<p>Usage data is collected from the logs of various web services
that the Jalview Desktop contacts through its normal operation.
These are described below:</p>
- <ul>
- <li><em>HTTP logs on the Jalview website</em><br> We
- record IP addresses of machines which access the web site, either
- via the browser when downloading the application, or when the
- Jalview Desktop user interface is launched.<br> <br>
- <ul>
- <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines release
- channels every time Jalview launches to determine if a new
- release is available.</li>
- <li><i>The questionnaire web service at
- www.jalview.org/cgi-bin/questionnaire.pl is checked and a
- unique cookie for the current questionnaire is stored in the
- Jalview properties file.</i></li>
- <li><i>The Jalview web services stack is contacted to
- retrieve the currently available web services. All
- interactions with the public Jalview web services are
- logged, but we delete all job data (input data and results)
- after about two weeks.</i></li>
- </ul> <br></li>
- <li><em>Google Analytics</em><br> Since Jalview 2.4.0b2,
- the Jalview Desktop records usage data with Google Analytics via
- the <a href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
- class.<br> The Google Analytics logs for Jalview version 2.4
- only record the fact that the application was started, but in the
- future, we will use this mechanism to improve the Desktop user
- interface, by tracking which parts of the user interface are being
- used most often.</li>
- </ul>
- </p>
+ <ul>
+ <li><em>HTTP logs on the Jalview website</em><br> We record
+ IP addresses of machines which access the web site, either via the
+ browser when downloading the application, or when the Jalview Desktop
+ user interface is launched.<br> <br>
+ <ul>
+ <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines
+ release channels every time Jalview launches to determine if a new
+ release is available.</li>
+ <li><i>The questionnaire web service at
+ www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique
+ cookie for the current questionnaire is stored in the Jalview
+ properties file.</i></li>
+ <li><i>The Jalview web services stack is contacted to
+ retrieve the currently available web services. All interactions
+ with the public Jalview web services are logged, but we delete all
+ job data (input data and results) after about two weeks.</i></li>
+ </ul> <br></li>
+ <li><em>Usage Analytics</em><br> Since Jalview 2.11.2.7, the
+ Jalview Desktop records usage data with a self-hosted instance of the
+ analytics stack <a href="https://plausible.io">Plausible.io</a> via a
+ custom GPLv3 client developed by Ben Soares. Prior to this, Jalview
+ versions as far back as 2.4 recorded application launches via <a
+ href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
+ .<br> Usage logs for Jalview record the fact that the
+ application was started, and details about the OS, installed Jalview
+ launcher (if any) and java version used. In the future, we will use
+ this mechanism to improve the Desktop user interface, by tracking
+ which parts of the user interface are being used most often.</li>
+ </ul>
<p>
<strong>Stopping Jalview from calling home</strong><br> If you
run Jalview in 'headless mode' via the command line, then the
--- /dev/null
+---
+version: 2.11.2.7
+date: 2023-06-30
+channel: "release"
+---
+
+## New Features
+- <!-- JAL-4001 --> Jalview now reports usage statistics via Plausible.io
+
+## Issues Resolved
+- <!-- JAL-4116 --> PDB structures slow to view when Jalview Java console is open
+- <!-- JAL-4216 --> chains in PDB or mmCIF files with negative RESNUMs not correctly parsed
---
version: 2.11.3.0
-date: 2023-06-07
+date: 2023-07-19
channel: "release"
---
- <!-- JAL-4089 --> Use selected columns for superposition
- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
+- <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
+
+
### Improved support for working with computationally determined models
- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
- <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
- <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
+- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
+
### Jalview on the command line
### Other improvements
- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
+- <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
+- <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
+
+- <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
+Add a command line option to set Jalview properties for this session only
+Add a command line option to suppress opening the startup file for this session
+
+
+JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser
+
+known issue ? <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
+
+
+- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
+- <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
## Still in progress (delete on release)
--- /dev/null
+Jalview 2.11.2.7 is a minor patch release - it includes patches affecting efficiency when importing structures and a small revision to the import processing of structures with negative residue numbering.
+
+With this release, Jalview usage statistics are now collected by a jalview.org hosted instance of the open source privacy-preserving analytics stack, Plausible.io.
+
+
The 2.11.3 series includes support for in-depth exploration of predicted alignment error matrices from AlphaFold in the context of multiple alignments, along with support for standard colourschemes for shading models according to their pLDDT.
+We're launching this release at ISMB 2023 - come find us !
+
It also introduces new support for native ARM-based OSX architectures, and a few other goodies!
label.interpret_tempfac_as = Interpret Temperature Factor as
label.add_pae_matrix_file = Add PAE matrix file
label.nothing_selected = Nothing selected
-prompt.google_analytics_title = Jalview Usage Statistics
-prompt.google_analytics = Do you want to help make Jalview better by enabling the collection of usage statistics with Google Analytics?\nYou can enable or disable usage tracking in the preferences.
