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Coverage Report

  1. Project Clover database Thu Nov 28 2024 18:06:40 GMT
  2. Package jalview.bin

File Cache.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
38% of files have more coverage

Code metrics

212
492
49
2
1,799
1,205
221
0.45
10.04
24.5
4.51

Classes

Class Line # Actions
Cache 244 472 216
0.566115756.6%
Cache.VersionChecker 561 20 5
0.740740774.1%
 

Contributing tests

This file is covered by 404 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.bin;
22   
23    import java.awt.Color;
24    import java.io.BufferedReader;
25    import java.io.File;
26    import java.io.FileInputStream;
27    import java.io.FileNotFoundException;
28    import java.io.FileOutputStream;
29    import java.io.IOException;
30    import java.io.InputStream;
31    import java.io.InputStreamReader;
32    import java.io.PrintWriter;
33    import java.io.StringWriter;
34    import java.net.Authenticator;
35    import java.net.PasswordAuthentication;
36    import java.net.URL;
37    import java.text.DateFormat;
38    import java.text.SimpleDateFormat;
39    import java.util.ArrayList;
40    import java.util.Arrays;
41    import java.util.Collection;
42    import java.util.Collections;
43    import java.util.Date;
44    import java.util.Enumeration;
45    import java.util.HashMap;
46    import java.util.List;
47    import java.util.Locale;
48    import java.util.Map;
49    import java.util.Properties;
50    import java.util.StringTokenizer;
51    import java.util.TreeSet;
52   
53    import javax.swing.LookAndFeel;
54    import javax.swing.UIManager;
55   
56    import jalview.analytics.Plausible;
57    import jalview.bin.argparser.Arg;
58    import jalview.bin.argparser.ArgParser;
59    import jalview.datamodel.PDBEntry;
60    import jalview.gui.Preferences;
61    import jalview.gui.UserDefinedColours;
62    import jalview.log.JLoggerLog4j;
63    import jalview.schemes.ColourSchemeLoader;
64    import jalview.schemes.ColourSchemes;
65    import jalview.schemes.UserColourScheme;
66    import jalview.structure.StructureImportSettings;
67    import jalview.urls.IdOrgSettings;
68    import jalview.util.ChannelProperties;
69    import jalview.util.ColorUtils;
70    import jalview.util.HttpUtils;
71    import jalview.util.LaunchUtils;
72    import jalview.util.MessageManager;
73    import jalview.util.Platform;
74    import jalview.ws.sifts.SiftsSettings;
75   
76    /**
77    * Stores and retrieves Jalview Application Properties Lists and fields within
78    * list entries are separated by '|' symbols unless otherwise stated (|) clauses
79    * are alternative values for a tag. <br>
80    * <br>
81    * Current properties include:
82    * <ul>
83    * <br>
84    * logs.Axis.Level - one of the stringified Levels for log4j controlling the
85    * logging level for axis (used for web services) <br>
86    * </li>
87    * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
88    * the logging level for castor (used for serialization) <br>
89    * </li>
90    * <li>logs.Jalview.Level - Cache.log stringified level. <br>
91    * </li>
92    * <li>SCREEN_WIDTH</li>
93    * <li>SCREEN_HEIGHT</li>
94    * <li>SCREEN_Y=285</li>
95    * <li>SCREEN_X=371</li>
96    * <li>SHOW_FULLSCREEN boolean</li>
97    * <li>FONT_NAME java font name for alignment text display</li>
98    * <li>FONT_SIZE size of displayed alignment text</li>
99    * <li>FONT_STYLE style of font displayed (sequence labels are always
100    * italic)</li>
101    * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
102    * <li>LAST_DIRECTORY last directory for browsing alignment</li>
103    * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
104    * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
105    * <li>SHOW_IDENTITY show percentage identity annotation</li>
106    * <li>SHOW_QUALITY show alignment quality annotation</li>
107    * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
108    * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
109    * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
110    * LABEL_AND_SEQUENCE</li>
111    * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
112    * sequence annotations</li>
113    * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
114    * annotation row</li>
115    * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
116    * <li>DEFAULT_FILE_FORMAT file format used to save</li>
117    * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
118    * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
119    * <li>VERSION the version of the jalview build</li>
120    * <li>BUILD_DATE date of this build</li>
121    * <li>LATEST_VERSION the latest jalview version advertised on the
122    * www.jalview.org</li>
123    * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
124    * descriptions</li>
125    * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
126    * suffix to file</li>
127    * <li>RECENT_URL list of recently retrieved URLs</li>
128    * <li>RECENT_FILE list of recently opened files</li>
129    * <li>USE_PROXY flag for whether a http proxy is to be used</li>
130    * <li>PROXY_SERVER the proxy</li>
131    * <li>PROXY_PORT</li>
132    * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
133    * service</li>
134    * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
135    * service</li>
136    * <li>USAGESTATS (false - user prompted) Enable analytics tracker for
137    * collecting usage statistics</li>
138    * <li>SHOW_OVERVIEW boolean for overview window display</li>
139    * <li>ANTI_ALIAS boolean for smooth fonts</li>
140    * <li>RIGHT_ALIGN_IDS boolean</li>
141    * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
142    * <li>PAD_GAPS boolean</li>
143    * <li>ID_ITALICS boolean</li>
144    * <li>SHOW_JV_SUFFIX</li>
145    * <li>WRAP_ALIGNMENT</li>
146    * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
147    * style check</li>
148    * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
149    * resolution</li>
150    * <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
151    * <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</li>
152    * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
153    * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
154    * $SEQUENCE_ID$</li>
155    * <li>STORED_LINKS list of name|url pairs which user has entered but are not
156    * currently used
157    * <li>DEFAULT_LINK name of single url to be used when user double clicks a
158    * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
159    * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
160    * jalview.utils.GroupURLLink for more info</li>
161    * <li>DEFAULT_BROWSER for unix</li>
162    * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
163    * (false)</li>
164    * <li>VERSION_CHECK (true) check for the latest release version from
165    * www.jalview.org (or the alias given by the www.jalview.org property)</li>
166    * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
167    * ID tooltip</li>
168    * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
169    * ID tooltip</li>
170    * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
171    * displayed as '.'</li>
172    * <li>SORT_BY_TREE (false) sort the current alignment view according to the
173    * order of a newly displayed tree</li>
174    * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
175    * sequence ID strings before attempting retrieval from any datasource</li>
176    * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
177    * alignment.</li>
178    * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
179    * in the alignment.</li>
180    * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
181    * histogram.</li>
182    * <li>SHOW_SSCONSENSUS_HISTOGRAM (false) Show secondary structure consensus
183    * annotation row's histogram.</li>
184    * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
185    * logo.</li>
186    * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
187    * logo normalised to row height rather than histogram height.</li>
188    * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
189    * respond to selections made in other alignments containing the same sequences.
190    * </li>
191    * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
192    * auto-discover JABAWS services</li>
193    * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
194    * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
195    * warning dialog box is displayed.</li>
196    * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
197    * when shading by annotation</li>
198    * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
199    * when shading by annotation</li>
200    * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
201    * requests to be redirected to a mirror of https://www.jalview.org</li>
202    * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
203    * alignment figure to accommodate even the longest sequence ID or annotation
204    * label.</li>
205    * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
206    * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
207    * will override this).</li>
208    * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
209    * record</li>
210    * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
211    * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
212    * display</li>
213    * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
214    * display</li>
215    * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
216    * display</li>
217    * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
218    * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
219    * </li>
220    * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
221    * <li>NOHTMLTEMPLATES - when set, the
222    * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
223    * not downloaded automatically</li>
224    * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
225    * available URL linkouts via www.jalview.org/services/identifiers</li>
226    * <li>
227    * </ul>
228    * Deprecated settings:
229    * <ul>
230    * *
231    * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
232    * startup (JWS1 services only)</li>
233    * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
234    * (JWS1 services only)</li>
235    * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
236    * services in the desktop GUI</li>
237    * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
238    * panel in web service preferences</li>
239    * </ul>
240    *
241    * @author $author$
242    * @version $Revision$
243    */
 
