
link = WebDriverWait(browser, 15).until(
......@@ -60,7 +70,7 @@ def test_admin_scheduling(browser):
link = WebDriverWait(browser, 10).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Scheduling"]'))
)
assert link.get_attribute("href") == "http://vipslogic/scheduling"
assert link.get_attribute("href") == f"{HOST_URL}/scheduling"
link.click()
assert browser.title == "Scheduling overview"
......@@ -70,7 +80,7 @@ def test_admin_organization_group(browser):
link = WebDriverWait(browser, 10).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Organization groups"]'))
)
assert link.get_attribute("href") == "http://vipslogic/organizationgroup"
assert link.get_attribute("href") == f"{HOST_URL}/organizationgroup"
link.click()
assert browser.title == "Organization groups"
......@@ -80,7 +90,7 @@ def test_admin_apple_fruit_moth(browser):
link = WebDriverWait(browser, 10).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Apple fruit moth"]'))
)
assert link.get_attribute("href") == "http://vipslogic/applefruitmoth"
assert link.get_attribute("href") == f"{HOST_URL}/applefruitmoth"
link.click()
assert browser.title == "Rognebærmøllstasjoner"
......@@ -90,7 +100,7 @@ def test_admin_users(browser):
link = WebDriverWait(browser, 20).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Users"]'))
)
assert link.get_attribute("href") == "http://vipslogic/user"
assert link.get_attribute("href") == f"{HOST_URL}/user"
link.click()
WebDriverWait(browser, 20).until(
EC.visibility_of_element_located((By.XPATH, "//h1[text()='Users']"))
......@@ -103,7 +113,7 @@ def test_admin_forecasts(browser):
link = WebDriverWait(browser, 20).until(
EC.element_to_be_clickable((By.XPATH, '//a[text()="Forecasts"]'))
)
assert link.get_attribute("href") == "http://vipslogic/forecastConfiguration"
assert link.get_attribute("href") == f"{HOST_URL}/forecastConfiguration"
link.click()
WebDriverWait(browser, 20).until(
EC.visibility_of_element_located((By.XPATH, "//h1[text()='Forecasts']"))
......
src/main/java/no/nibio/vips/logic/controller/servlet/LoginController.java
View file @ aa5eda39
......@@ -19,13 +19,6 @@
package no.nibio.vips.logic.controller.servlet;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.api.client.googleapis.auth.oauth2.GoogleAuthorizationCodeRequestUrl;
import com.google.api.client.googleapis.auth.oauth2.GoogleAuthorizationCodeTokenRequest;
import com.google.api.client.googleapis.auth.oauth2.GoogleIdToken;
import com.google.api.client.googleapis.auth.oauth2.GoogleIdToken.Payload;
import com.google.api.client.googleapis.auth.oauth2.GoogleTokenResponse;
import com.google.api.client.http.javanet.NetHttpTransport;
import com.google.api.client.json.jackson2.JacksonFactory;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
......@@ -88,70 +81,9 @@ public class LoginController extends HttpServlet {
// We remove the session attribute, so it doesn't stick
request.getSession().removeAttribute(LoginController.RETURN_UUID_PARAMETER_NAME);
// This means that an OpenId authentication has returned the user to this URL
// See code below
if(request.getServletPath().contains("oauth2callback"))
{
// Is it an authorization response?
if(request.getParameter("code") != null)
{
String authorizationCode = request.getParameter("code");
// Verify state
String storedState = (String) request.getSession().getAttribute("state");
String receivedState = request.getParameter("state");
if(receivedState == null || storedState == null || ! storedState.equals(receivedState))
{
request.setAttribute("errorMessageKey", "invalidcredentials");
request.getRequestDispatcher("/login.ftl").forward(request, response);
return;
}
// Use code, make request to Google for getting token with user information
GoogleTokenResponse tokenResponse = new GoogleAuthorizationCodeTokenRequest(
new NetHttpTransport(),
new JacksonFactory(),
System.getProperty("no.nibio.vips.logic.GOOGLE_OPENID_CLIENT_ID"),
System.getProperty("no.nibio.vips.logic.GOOGLE_OPENID_CLIENT_SECRET"),
authorizationCode,
Globals.PROTOCOL + "://" + ServletUtil.getServerName(request) + "/oauth2callback"
).execute();
GoogleIdToken idToken = GoogleIdToken.parse(new JacksonFactory(), tokenResponse.getIdToken());
Payload payload = idToken.getPayload();
// Try to find the user
VipsLogicUser user = userBean.getUser(payload.getSubject(), UserAuthenticationType.TYPE_OPENID_GOOGLE);
if(user != null)
{
request.getSession().setAttribute("user", user);
UUID uUUID = this.handleRememberUser(request, response, user, returnUUID);
if(returnUUID)
{
nextPage += (nextPage.contains("?") ? "&": "?") + "returnUUID=" + uUUID.toString();
}
if(nextPage.indexOf(Globals.PROTOCOL) == 0)
{
System.out.println("nextPage=" + nextPage);
response.sendRedirect(nextPage);
}
else
{
response.sendRedirect(new StringBuilder(Globals.PROTOCOL + "://").append(ServletUtil.getServerName(request)).append(nextPage).toString());
}
}
else
{
// This might be
// * a new user
// * an existing user logging in with OpenId/Google for the first time.