+prompt.analytics_title = Jalview Usage Statistics
+prompt.analytics = Do you want to help make Jalview better by enabling the collection of usage statistics with Plausible analytics?\nYou can enable or disable usage tracking in the preferences.
label.working_ellipsis = Working ...
action.show_groups_on_matrix = Show groups on matrix
action.show_groups_on_matrix_tooltip = When enabled, clusters defined on the matrix's associated tree or below the assigned threshold are shown as different colours on the matrix annotation row
label.tftype_plddt = pLDDT
label.add_pae_matrix_file = Añadir un fichero de matriz PAE
label.nothing_selected = Nada seleccionado
-prompt.google_analytics_title = Jalview Estadísticas de Uso
-prompt.google_analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con Google Analytics?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+prompt.analytics_title = Jalview Estadísticas de Uso
+prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
pdbpos++;
}
- if (allowmismatch || c1 == c2)
+ // ignore case differences
+ if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
{
// extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
* @param alignment
* the alignment to add them to
* @param selectionGroup
- * current selection group (or null if none)
+ * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
* @param seq
* @param ann
* @param selectionGroup
- * - may be null
+ * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
* @return annotation added to {@code seq and {@code alignment}
*/
public static AlignmentAnnotation addReferenceAnnotationTo(
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analytics;
+import java.io.BufferedReader;
import java.io.IOException;
+import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.UnsupportedEncodingException;
+import java.lang.invoke.MethodHandles;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.List;
import java.util.Map;
import java.util.Random;
-import java.util.UUID;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.util.ChannelProperties;
+import jalview.util.HttpUtils;
-public class GoogleAnalytics4
+public class Plausible
{
+ private static final String USER_AGENT;
+
private static final String JALVIEW_ID = "Jalview Desktop";
- private static final String SESSION_ID = new Random().toString();
+ private static final String DOMAIN = "jalview.org";
- private static final String MEASUREMENT_ID = "G-6TMPHMXEQ0";
+ private static final String CONFIG_API_BASE_URL = "https://www.jalview.org/services/config/analytics/url";
- private static final String API_SECRET = "Qb9NSbqkRDqizG6j2BBJ2g";
+ private static final String DEFAULT_API_BASE_URL = "https://analytics.jalview.org/api/event";
- // This will generate a different CLIENT_ID each time the application is
- // launched. Do we want to store it in .jalview_properties?
- private static final String CLIENT_ID = UUID.randomUUID().toString();
+ private static final String API_BASE_URL;
- private static final String BASE_URL = "https://www.google-analytics.com/mp/collect";
+ private static final String clientId;
- private static final String DESKTOP_EVENT = "desktop_event";
+ public static final String APPLICATION_BASE_URL = "desktop://localhost";
private List<Map.Entry<String, String>> queryStringValues;
private List<Map.Entry<String, Object>> jsonObject;
- private List<Event> events;
-
private List<Map.Entry<String, String>> cookieValues;
private static boolean ENABLED = false;
- private static GoogleAnalytics4 instance = null;
+ private static boolean DEBUG = true;
- private static final Map<String, String> defaultParams;
+ private static Plausible instance = null;
+
+ private static final Map<String, String> defaultProps;
static
{
- defaultParams = new HashMap<>();
- defaultParams.put("app_name",
+ defaultProps = new HashMap<>();
+ defaultProps.put("app_name",
ChannelProperties.getProperty("app_name") + " Desktop");
- defaultParams.put("version", Cache.getProperty("VERSION"));
- defaultParams.put("build_date",
+ defaultProps.put("version", Cache.getProperty("VERSION"));
+ defaultProps.put("build_date",
Cache.getDefault("BUILD_DATE", "unknown"));
- defaultParams.put("java_version", System.getProperty("java.version"));
+ defaultProps.put("java_version", System.getProperty("java.version"));
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
- defaultParams.put("install4j_version", val);
+ defaultProps.put("install4j_version", val);
}
val = System.getProperty("installer_template_version");
if (val != null)
{
- defaultParams.put("install4j_template_version", val);
+ defaultProps.put("install4j_template_version", val);
}
val = System.getProperty("launcher_version");
if (val != null)
{
- defaultParams.put("launcher_version", val);
+ defaultProps.put("launcher_version", val);
}
- defaultParams.put("java_arch",
+ defaultProps.put("java_arch",
System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ defaultProps.put("os", System.getProperty("os.name"));
+ defaultProps.put("os_version", System.getProperty("os.version"));
+ defaultProps.put("os_arch", System.getProperty("os.arch"));
+ String installation = Cache.applicationProperties
+ .getProperty("INSTALLATION");
+ if (installation != null)
+ {
+ defaultProps.put("installation", installation);
+ }
+
+ // ascertain the API_BASE_URL
+ API_BASE_URL = getAPIBaseURL();
+
+ // random clientId to make User-Agent unique (to register analytic)
+ clientId = String.format("%08x", new Random().nextInt());
+
+ USER_AGENT = HttpUtils.getUserAgent(
+ MethodHandles.lookup().lookupClass().getCanonicalName() + " "
+ + clientId);
}
- private GoogleAnalytics4()
+ private Plausible()
{
this.resetLists();
}
ENABLED = b;
}
- public void sendAnalytics(String eventName, String... paramsStrings)
+ public void sendEvent(String eventName, String urlString,
+ String... propsStrings)
{
- sendAnalytics(eventName, false, paramsStrings);
+ sendEvent(eventName, urlString, false, propsStrings);
}
/**
* The simplest way to send an analytic event.