244    public class Cache
245    {
246    /**
247    * property giving log4j level for CASTOR loggers
248    */
249    public static final String CASTORLOGLEVEL = "logs.Castor.level";
250   
251    /**
252    * property giving log4j level for AXIS loggers
253    */
254    public static final String AXISLOGLEVEL = "logs.Axis.level";
255   
256    /**
257    * property giving log4j level for Jalview Log
258    */
259    public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
260   
261    // for tests
262    public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
263   
264    /**
265    * Sifts settings
266    */
267    public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
268    .getProperty("user.home") + File.separatorChar
269    + ".sifts_downloads" + File.separatorChar;
270   
271    private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
272   
273    private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
274   
275    /**
276    * Identifiers.org download settings
277    */
278    private static final String ID_ORG_FILE = System.getProperty("user.home")
279    + File.separatorChar + ".identifiers.org.ids.json";
280   
281    /**
282    * Allowed values are PDB or mmCIF
283    */
284    private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
285    .toString();
286   
287    private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
288    .toString();
289   
290    /*
291    * a date formatter using a fixed (rather than the user's) locale;
292    * this ensures that date properties can be written and re-read successfully
293    * even if the user changes their locale setting
294    */
295    private static final DateFormat date_format = SimpleDateFormat
296    .getDateTimeInstance(SimpleDateFormat.MEDIUM,
297    SimpleDateFormat.MEDIUM, Locale.UK);
298   
299    /**
300    * Initialises the Jalview Application Log
301    */
302   
303    public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
304   
305    // save the proxy properties set at startup
306    public final static String[] startupProxyProperties = {
307    System.getProperty("http.proxyHost"),
308    System.getProperty("http.proxyPort"),
309    System.getProperty("https.proxyHost"),
310    System.getProperty("https.proxyPort"),
311    System.getProperty("http.proxyUser"),
312    System.getProperty("http.proxyPassword"),
313    System.getProperty("https.proxyUser"),
314    System.getProperty("https.proxyPassword"),
315    System.getProperty("http.nonProxyHosts") };
316   
317    public final static String PROXYTYPE_NONE = "none";
318   
319    // "false" and "true" for backward compatibility
320    public final static String PROXYTYPE_SYSTEM = "false";
321   
322    public final static String PROXYTYPE_CUSTOM = "true";
323   
324    // in-memory only storage of proxy password, safer to use char array
325    public static char[] proxyAuthPassword = null;
326   
327    /**
328    * Session properties, set by command line, try not to affect stored
329    * properties!
330    */
331    private static Map<String, String> sessionProperties = new HashMap<>();
332   
333    private static boolean bypassSessionProperties = false;
334   
 