// Sending user to form asking this question
request.setAttribute("userAuthenticationTypeId", UserAuthenticationType.TYPE_OPENID_GOOGLE);
request.getSession().setAttribute("openId", payload.getSubject());
request.getRequestDispatcher("/registerOpenIdForm.ftl").forward(request, response);
}
}
}
// A log out request
else if(request.getServletPath().contains("logout"))
if(request.getServletPath().contains("logout"))
{
request.getSession().removeAttribute("user");
Cookie rememberedUser = ServletUtil.getCookie(request, "rememberedUser");
......@@ -230,39 +162,6 @@ public class LoginController extends HttpServlet {
}
}
/* Login with Google OpenConnect/OAuth2
For documentation about how this is done, see:
https://developers.google.com/accounts/docs/OAuth2WebServer
and https://developers.google.com/accounts/docs/OpenIDConnect
ClientID, ClientSecret, callbacks etc. has been created by logging
in to https://console.developers.google.com as tor-einar.skog@nibio.no
*/
else if(userAuthenticationTypeId.equals(UserAuthenticationType.TYPE_OPENID_GOOGLE))
{
// configure the return_to URL where your application will receive
// the authentication responses from the OpenID Connect provider
String serverName = ServletUtil.getServerName(request);
String callbackUrl = Globals.PROTOCOL + "://" + serverName + "/oauth2callback" ;
// We store the information about the next page in a session
// as Google does not accept to forward it
request.getSession().setAttribute("nextPage", URLEncoder.encode(nextPage, "UTF-8"));
request.getSession().setAttribute(LoginController.RETURN_UUID_PARAMETER_NAME, returnUUID);
request.getSession().setAttribute("rememberUser", request.getParameter("rememberUser"));
// Token to check for security (avoid man-in-the-middle)
String state = new BigInteger(130, new SecureRandom()).toString(32);
request.getSession().setAttribute("state", state);
String url =
new GoogleAuthorizationCodeRequestUrl(
System.getProperty("no.nibio.vips.logic.GOOGLE_OPENID_CLIENT_ID"),
callbackUrl,
Arrays.asList(
"https://www.googleapis.com/auth/userinfo.email")
)
.setState(state).build();
// Redirect to Google for authentication
response.sendRedirect(url);
}
// Authentication method not recognized, redirect to standard form
else
{
......
src/main/java/no/nibio/vips/logic/controller/session/SessionControllerGetter.java
View file @ aa5eda39
......@@ -34,7 +34,7 @@ public class SessionControllerGetter {
// This obviously has to be changed when changing the application name in Maven
// TODO: Refactor out to System properties (e.g. in standalone.xml in JBoss/WildFly)
public static final String JNDI_PATH = "java:global/VIPSLogic-2023.1/";
public static final String JNDI_PATH = "java:global/VIPSLogic-2024.1/";
public static SchedulingBean getSchedulingBean()
{
......
src/main/java/no/nibio/vips/logic/modules/barkbeetle/BarkbeetleBean.java
View file @ aa5eda39
......@@ -50,10 +50,7 @@ import javax.persistence.PersistenceContext;
import org.geotools.geometry.jts.JTS;
import org.geotools.referencing.CRS;
import org.opengis.referencing.FactoryException;
import org.opengis.referencing.crs.CoordinateReferenceSystem;
import org.opengis.referencing.operation.MathTransform;
import org.opengis.referencing.operation.TransformException;
import no.nibio.vips.logic.controller.session.SessionControllerGetter;
import no.nibio.vips.logic.controller.session.UserBean;
......@@ -67,6 +64,10 @@ import no.nibio.vips.logic.messaging.UniversalMessageFormat;
import no.nibio.vips.logic.util.GISEntityUtil;
import no.nibio.vips.logic.util.Globals;
import no.nibio.vips.logic.util.SimpleMailSender;
import org.geotools.api.referencing.FactoryException;
import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
import org.geotools.api.referencing.operation.MathTransform;
import org.geotools.api.referencing.operation.TransformException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
......
src/main/java/no/nibio/vips/logic/service/ModelFormService.java
View file @ aa5eda39
......@@ -195,7 +195,6 @@ public class ModelFormService {
ModelConfiguration mConf = new SeptoriaHumidityModelPreprocessor().getModelConfiguration(fConf);
Integer VIPSCoreUserId = organization.getDefaultVipsCoreUserId();
System.out.println("defaultVIPScoreUserId = " + VIPSCoreUserId);
List<Result>results = forecastBean.runForecast(mConf, VIPSCoreUserId);
......
src/main/webapp/templates/login.ftl
View file @ aa5eda39
......@@ -49,14 +49,6 @@
<a href="/user?action=registerNewUserForm&userAuthenticationTypeId=1">${i18nBundle.registerNewUser}</a><br/>
<a href="/user?action=resetPasswordRequestForm">${i18nBundle.forgottenPassword}</a>
</form>
<form class="form-signin" action="/loginsubmit" method="POST">
<input type="hidden" name="userAuthenticationTypeId" value="3"/>
<input type="hidden" name="nextPage" value="${nextPage!"/"}"/>
<input type="hidden" name="returnUUID" value="<#if returnUUID?has_content>${returnUUID?c!""}</#if>"/>
<h2 class="form-signin-heading">${i18nBundle.or}</h2>
<input type="image" src="/images/btn_sign_in_with_google.png" alt="${i18nBundle.signInWith} Google"/><br/>
<input type="checkbox" name="rememberUser"<#if checkRemember?has_content && checkRemember> checked="checked"</#if>/> ${i18nBundle.rememberLogin}
</form>
</div>
</#macro>
<@page_html/>