*
* @param eventName
- * The event name. To emulate a webpage view use "page_view" and set
- * a "page_location" parameter. See
- * https://developers.google.com/analytics/devguides/collection/ga4/events?client_type=gtag
- * @param sendDefaultParams
- * Flag whether to add the default params about the application.
- * @param paramsStrings
+ * The event name. To emulate a webpage view use "pageview" and set a
+ * "url" key/value. See https://plausible.io/docs/events-api
+ * @param sendDefaultProps
+ * Flag whether to add the default props about the application.
+ * @param propsStrings
* Optional multiple Strings in key, value pairs (there should be an
- * even number of paramsStrings) to be set as parameters of the
- * event. To emulate a webpage view use "page_location" as the URL in
- * a "page_view" event.
+ * even number of propsStrings) to be set as property of the event.
+ * To emulate a webpage view set "url" as the URL in a "pageview"
+ * event.
*/
- public void sendAnalytics(String eventName, boolean sendDefaultParams,
- String... paramsStrings)
+ public void sendEvent(String eventName, String urlString,
+ boolean sendDefaultProps, String... propsStrings)
{
// clear out old lists
this.resetLists();
if (!ENABLED)
{
- Console.debug("GoogleAnalytics4 not enabled.");
+ Console.debug("Plausible not enabled.");
return;
}
- Map<String, String> params = new HashMap<>();
- params.put("event_category", DESKTOP_EVENT);
- params.put("event_label", eventName);
+ Map<String, String> props = new HashMap<>();
// add these to all events from this application instance
- if (sendDefaultParams)
+ if (sendDefaultProps)
{
- params.putAll(defaultParams);
+ props.putAll(defaultProps);
}
- // add (and overwrite with) the passed in params
- if (paramsStrings != null && paramsStrings.length > 0)
+ // add (and overwrite with) the passed in props
+ if (propsStrings != null && propsStrings.length > 0)
{
- if (paramsStrings.length % 2 != 0)
+ if (propsStrings.length % 2 != 0)
{
Console.warn(
- "Cannot addEvent with odd number of paramsStrings. Ignoring the last one.");
+ "Cannot addEvent with odd number of propsStrings. Ignoring the last one.");
}
- for (int i = 0; i < paramsStrings.length - 1; i += 2)
+ for (int i = 0; i < propsStrings.length - 1; i += 2)
{
- String key = paramsStrings[i];
- String value = paramsStrings[i + 1];
- params.put(key, value);
+ String key = propsStrings[i];
+ String value = propsStrings[i + 1];
+ props.put(key, value);
}
}
- addEvent(eventName, params);
- addQueryStringValue("measurement_id", MEASUREMENT_ID);
- addQueryStringValue("api_secret", API_SECRET);
- addJsonValue("client_id", CLIENT_ID);
- addJsonValues("events", Event.toObjectList(events));
+ addJsonValue("domain", DOMAIN);
+ addJsonValue("name", eventName);
+ StringBuilder eventUrlSb = new StringBuilder(APPLICATION_BASE_URL);
+ if (!APPLICATION_BASE_URL.endsWith("/") && !urlString.startsWith("/"))
+ {
+ eventUrlSb.append("/");
+ }
+ eventUrlSb.append(urlString);
+ addJsonValue("url", eventUrlSb.toString());
+ addJsonObject("props", props);
StringBuilder urlSb = new StringBuilder();
- urlSb.append(BASE_URL);
- urlSb.append('?');
- urlSb.append(buildQueryString());
+ urlSb.append(API_BASE_URL);
+ String qs = buildQueryString();
+ if (qs != null && qs.length() > 0)
+ {
+ urlSb.append('?');
+ urlSb.append(qs);
+ }
try
{
URL url = new URL(urlSb.toString());
String jsonString = buildJson();
- Console.debug("GA4: HTTP Request is: '" + urlSb.toString() + "'");
- Console.debug("GA4: POSTed JSON is:\n" + jsonString);
+ Console.debug(
+ "Plausible: HTTP Request is: '" + urlSb.toString() + "'");
+ if (DEBUG)
+ {
+ Console.debug("Plausible: User-Agent is: '" + USER_AGENT + "'");
+ }
+ Console.debug("Plausible: POSTed JSON is:\n" + jsonString);
byte[] jsonBytes = jsonString.getBytes(StandardCharsets.UTF_8);
int jsonLength = jsonBytes.length;
httpURLConnection.setFixedLengthStreamingMode(jsonLength);
httpURLConnection.setRequestProperty("Content-Type",
- "application/json; charset=UTF-8");
+ "application/json");
+ httpURLConnection.setRequestProperty("User-Agent", USER_AGENT);
httpURLConnection.connect();
try (OutputStream os = httpURLConnection.getOutputStream())
{
}
int responseCode = httpURLConnection.getResponseCode();
String responseMessage = httpURLConnection.getResponseMessage();
+
if (responseCode < 200 || responseCode > 299)
{
- Console.warn("GoogleAnalytics4 connection failed: '" + responseCode
- + " " + responseMessage + "'");
+ Console.warn("Plausible connection failed: '" + responseCode + " "
+ + responseMessage + "'");
}
else
{
- Console.debug("GoogleAnalytics4 connection succeeded: '"
- + responseCode + " " + responseMessage + "'");
+ Console.debug("Plausible connection succeeded: '" + responseCode
+ + " " + responseMessage + "'");
+ }
+
+ if (DEBUG)
+ {
+ BufferedReader br = new BufferedReader(new InputStreamReader(
+ (httpURLConnection.getInputStream())));
+ StringBuilder sb = new StringBuilder();
+ String response;
+ while ((response = br.readLine()) != null)
+ {