335  10 toggle public static void enableSessionProperties()
336    {
337  10 bypassSessionProperties = false;
338    }
339   
 
340  10 toggle public static void disableSessionProperties()
341    {
342  10 bypassSessionProperties = true;
343    }
344   
345    /** Jalview Properties */
346    public static Properties applicationProperties = new Properties()
347    {
348    // override results in properties output in alphabetical order
 
349  0 toggle @Override
350    public synchronized Enumeration<Object> keys()
351    {
352  0 return Collections.enumeration(new TreeSet<>(super.keySet()));
353    }
354    };
355   
356    /* build Properties (not all saved to .jalview_properties) */
357    public static Properties buildProperties = new Properties();
358   
359    /** Default file is ~/.jalview_properties */
360    static String propertiesFile;
361   
362    private static final String fallbackPropertiesFile = ".jalview_properties";
363   
364    private static boolean propsAreReadOnly = Platform.isJS();
365   
 
366  0 toggle public static boolean isPropsAreReadOnly()
367    {
368  0 return propsAreReadOnly;
369    }
370   
 
371  32 toggle public static void setPropsAreReadOnly(boolean propsAreReadOnly)
372    {
373  32 Cache.propsAreReadOnly = propsAreReadOnly;
374    }
375   
376    private final static String JS_PROPERTY_PREFIX = "jalview_";
377   
378    /**
379    * Loads properties from the given properties file. Any existing properties
380    * are first cleared.
381    */
 
382  307 toggle public static void loadProperties(String propsFile)
383    {
384  307 propertiesFile = propsFile;
385  307 String releasePropertiesFile = null;
386  307 boolean defaultProperties = false;
387  307 if (propsFile == null && !propsAreReadOnly)
388    {
389  42 String channelPrefsFilename = ChannelProperties
390    .getProperty("preferences.filename");
391  42 String releasePrefsFilename = fallbackPropertiesFile;
392  42 propertiesFile = System.getProperty("user.home") + File.separatorChar
393    + channelPrefsFilename;
394  42 releasePropertiesFile = System.getProperty("user.home")
395    + File.separatorChar + releasePrefsFilename;
396  42 defaultProperties = true;
397    }
398    else
399    {
400    // don't corrupt the file we've been given.
401  265 propsAreReadOnly = true;
402    }
403   
404  307 if (propertiesFile == null)
405    { // BH 2019
406  59 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
407    applicationProperties);
408    }
409    else
410    {
411  248 try
412    {
413  248 InputStream fis;
414  248 try
415    {
416    // props file provided as URL
417  248 fis = HttpUtils.openStream(new URL(propertiesFile));
418  0 if (!Jalview.quiet())
419    {
420  0 jalview.bin.Console.outPrintln(
421    "Loading jalview properties from : " + propertiesFile);
422  0 jalview.bin.Console.outPrintln(
423    "Disabling Jalview writing to user's local properties file.");
424    }
425  0 propsAreReadOnly = true;
426    } catch (Exception ex)
427    {
428  248 fis = null;
429    }
430  248 if (fis == null)
431    {
432  248 String readPropertiesFile = propertiesFile;
433    // if we're using the usual properties file and the channel properties
434    // file doesn't exist, read .jalview_properties
435    // (but we'll still save to the channel properties file).
436  248 if (defaultProperties && (!new File(propertiesFile).exists())
437    && (new File(releasePropertiesFile).exists()))
438    {
439  0 readPropertiesFile = releasePropertiesFile;
440    }
441  248 fis = new FileInputStream(readPropertiesFile);
442    }
443  247 applicationProperties.clear();
444  247 applicationProperties.load(fis);
445   
446    // remove any old build properties
447   
448  247 deleteBuildProperties();
449  247 fis.close();
450    } catch (Exception ex)
451    {
452  1 if (!Jalview.quiet())
453  1 jalview.bin.Console
454    .outPrintln("Error reading properties file: " + ex);
455    }
456    }
457   
458    /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
459    if (getDefault("USE_PROXY", false))
460    {
461    String proxyServer = getDefault("PROXY_SERVER", ""),
462    proxyPort = getDefault("PROXY_PORT", "8080");
463    }
464    */
465   
466    // PROXY TYPE settings (now three options "none", "false", "true", but using
467    // backward compatible strings)
468  307 String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
469    // default to upgrading old settings
470  307 switch (proxyType)
471    {
472  0 case PROXYTYPE_NONE:
473  0 clearProxyProperties();
474  0 break;
475  307 case PROXYTYPE_SYSTEM: // use system settings
476  307 resetProxyProperties();
477  307 break;
478  0 case PROXYTYPE_CUSTOM: // use specified proxy settings
479  0 String httpHost = getDefault("PROXY_SERVER", "");
480  0 String httpPort = getDefault("PROXY_PORT", "8080");
481  0 String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
482  0 String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
483  0 String httpUser = getDefault("PROXY_AUTH_USER", null);
484    // https.proxyUser and https.proxyPassword are not able to be
485    // independently set in Preferences yet (or http.nonProxyHosts)
486  0 String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
487  0 setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
488    proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
489  0 break;
490  0 default:
491  0 String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
492    + proxyType;
493  0 Console.warn(message);
494    }
495   
496    // LOAD THE AUTHORS FROM THE authors.props file
497  307 String authorDetails = resolveResourceURLFor("/authors.props");
498   
499  307 try
500    {
501  307 if (authorDetails != null)
502    {
503  307 URL localJarFileURL = new URL(authorDetails);
504  307 InputStream in = localJarFileURL.openStream();
505  307 applicationProperties.load(in);
506  307 in.close();
507    }
508    } catch (Exception ex)
509    {
510  0 if (!Jalview.quiet())
511  0 jalview.bin.Console
512    .outPrintln("Error reading author details: " + ex);
513  0 authorDetails = null;
514    }
515  307 if (authorDetails == null)
516    {
517  0 applicationProperties.remove("AUTHORS");
518  0 applicationProperties.remove("AUTHORFNAMES");
519  0 applicationProperties.remove("YEAR");
520    }
521   
522  307 loadBuildProperties(false);
523   
524  307 SiftsSettings
525    .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
526   
527  307 SiftsSettings.setSiftDownloadDirectory(Cache
528    .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
529   
530  307 SiftsSettings.setFailSafePIDThreshold(
531    Cache.getDefault("sifts_fail_safe_pid_threshold",
532    DEFAULT_FAIL_SAFE_PID_THRESHOLD));
533   
534  307 SiftsSettings.setCacheThresholdInDays(
535    Cache.getDefault("sifts_cache_threshold_in_days",
536    DEFAULT_CACHE_THRESHOLD_IN_DAYS));
537   
538  307 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
539    "https://www.jalview.org/services/identifiers"));
540  307 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
541   
542  307 StructureImportSettings.setDefaultStructureFileFormat(
543    Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
544  307 StructureImportSettings
545    .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
546    // StructureImportSettings
547    // .setDefaultPDBFileParser(Cache.getDefault(
548    // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
549   
550  307 String jnlpVersion = System.getProperty("jalview.version");
551   
552    // jnlpVersion will be null if a latest version check for the channel needs
553    // to be done
554    // Dont do this check if running in headless mode
555   
556  307 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
557    && (System.getProperty("java.awt.headless") == null || System
558    .getProperty("java.awt.headless").equals("false")))
559    {
560   
 