+ sb.append(response);
+ }
+ String body = sb.toString();
+ Console.debug("Plausible response content:\n" + body);
}
} catch (MalformedURLException e)
{
Console.debug(
- "Somehow the GoogleAnalytics4 BASE_URL and queryString is malformed.",
+ "Somehow the Plausible BASE_URL and queryString is malformed: '"
+ + urlSb.toString() + "'",
e);
return;
} catch (IOException e)
{
- Console.debug("Connection to GoogleAnalytics4 BASE_URL '" + BASE_URL
+ Console.debug("Connection to Plausible BASE_URL '" + API_BASE_URL
+ "' failed.", e);
} catch (ClassCastException e)
{
Console.debug(
- "Couldn't cast URLConnection to HttpURLConnection in GoogleAnalytics4.",
+ "Couldn't cast URLConnection to HttpURLConnection in Plausible.",
e);
}
}
- public void addEvent(String name, Map<String, String> params)
+ private void addJsonObject(String key, Map<String, String> map)
{
- Event event = new Event(name);
- if (params != null && params.size() > 0)
+ List<Map.Entry<String, ? extends Object>> list = new ArrayList<>();
+ for (String k : map.keySet())
{
- for (String key : params.keySet())
- {
- String value = params.get(key);
- event.addParam(key, value);
- }
+ list.add(stringEntry(k, map.get(k)));
}
- events.add(event);
+ addJsonObject(key, list);
+
}
private void addJsonObject(String key,
- List<Map.Entry<String, Object>> object)
+ List<Map.Entry<String, ? extends Object>> object)
{
jsonObject.add(objectEntry(key, object));
}
private void resetLists()
{
jsonObject = new ArrayList<>();
- events = new ArrayList<Event>();
queryStringValues = new ArrayList<>();
cookieValues = new ArrayList<>();
}
- public static GoogleAnalytics4 getInstance()
+ public static Plausible getInstance()
{
if (instance == null)
{
- instance = new GoogleAnalytics4();
+ instance = new Plausible();
}
return instance;
}
{
return new AbstractMap.SimpleEntry<String, String>(s, v);
}
-}
-
-class Event
-{
- private String name;
- private List<Map.Entry<String, String>> params;
-
- @SafeVarargs
- public Event(String name, Map.Entry<String, String>... paramEntries)
+ private static String getAPIBaseURL()
{
- this.name = name;
- this.params = new ArrayList<Map.Entry<String, String>>();
- for (Map.Entry<String, String> paramEntry : paramEntries)
+ try
{
- if (paramEntry == null)
+ URL url = new URL(CONFIG_API_BASE_URL);
+ URLConnection urlConnection = url.openConnection();
+ HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection;
+ httpURLConnection.setRequestMethod("GET");
+ httpURLConnection.setRequestProperty("User-Agent", USER_AGENT);
+ httpURLConnection.setConnectTimeout(5000);
+ httpURLConnection.setReadTimeout(3000);
+ httpURLConnection.connect();
+ int responseCode = httpURLConnection.getResponseCode();
+ String responseMessage = httpURLConnection.getResponseMessage();
+
+ if (responseCode < 200 || responseCode > 299)
{
- continue;
+ Console.warn("Config URL connection to '" + CONFIG_API_BASE_URL
+ + "' failed: '" + responseCode + " " + responseMessage
+ + "'");
}
- params.add(paramEntry);
- }
- }
- public void addParam(String param, String value)
- {
- params.add(GoogleAnalytics4.stringEntry(param, value));
- }
+ BufferedReader br = new BufferedReader(
+ new InputStreamReader((httpURLConnection.getInputStream())));
+ StringBuilder sb = new StringBuilder();
+ String response;
+ while ((response = br.readLine()) != null)
+ {
+ sb.append(response);
+ }
+ if (sb.length() > 7 && sb.substring(0, 5).equals("https"))
+ {
+ return sb.toString();
+ }
- protected List<Map.Entry<String, Object>> toObject()
- {
- List<Map.Entry<String, Object>> object = new ArrayList<>();
- object.add(GoogleAnalytics4.objectEntry("name", (Object) name));
- if (params.size() > 0)
+ } catch (MalformedURLException e)
{
- object.add(GoogleAnalytics4.objectEntry("params", (Object) params));
- }
- return object;
- }
-
- protected static List<Object> toObjectList(List<Event> events)
- {
- List<Object> eventObjectList = new ArrayList<>();
- for (Event event : events)
+ Console.debug("Somehow the config URL is malformed: '"
+ + CONFIG_API_BASE_URL + "'", e);
+ } catch (IOException e)
{
- eventObjectList.add((Object) event.toObject());
+ Console.debug("Connection to Plausible BASE_URL '" + API_BASE_URL
+ + "' failed.", e);
+ } catch (ClassCastException e)
+ {
+ Console.debug(
+ "Couldn't cast URLConnection to HttpURLConnection in Plausible.",
+ e);
}
- return eventObjectList;
+ return DEFAULT_API_BASE_URL;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import java.util.Date;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import jalview.analytics.GoogleAnalytics4;
+import jalview.analytics.Plausible;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
* service</li>
* <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
* service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * <li>USAGESTATS (false - user prompted) Enable analytics tracker for
* collecting usage statistics</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
}
/**
- * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
- * enabled.
+ * Initialise the tracker if it is not done already.
*/
- protected static Object tracker = null;
-
- protected static Class trackerfocus = null;
-
- protected static Class jgoogleanalyticstracker = null;
-
- private static boolean useGA4 = true;
-
- /**
- * Initialise the google tracker if it is not done already.
- */
- public static void initGoogleTracker()
+ public static void initAnalytics()
{
- if (useGA4)
- {
- GoogleAnalytics4.setEnabled(true);
+ Plausible.setEnabled(true);
- String appName = ChannelProperties.getProperty("app_name")
- + " Desktop";
- String version = Cache.getProperty("VERSION") + "_"
- + Cache.getDefault("BUILD_DATE", "unknown");
- String path;
- /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
- try
- {
- path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
- URLEncoder.encode(version, "UTF-8"),
- URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
- } catch (UnsupportedEncodingException e)
- {
- */
- path = ("/" + String.join("/", appName, version, APPLICATION_STARTED))
- .replace(' ', '+');
- /*
- }
- */
- GoogleAnalytics4 ga4 = GoogleAnalytics4.getInstance();
-
- // This will add a page_view similar to the old UA analytics.
- // We probably want to get rid of this once the application_launch event
- // is being processed properly.
- ga4.sendAnalytics("page_view", "page_location", path, "page_title",
- APPLICATION_STARTED);
-
- // This will send a new "application_launch" event with parameters
- // including the old-style "path", the channel name and version
- ga4.sendAnalytics("application_launch", true, "page_location", path);
- }
- else
+ String appName = ChannelProperties.getProperty("app_name") + " Desktop";
+ String version = Cache.getProperty("VERSION") + "_"
+ + Cache.getDefault("BUILD_DATE", "unknown");
+ String path;
+ /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
+ try
{
- if (tracker == null)
- {
- if (jgoogleanalyticstracker == null)
- {
- // try to get the tracker class
- try
- {
- jgoogleanalyticstracker = Cache.class.getClassLoader()
- .loadClass(
- "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
- trackerfocus = Cache.class.getClassLoader().loadClass(
- "com.boxysystems.jgoogleanalytics.FocusPoint");
- } catch (Exception e)
- {
- Console.debug(
- "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
- tracker = null;
- jgoogleanalyticstracker = null;
- trackerfocus = null;
- return;
- }
- }
- // now initialise tracker
- Exception re = null, ex = null;
- Error err = null;
- String vrs = "No Version Accessible";
- try
- {
- // Google analytics tracking code for Library Finder
- tracker = jgoogleanalyticstracker
- .getConstructor(new Class[]
- { String.class, String.class, String.class })
- .newInstance(new Object[]
- { ChannelProperties.getProperty("app_name") + " Desktop",
- (vrs = Cache.getProperty("VERSION") + "_"
- + Cache.getDefault("BUILD_DATE", "unknown")),
- "UA-9060947-1" });
- jgoogleanalyticstracker
- .getMethod("trackAsynchronously", new Class[]
- { trackerfocus })
- .invoke(tracker, new Object[]
- { trackerfocus
- .getConstructor(new Class[]
- { String.class })
- .newInstance(new Object[]
- { APPLICATION_STARTED }) });
- } catch (RuntimeException e)
- {
- re = e;
- } catch (Exception e)
- {
- ex = e;
- } catch (Error e)
- {
- err = e;
- }
- if (re != null || ex != null || err != null)
- {
- if (re != null)
- {
- Console.debug("Caught runtime exception in googletracker init:",
- re);
- }
- if (ex != null)
- {
- Console.warn(
- "Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs,
- ex);
- }
- if (err != null)
- {
- Console.error(
- "Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs,
- err);
- }
- }
- else
- {
- Console.debug("Successfully initialised tracker.");
- }
- }
+ path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
+ URLEncoder.encode(version, "UTF-8"),
+ URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
+ } catch (UnsupportedEncodingException e)
+ {
+ */
+ List<String> pathParts = new ArrayList<>();
+ pathParts.add(appName);
+ pathParts.add(version);
+ pathParts.add(APPLICATION_STARTED);
+ path = ("/" + String.join("/", pathParts)).replace(' ', '+');
+ /*
}
+ */
+ Plausible plausible = Plausible.getInstance();
+
+ // This will send a new "application_launch" event with parameters
+ // including the old-style "path", the channel name and version
+ plausible.sendEvent("application_launch", path, true);
}
- private static final String APPLICATION_STARTED = "Application Started.";
+ private static final String APPLICATION_STARTED = "Application Started";
/**
* get the user's default colour if available
Console.error("Failed to import and open structure view.");
continue;
}
- while (sv.isBusy())
+ try
{
- try {
+ long tries=1000;
+ while (sv.isBusy() && tries>0)
+ {
Thread.sleep(25);
+ if (sv.isBusy())
+ {
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
+ }
}
- catch (Exception x)
+ if (tries==0 && sv.isBusy())
{
-
+ Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
}
+ } catch (Exception x)
+ {
+ Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x);
}
-
+ Console.debug("Successfully opened viewer for "+structureFilepath);
String structureImageFilename = ArgParser.getValueFromSubValOrArg(
avm, av, Arg.STRUCTUREIMAGE, subVals);
if (sv != null && structureImageFilename != null)
}
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
switch (StructureViewer.getViewerType())
{
case JMOL:
try
{
- Thread.sleep(1000);
+ Thread.sleep(1000); // WHY ???