561    class VersionChecker extends Thread
562    {
563   
 
564  123 toggle @Override
565    public void run()
566    {
567  123 String remoteBuildPropertiesUrl = Cache
568    .getAppbaseBuildProperties();
569   
570  122 String orgtimeout = System
571    .getProperty("sun.net.client.defaultConnectTimeout");
572  122 if (orgtimeout == null)
573    {
574  17 orgtimeout = "30";
575  17 Console.debug("Setting default net timeout to " + orgtimeout
576    + " seconds.");
577    }
578  122 String remoteVersion = null;
579  122 if (remoteBuildPropertiesUrl.startsWith("http"))
580    {
581  122 try
582    {
583  122 System.setProperty("sun.net.client.defaultConnectTimeout",
584    "5000");
585   
586  122 URL url = new URL(remoteBuildPropertiesUrl);
587   
588  122 BufferedReader in = new BufferedReader(
589    new InputStreamReader(HttpUtils.openStream(url)));
590   
591  122 Properties remoteBuildProperties = new Properties();
592  122 remoteBuildProperties.load(in);
593  122 remoteVersion = remoteBuildProperties.getProperty("VERSION");
594    } catch (Exception ex)
595    {
596  0 if (!Jalview.quiet())
597    {
598  0 jalview.bin.Console.errPrintln(
599    "Non-fatal exception when checking version at "
600    + remoteBuildPropertiesUrl + ":");
601  0 jalview.bin.Console.printStackTrace(ex);
602    }
603  0 remoteVersion = getProperty("VERSION");
604    }
605    }
606  122 System.setProperty("sun.net.client.defaultConnectTimeout",
607    orgtimeout);
608   
609  122 setProperty("LATEST_VERSION", remoteVersion);
610    }
611    }
612   
613  123 VersionChecker vc = new VersionChecker();
614  123 vc.start();
615    }
616    else
617    {
618  184 if (jnlpVersion != null)
619    {
620  0 setProperty("LATEST_VERSION", jnlpVersion);
621    }
622    else
623    {
624  184 applicationProperties.remove("LATEST_VERSION");
625    }
626    }
627   
628    // LOAD USERDEFINED COLOURS
629  307 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
630  307 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
631    false);
632    }
633   
634    /**
635    * construct a resource URL for the given absolute resource pathname
636    *
637    * @param resourcePath
638    * @return
639    */
 
640  745 toggle private static String resolveResourceURLFor(String resourcePath)
641    {
642  745 String url = null;
643  745 if (Platform.isJS() || !Cache.class.getProtectionDomain()
644    .getCodeSource().getLocation().toString().endsWith(".jar"))
645    {
646  745 try
647    {
648  745 url = Cache.class.getResource(resourcePath).toString();
649    } catch (Exception ex)
650    {
651  0 jalview.bin.Console.errPrintln("Failed to resolve resource "
652    + resourcePath + ": " + ex.getMessage());
653    }
654    }
655    else
656    {
657  0 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
658    .getLocation().toString().concat("!" + resourcePath));
659    }
660  745 return url;
661    }
662   
 
663  438 toggle public static void loadBuildProperties(boolean reportVersion)
664    {
665  438 String codeInstallation = getProperty("INSTALLATION");
666  438 boolean printVersion = codeInstallation == null;
667   
668    /*
669    * read build properties - from the Jalview jar for a Java distribution,
670    * or from codebase file in test or JalviewJS context
671    */
672  438 try
673    {
674  438 String buildDetails = resolveResourceURLFor("/.build_properties");
675  438 URL localJarFileURL = new URL(buildDetails);
676  438 InputStream in = localJarFileURL.openStream();
677  438 buildProperties.load(in);
678  438 in.close();
679  438 if (buildProperties.getProperty("BUILD_DATE", null) != null)
680    {
681  438 applicationProperties.put("BUILD_DATE",
682    buildProperties.getProperty("BUILD_DATE"));
683    }
684  438 if (buildProperties.getProperty("INSTALLATION", null) != null)
685    {
686  438 applicationProperties.put("INSTALLATION",
687    buildProperties.getProperty("INSTALLATION"));
688    }
689  438 if (buildProperties.getProperty("VERSION", null) != null)
690    {
691  438 applicationProperties.put("VERSION",
692    buildProperties.getProperty("VERSION"));
693    }
694  438 if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null)
695    {
696  438 applicationProperties.put("JAVA_COMPILE_VERSION",
697    buildProperties.getProperty("JAVA_COMPILE_VERSION"));
698    }
699    } catch (Exception ex)
700    {
701  0 if (!Jalview.quiet())
702  0 jalview.bin.Console
703    .outPrintln("Error reading build details: " + ex);
704  0 applicationProperties.remove("VERSION");
705    }
706  438 String codeVersion = getProperty("VERSION");
707  438 codeInstallation = getProperty("INSTALLATION");
708   
709  438 if (codeVersion == null)
710    {
711    // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
712  0 codeVersion = "Test";
713  0 codeInstallation = "";
714    }
715    else
716    {
717  438 codeInstallation = " (" + codeInstallation + ")";
718    }
719  438 setProperty("VERSION", codeVersion);
720  438 new BuildDetails(codeVersion, null, codeInstallation);
721  438 if (printVersion && reportVersion)
722    {
723  51 jalview.bin.Console
724    .outPrintln(ChannelProperties.getProperty("app_name")
725    + " version: " + codeVersion + codeInstallation);
726    }
727    }
728   
 
729  247 toggle private static void deleteBuildProperties()
730    {
731  247 applicationProperties.remove("LATEST_VERSION");
732  247 applicationProperties.remove("VERSION");
733  247 applicationProperties.remove("AUTHORS");
734  247 applicationProperties.remove("AUTHORFNAMES");
735  247 applicationProperties.remove("YEAR");
736  247 applicationProperties.remove("BUILD_DATE");
737  247 applicationProperties.remove("INSTALLATION");
738    }
739   
740    /**
741    * Gets Jalview application property of given key. Returns null if key not
742    * found
743    *
744    * @param key
745    * Name of property
746    *
747    * @return Property value
748    */
 
749  315207 toggle public static String getProperty(String key)
750    {
751  315206 return getProperty(key, false);
752    }
753   
 
754  315203 toggle public static String getProperty(String key,
755    boolean skipSessionProperties)
756    {
757  315204 String prop = null;
758  315204 if (!(skipSessionProperties || bypassSessionProperties))
759    {
760  315106 prop = getSessionProperty(key);
761    }
762  315207 if (prop == null)
763    {
764  315207 prop = applicationProperties.getProperty(key);
765    }
766  315210 if (prop == null && Platform.isJS())
767    {
768  0 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
769    + "_" + JS_PROPERTY_PREFIX + key);
770    }
771  315207 return prop;
772    }
773   
774    /**
775    * These methods are used when checking if the saved preference is different
776    * to the default setting
777    */
778   
 
779  296622 toggle public static boolean getDefault(String property, boolean def)
780    {
781  296621 String string = getProperty(property);
782  296619 if (string != null)
783    {
784  225333 def = Boolean.valueOf(string).booleanValue();
785    }
786   
787  296622 return def;
788    }
789   
 
790  302 toggle public static int getDefault(String property, int def)
791    {
792  302 String string = getProperty(property);
793  302 if (string != null)
794    {
795  8 try
796    {
797  8 def = Integer.parseInt(string);
798    } catch (NumberFormatException e)
799    {
800  0 if (!Jalview.quiet())
801  0 jalview.bin.Console.errPrintln("Error parsing int property '"
802    + property + "' with value '" + string + "'");
803    }
804    }
805   
806  302 return def;
807    }
808   
 