} catch (InterruptedException e)
{
// TODO Auto-generated catch block
{
AppJmol jmol = (AppJmol) sview;
try {
+ Console.debug("Rendering image to "+structureImageFile);
jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
+ Console.debug("Finished Rendering image to "+structureImageFile);
+
}
catch (ImageOutputException ioexc)
{
{
headless = true;
}
- System.setProperty("http.agent",
- "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+ System.setProperty("http.agent", HttpUtils.getUserAgent());
try
{
// Run Commands from cli
cmds = new Commands(argparser, headlessArg);
boolean commandsSuccess = cmds.argsWereParsed();
+
if (commandsSuccess)
{
if (headlessArg)
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ "-nonews\tTurn off check for Jalview news.\n"
- + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ + "-nousagestats\tTurn off analytics tracking for this session.\n"
+ "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
// +
// "-setprop PROPERTY=VALUE\tSet the given Jalview property,
*/
PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
"USAGESTATS",
- MessageManager.getString("prompt.google_analytics_title"),
- MessageManager.getString("prompt.google_analytics"),
+ MessageManager.getString("prompt.plausible_analytics_title"),
+ MessageManager.getString("prompt.plausible_analytics"),
new Runnable()
{
@Override
public void run()
{
- Console.debug(
- "Initialising googletracker for usage stats.");
- Cache.initGoogleTracker();
+ Console.debug("Initialising analytics for usage stats.");
+ Cache.initAnalytics();
Console.debug("Tracking enabled.");
}
}, new Runnable()
@Override
public void run()
{
- Console.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling analytics.");
}
}, null, true);
desktop.addDialogThread(prompter);
public static boolean isPrimaryCandidate(String ucversion)
{
+ if (ucversion==null)
+ {
+ // Null/empty version is not a real reference ?
+ return false;
+ }
// tricky - this test really needs to search the sequence's set of dbrefs to
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
transferAnnotation(entry.getDatasetSequence(), mp);
return;
}
+ // transfer from entry to sequence
+ // if entry has a description and sequence doesn't, then transfer
+ if (entry.getDescription()!=null && (description==null || description.trim().length()==0))
+ {
+ description = entry.getDescription();
+ }
+
// transfer any new features from entry onto sequence
if (entry.getSequenceFeatures() != null)
{
{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.io.File;
+import java.lang.reflect.InvocationTargetException;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.concurrent.Callable;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
};
String view = MessageManager.getString("action.view")
.toLowerCase(Locale.ROOT);
- ImageExporter exporter = new ImageExporter(writer,
+ final ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
- exporter.doExport(file, this, width, height, view, renderer, userBis);
-
+ final Throwable[] exceptions = new Throwable[1];
+ exceptions[0] = null;
+ final AppJmol us = this;
+ try
+ {
+ Thread runner = Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ exporter.doExport(file, us, width, height, view, renderer,
+ userBis);
+ } catch (Throwable t)
+ {
+ exceptions[0] = t;
+ }
+ }
+ });
+ runner.start();
+ do { Thread.sleep(25); } while (runner.isAlive());
+ } catch (Throwable e)
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", e);
+ }
+ if (exceptions[0] != null)
+ {
+ if (exceptions[0] instanceof ImageOutputException)
+ {
+ throw ((ImageOutputException) exceptions[0]);
+ }
+ else
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", exceptions[0]);
+ }
+ }
}
@Override
setKeyBindings(frame);
- desktop.add(frame);
+ // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
+ int tries=3;
+ boolean shown=false;
+ Exception last=null;
+ do
+ {
+ try
+ {
+ desktop.add(frame);
+ shown=true;
+ } catch (IllegalArgumentException iaex)
+ {
+ last=iaex;
+ tries--;
+ jalview.bin.Console.info(
+ "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
+ iaex);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException iex)
+ {
+ }
+ ;
+ }
+ } while (!shown && tries > 0);
+ if (!shown)
+ {
+ jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+ }
windowMenu.add(menuItem);
{
Desktop.instance.closeAll_actionPerformed(null);
Desktop.instance.setVisible(false);
- Desktop.instance.dispose();
+ Desktop us = Desktop.instance;
Desktop.instance = null;
+ // call dispose in a separate thread - try to avoid indirect deadlocks
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ ExecutorService dex = us.dialogExecutor;
+ if (dex!=null) {
+ dex.shutdownNow();
+ us.dialogExecutor=null;
+ us.block.drainPermits();
+ }
+ us.dispose();
+ }
+ }).start();
}
}
*/
if (file == null && !Jalview.isHeadlessMode())
{
+ if (Desktop.instance.isInBatchMode())
+ {
+ // defensive error report - we could wait for user input.. I guess ?