809  43 toggle public static float getDefault(String property, float def)
810    {
811  43 String string = getProperty(property);
812  43 if (string != null)
813    {
814  4 try
815    {
816  4 def = Float.parseFloat(string);
817    } catch (NumberFormatException e)
818    {
819  0 if (!Jalview.quiet())
820  0 jalview.bin.Console.errPrintln("Error parsing float property '"
821    + property + "' with value '" + string + "'");
822    }
823    }
824   
825  43 return def;
826    }
827   
828    /**
829    * Answers the value of the given property, or the supplied default value if
830    * the property is not set
831    */
 
832  11971 toggle public static String getDefault(String property, String def)
833    {
834  11971 String value = getProperty(property);
835  11972 return value == null ? def : value;
836    }
837   
838    /**
839    * Stores property in the file "HOME_DIR/.jalview_properties"
840    *
841    * @param key
842    * Name of object
843    * @param obj
844    * String value of property
845    *
846    * @return previous value of property (or null)
847    */
 
848  2577 toggle public static Object setProperty(String key, String obj)
849    {
850  2577 Object oldValue = null;
851  2577 try
852    {
853  2577 oldValue = applicationProperties.setProperty(key, obj);
854  2577 if (propertiesFile != null && !propsAreReadOnly
855    // don't rewrite if new value is same as old value
856    && !((obj == null && oldValue == null)
857    || (obj != null && obj.equals(oldValue))))
858    {
859    // reset the session property too
860  16 if (sessionProperties.containsKey(key))
861    {
862  0 sessionProperties.remove(key);
863    }
864  16 FileOutputStream out = new FileOutputStream(propertiesFile);
865  16 applicationProperties.store(out, "---JalviewX Properties File---");
866  16 out.close();
867    }
868    } catch (Exception ex)
869    {
870  0 if (!Jalview.quiet())
871  0 jalview.bin.Console.errPrintln(
872    "Error setting property: " + key + " " + obj + "\n" + ex);
873    }
874  2577 return oldValue;
875    }
876   
877    /**
878    * remove the specified property from the jalview properties file
879    *
880    * @param string
881    */
 
882  27 toggle public static void removeProperty(String string)
883    {
884  27 applicationProperties.remove(string);
885  27 saveProperties();
886    }
887   
888    /**
889    * save the properties to the jalview properties path
890    */
 
891  27 toggle public static void saveProperties()
892    {
893  27 if (!propsAreReadOnly)
894    {
895  0 try
896    {
897  0 FileOutputStream out = new FileOutputStream(propertiesFile);
898  0 applicationProperties.store(out, "---JalviewX Properties File---");
899  0 out.close();
900    } catch (Exception ex)
901    {
902  0 if (!Jalview.quiet())
903  0 jalview.bin.Console.errPrintln("Error saving properties: " + ex);
904    }
905    }
906    }
907   
908    /**
909    * internal vamsas class discovery state
910    */
911    private static int vamsasJarsArePresent = -1;
912   
913    /**
914    * Searches for vamsas client classes on class path.
915    *
916    * @return true if vamsas client is present on classpath
917    */
 
918  0 toggle public static boolean vamsasJarsPresent()
919    {
920  0 if (vamsasJarsArePresent == -1)
921    {
922  0 try
923    {
924  0 if (jalview.jbgui.GDesktop.class.getClassLoader()
925    .loadClass("uk.ac.vamsas.client.VorbaId") != null)
926    {
927  0 Console.debug(
928    "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
929  0 vamsasJarsArePresent = 1;
930  0 JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
931    Console.getCachedLogLevel("logs.Vamsas.Level"));
932  0 JLoggerLog4j.addAppender(lvclient, Console.log,
933    JALVIEW_LOGGER_NAME);
934    // Tell the user that debug is enabled
935  0 lvclient.debug(ChannelProperties.getProperty("app_name")
936    + " Vamsas Client Debugging Output Follows.");
937    }
938    } catch (Exception e)
939    {
940  0 vamsasJarsArePresent = 0;
941  0 Console.debug("Vamsas Classes are not present");
942    }
943    }
944  0 return (vamsasJarsArePresent > 0);
945    }
946   
947    /**
948    * internal vamsas class discovery state
949    */
950    private static int groovyJarsArePresent = -1;
951   
952    /**
953    * Searches for vamsas client classes on class path.
954    *
955    * @return true if vamsas client is present on classpath
956    */
 
957  0 toggle public static boolean groovyJarsPresent()
958    {
959  0 if (groovyJarsArePresent == -1)
960    {
961  0 try
962    {
963  0 if (Cache.class.getClassLoader()
964    .loadClass("groovy.lang.GroovyObject") != null)
965    {
966  0 Console.debug(
967    "Found Groovy (groovy.lang.GroovyObject can be loaded)");
968  0 groovyJarsArePresent = 1;
969  0 JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
970    Console.getCachedLogLevel("logs.Groovy.Level"));
971  0 JLoggerLog4j.addAppender(lgclient, Console.log,
972    JALVIEW_LOGGER_NAME);
973    // Tell the user that debug is enabled
974  0 lgclient.debug(ChannelProperties.getProperty("app_name")
975    + " Groovy Client Debugging Output Follows.");
976    }
977    } catch (Error e)
978    {
979  0 groovyJarsArePresent = 0;
980  0 Console.debug("Groovy Classes are not present", e);
981    } catch (Exception e)
982    {
983  0 groovyJarsArePresent = 0;
984  0 Console.debug("Groovy Classes are not present");
985    }
986    }
987  0 return (groovyJarsArePresent > 0);
988    }
989   
990    /**
991    * Initialise the tracker if it is not done already.
992    */
 
993  0 toggle public static void initAnalytics()
994    {
995  0 Plausible.setEnabled(true);
996   
997  0 String appName = ChannelProperties.getProperty("app_name") + " Desktop";
998  0 String version = Cache.getProperty("VERSION") + "_"
999    + Cache.getDefault("BUILD_DATE", "unknown");
1000  0 String path;
1001    /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
1002    try
1003    {
1004    path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
1005    URLEncoder.encode(version, "UTF-8"),
1006    URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
1007    } catch (UnsupportedEncodingException e)
1008    {
1009    */
1010  0 List<String> pathParts = new ArrayList<>();
1011  0 pathParts.add(appName);
1012  0 pathParts.add(version);
1013  0 pathParts.add(APPLICATION_STARTED);
1014  0 path = ("/" + String.join("/", pathParts)).replace(' ', '+');
1015    /*
1016    }
1017    */
1018  0 Plausible plausible = Plausible.getInstance();
1019   
1020    // This will send a new "application_launch" event with parameters
1021    // including the old-style "path", the channel name and version
1022  0 plausible.sendEvent("application_launch", path, true);
1023    }
1024   
1025    private static final String APPLICATION_STARTED = "Application Started";
1026   
1027    /**
1028    * get the user's default colour if available
1029    *
1030    * @param property
1031    * @param defcolour
1032    * @return
1033    */
 
1034  86 toggle public static Color getDefaultColour(String property, Color defcolour)
1035    {
1036  86 String colprop = getProperty(property);
1037  86 if (colprop == null)
1038    {
1039  12 return defcolour;
1040    }
1041  74 Color col = ColorUtils.parseColourString(colprop);
1042  74 if (col == null)
1043    {
1044  0 Console.warn("Couldn't parse '" + colprop + "' as a colour for "
1045    + property);
1046    }
1047  74 return (col == null) ? defcolour : col;
1048    }
1049   
1050    /**
1051    * store a colour as a Jalview user default property
1052    *
1053    * @param property
1054    * @param colour
1055    */
 
1056  4 toggle public static void setColourProperty(String property, Color colour)
1057    {
1058  4 setProperty(property, jalview.util.Format.getHexString(colour));
1059    }
1060   
1061    /**
1062    * Stores a formatted date in a jalview property, using a fixed locale.
1063    *
1064    * @param propertyName
1065    * @param date
1066    * @return the formatted date string
1067    */
 
1068  132 toggle public static String setDateProperty(String propertyName, Date date)
1069    {
1070  132 String formatted = date_format.format(date);
1071  132 setProperty(propertyName, formatted);
1072  132 return formatted;
1073    }
1074   
1075    /**
1076    * Reads a date stored in a Jalview property, parses it (using a fixed locale
1077    * format) and returns as a Date, or null if parsing fails
1078    *
1079    * @param propertyName
1080    * @return
1081    *
1082    */
 
1083  42 toggle public static Date getDateProperty(String propertyName)
1084    {
1085  42 String val = getProperty(propertyName);
1086  42 if (val != null)
1087    {
1088  42 try
1089    {
1090  42 return date_format.parse(val);
1091    } catch (Exception ex)
1092    {
1093  8 jalview.bin.Console
1094    .errPrintln("Invalid or corrupt date in property '"
1095    + propertyName + "' : value was '" + val + "'");
1096    }
1097    }
1098  8 return null;
1099    }
1100   
1101    /**
1102    * get and parse a property as an integer. send any parsing problems to
1103    * System.err
1104    *
1105    * @param property
1106    * @return null or Integer
1107    */
 
1108  76 toggle public static Integer getIntegerProperty(String property)
1109    {
1110  76 String val = getProperty(property);
1111  ? if (val != null && (val = val.trim()).length() > 0)
1112    {
1113  0 try
1114    {
1115  0 return Integer.valueOf(val);
1116    } catch (NumberFormatException x)
1117    {
1118  0 jalview.bin.Console.errPrintln("Invalid integer in property '"
1119    + property + "' (value was '" + val + "')");
1120    }
1121    }
1122  76 return null;
1123    }
1124   
1125    /**
1126    * Set the specified value, or remove it if null or empty. Does not save the
1127    * properties file.
1128    *
1129    * @param propName
1130    * @param value
1131    */
 
1132  0 toggle public static void setOrRemove(String propName, String value)
1133    {
1134  0 if (propName == null)
1135    {
1136  0 return;
1137    }
1138  0 if (value == null || value.trim().length() < 1)
1139    {
1140  0 Cache.applicationProperties.remove(propName);
1141    }
1142    else
1143    {
1144  0 Cache.applicationProperties.setProperty(propName, value);
1145    }
1146    }
1147   
1148    /**
1149    * Loads in user colour schemes from files.
1150    *
1151    * @param files
1152    * a '|'-delimited list of file paths
1153    */
 