+ throw(new ImageOutputException("Need an output file to render to when exporting images in batch mode!"));
+ }
JalviewFileChooser chooser = imageType.getFileChooser();
chooser.setFileView(new JalviewFileView());
MessageManager.formatMessage("label.create_image_of",
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ null);
refresh();
}
import java.net.HttpURLConnection;
import java.net.ProtocolException;
import java.net.URL;
-import java.util.List;
import javax.ws.rs.HttpMethod;
+import jalview.bin.Cache;
+
public class HttpUtils
{
return connection.getResponseCode() == 200;
}
+ public static String getUserAgent()
+ {
+ return getUserAgent(null);
+ }
+
+ public static String getUserAgent(String className)
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview");
+ sb.append('/');
+ sb.append(Cache.getDefault("VERSION", "Unknown"));
+ sb.append(" (");
+ sb.append(System.getProperty("os.name"));
+ sb.append("; ");
+ sb.append(System.getProperty("os.arch"));
+ sb.append(' ');
+ sb.append(System.getProperty("os.name"));
+ sb.append(' ');
+ sb.append(System.getProperty("os.version"));
+ sb.append("; ");
+ sb.append("java/");
+ sb.append(System.getProperty("java.version"));
+ sb.append("; ");
+ sb.append("jalview/");
+ sb.append(ChannelProperties.getProperty("channel"));
+ if (className != null)
+ {
+ sb.append("; ");
+ sb.append(className);
+ }
+ String installation = Cache.applicationProperties
+ .getProperty("INSTALLATION");
+ if (installation != null)
+ {
+ sb.append("; ");
+ sb.append(installation);
+ }
+ sb.append(')');
+ sb.append(" help@jalview.org");
+ return sb.toString();
+ }
+
}
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/";
private final static String NEWLINE = System.lineSeparator();
pdbId = pdbId.replace(".cif", "");
}
String siftFile = pdbId + ".xml.gz";
- String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
+ String siftsFileFTPURL = getDownloadUrlFor(siftFile);
/*
* Download the file from URL to either
return downloadTo;
}
+ public static String getDownloadUrlFor(String siftFile)
+ {
+ return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile;
+ }
+
/**
* Delete the SIFTs file for the given PDB Id in the local SIFTs download
* directory
import jalview.gui.JvOptionPane;
import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import com.google.common.base.Charsets;
+
/**
* Test the alignment -> Mapping routines
*
assertEquals(as.getAStr1(), as.getAStr2());
Mapping s1tos2 = as.getMappingFromS1(false);
+ checkMapping(s1tos2,s1,s2);
+ }
+
+ public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+ {
System.out.println(s1tos2.getMap().toString());
- for (int i = s2.getStart(); i < s2.getEnd(); i++)
+ for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
{
- System.out.println("Position in s2: " + i
- + " maps to position in s1: " + s1tos2.getPosition(i));
- // TODO fails: getCharAt doesn't allow for the start position??
- // assertEquals(String.valueOf(s2.getCharAt(i)),
- // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
+ int p=s1tos2.getPosition(i);
+ char s2c=_s2.getCharAt(i-_s2.getStart());
+ char s1c=_s1.getCharAt(p-_s1.getStart());
+ System.out.println("Position in s2: " + i +s2c
+ + " maps to position in s1: " +p+s1c);
+ assertEquals(s1c,s2c);
}
}
+ @Test(groups = { "Functional" })
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void testGetMappingForS1_withLowerCase()
+ {
+ // make one of the sequences lower case
+ SequenceI ns2 = new Sequence(s2);
+ ns2.replace('D', 'd');
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
+ System.out.println("s1: " + as.getAStr1());
+ System.out.println("s2: " + as.getAStr2());
+
+ // aligned results match
+ assertEquals("ASDFA", as.getAStr1());
+ assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
+ assertEquals("ASdFA",as.getAStr2());
+ // verify mapping is consistent between original all-caps sequences
+ checkMapping(s1tos2,s1,s2);
+ }
@Test(groups = { "Functional" })
public void testExtractGaps()
import jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
-@Test
public class CommandsTest
{
private static final String testfiles = "test/jalview/bin/argparser/testfiles";
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
- String[] args = (cmdLine + " --gui").split("\\s+");
- callJalviewMain(args);
- Commands cmds = Jalview.getInstance().getCommands();
- Assert.assertNotNull(cmds);
- Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
- "Commands were not provided in the args");
- Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
- "Overall command parse and operation is false");
+ try
+ {
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
+ "Commands were not provided in the args");
+ Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
+ "Overall command parse and operation is false");
- Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
- "Wrong number of AlignFrames");
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ "Wrong number of AlignFrames");
- if (sequences != null)
- {
- Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
- for (AlignFrame af : afs)
+ if (sequences != null)
{
- openedSequenceNames
- .addAll(af.getViewport().getAlignment().getSequenceNames());
- }
- for (String sequence : sequences)
- {
- Assert.assertTrue(openedSequenceNames.contains(sequence),
- "Sequence '" + sequence
- + "' was not found in opened alignment files: "
- + cmdLine + ".\nOpened sequence names are:\n"
- + String.join("\n", openedSequenceNames));
+ Set<String> openedSequenceNames = new HashSet<>();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ openedSequenceNames.addAll(
+ af.getViewport().getAlignment().getSequenceNames());
+ }
+ for (String sequence : sequences)
+ {
+ Assert.assertTrue(openedSequenceNames.contains(sequence),
+ "Sequence '" + sequence
+ + "' was not found in opened alignment files: "
+ + cmdLine + ".\nOpened sequence names are:\n"
+ + String.join("\n", openedSequenceNames));
+ }
}
- }
- Assert.assertFalse(
- lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during commandsOpenTest", x);
+ } finally
+ {
+ tearDown();
+
+ }
}
@Test(groups = "Functional", dataProvider = "structureImageOutputFiles")
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
- callJalviewMain(args);
- Commands cmds = Jalview.getInstance().getCommands();
- Assert.assertNotNull(cmds);
- File lastFile = null;
- for (String filename : filenames)
+ try
{
- File file = new File(filename);
- Assert.assertTrue(file.exists(), "File '" + filename
- + "' was not created by '" + cmdLine + "'");
- Assert.assertTrue(file.isFile(), "File '" + filename
- + "' is not a file from '" + cmdLine + "'");
- Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
- + "' has no content from '" + cmdLine + "'");
- // make sure the successive output files get bigger!
- if (lastFile != null)
- Assert.assertTrue(
- Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ File lastFile = null;
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ Assert.assertTrue(file.exists(), "File '" + filename
+ + "' was not created by '" + cmdLine + "'");
+ Assert.assertTrue(file.isFile(), "File '" + filename
+ + "' is not a file from '" + cmdLine + "'");
+ Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ + "' has no content from '" + cmdLine + "'");
+ // make sure the successive output files get bigger!
+ if (lastFile != null)
+ Assert.assertTrue(Files.size(file.toPath()) > Files
+ .size(lastFile.toPath()));
+ }
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during structureImageOutputTest",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
}
- cleanupFiles(filenames);
- tearDown();
}
@Test(groups = "Functional", dataProvider = "argfileOutputFiles")
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
+ try {
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
Assert.assertTrue(
Files.size(file.toPath()) > Files.size(lastFile.toPath()));
}
- cleanupFiles(filenames);
- tearDown();
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
+ }
}
@DataProvider(name = "structureImageOutputFiles")
{
Sequence origSeq = new Sequence("MYSEQ", "THISISASEQ");
Sequence toSeq = new Sequence("MYSEQ", "THISISASEQ");
+ origSeq.setDescription("DESCRIPTION");
origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
+
+ toSeq.transferAnnotation(origSeq, null);
+ assertEquals("DESCRIPTION",toSeq.getDescription());
+ toSeq = new Sequence("MYSEQ", "THISISASEQ");
+ toSeq.setDescription("unchanged");
toSeq.transferAnnotation(origSeq, null);
+ assertEquals("unchanged",toSeq.getDescription());
+
assertTrue(toSeq.getDBRefs().size() == 1);
assertTrue(toSeq.getDBRefs().get(0).isCanonical());
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
+
pdbFile = new PDBfile(false, false, false,
"test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
+ // TODO: this uses a network connection - we should mock the sifts testPDBId.xml.gz
siftsClient = new SiftsClient(pdbFile);
}
{
siftsClient = null;
}
+
+ @Test(groups= {"Functional"})
+ public void testSIFTsDownloadURL() {
+ String expectedUrl = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.sifts.xml.gz";
+ Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"), expectedUrl);
+ }
@Test(groups = { "Network" })
public void getSIFTsFileTest() throws SiftsException, IOException
long t1 = siftsFile.lastModified();
// re-read file should be returned from cache
- siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ siftsFile = SiftsClient.getSiftsFile(testPDBId);
FileAssert.assertFile(siftsFile);
long t2 = siftsFile.lastModified();
assertEquals(t1, t2);
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
DBRefEntry invalidDBRef = new DBRefEntry();
- invalidDBRef.setAccessionId("BLAR");
+ invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also invalid
invalidTestSeq.addDBRef(invalidDBRef);
siftsClient.getValidSourceDBRef(invalidTestSeq);
}
git://source.jalview.org / jalview.git / commitdiff