1154  307 toggle public static void initUserColourSchemes(String files)
1155    {
1156  307 if (files == null || files.length() == 0)
1157    {
1158  307 return;
1159    }
1160   
1161    // In case colours can't be loaded, we'll remove them
1162    // from the default list here.
1163  0 StringBuffer coloursFound = new StringBuffer();
1164  0 StringTokenizer st = new StringTokenizer(files, "|");
1165  0 while (st.hasMoreElements())
1166    {
1167  0 String file = st.nextToken();
1168  0 try
1169    {
1170  0 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1171  0 if (ucs != null)
1172    {
1173  0 if (coloursFound.length() > 0)
1174    {
1175  0 coloursFound.append("|");
1176    }
1177  0 coloursFound.append(file);
1178  0 ColourSchemes.getInstance().registerColourScheme(ucs);
1179    }
1180    } catch (Exception ex)
1181    {
1182  0 if (!Jalview.quiet())
1183  0 jalview.bin.Console
1184    .outPrintln("Error loading User ColourFile\n" + ex);
1185    }
1186    }
1187  0 if (!files.equals(coloursFound.toString()))
1188    {
1189  0 if (coloursFound.toString().length() > 1)
1190    {
1191  0 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1192    coloursFound.toString());
1193    }
1194    else
1195    {
1196  0 applicationProperties
1197    .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1198    }
1199    }
1200    }
1201   
1202    /**
1203    * Initial logging information helper for various versions output
1204    *
1205    * @param prefix
1206    * @param value
1207    * @param defaultValue
1208    */
 
1209  2884 toggle private static void appendIfNotNull(StringBuilder sb, String prefix,
1210    String value, String suffix, String defaultValue)
1211    {
1212  2884 if (value == null && defaultValue == null)
1213    {
1214  1854 return;
1215    }
1216  1030 if (prefix != null)
1217  1030 sb.append(prefix);
1218  1030 sb.append(value == null ? defaultValue : value);
1219  1030 if (suffix != null)
1220  1030 sb.append(suffix);
1221    }
1222   
1223    /**
1224    *
1225    * @return Jalview version, build details and JVM platform version for console
1226    */
 
1227  206 toggle public static String getVersionDetailsForConsole()
1228    {
1229  206 boolean extra = Console.isDebugEnabled()
1230    || !"release".equals(ChannelProperties.getProperty("channel"));
1231  206 StringBuilder sb = new StringBuilder();
1232  206 sb.append(ChannelProperties.getProperty("app_name"))
1233    .append(" Version: ");
1234  206 sb.append(Cache.getDefault("VERSION", "TEST"));
1235  206 sb.append("\n");
1236  206 sb.append(ChannelProperties.getProperty("app_name"))
1237    .append(" Installation: ");
1238  206 sb.append(Cache.getDefault("INSTALLATION", "unknown"));
1239  206 sb.append("\n");
1240  206 appendIfNotNull(sb, "Channel: ",
1241    ChannelProperties.getProperty("channel"), "\n", null);
1242  206 sb.append("Build Date: ");
1243  206 sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
1244  206 sb.append("\n");
1245  206 if (extra)
1246    {
1247  206 appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
1248    "unknown");
1249  206 appendIfNotNull(sb, "Log file: ",
1250    System.getProperty("installer.logfile"), "\n", "unknown");
1251    }
1252  206 sb.append("Java version: ");
1253  206 sb.append(System.getProperty("java.version"));
1254  206 sb.append("\n");
1255  206 if (extra)
1256    {
1257  206 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1258    "\n", "unknown");
1259  206 appendIfNotNull(sb, "Java launch class: ",
1260    System.getProperty("sun.java.command"), "\n", "unknown");
1261  206 sb.append("Java platform: ");
1262  206 sb.append(System.getProperty("os.name"));
1263  206 sb.append(" ");
1264  206 sb.append(System.getProperty("os.version"));
1265  206 sb.append(" (");
1266  206 sb.append(System.getProperty("os.arch"));
1267  206 sb.append(")");
1268  206 sb.append("\n");
1269  206 LookAndFeel laf = UIManager.getLookAndFeel();
1270  206 String lafName = laf == null ? "Not obtained" : laf.getName();
1271  206 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1272  206 sb.append("Java LAF: ");
1273  206 sb.append(lafName);
1274  206 sb.append(" (");
1275  206 sb.append(lafClass);
1276  206 sb.append(")\n");
1277    // pid() only available in Java 9+
1278  206 if (LaunchUtils.getJavaVersion() > 8)
1279    {
1280  206 sb.append("Java Virtual Machine PID: ");
1281  206 sb.append(ProcessHandle.current().pid());
1282  206 sb.append("\n");
1283    }
1284   
1285    }
1286  206 appendIfNotNull(sb, "Installer version: ",
1287    System.getProperty("sys.install4jVersion"), "\n", null);
1288  206 if (extra)
1289    {
1290  206 String installerAppdir = System.getProperty("installer.appdir");
1291  206 if (installerAppdir != null)
1292    {
1293  0 try
1294    {
1295  0 String temp = new File(installerAppdir).getCanonicalPath();
1296  0 installerAppdir = temp;
1297    } catch (IOException e)
1298    {
1299  0 installerAppdir = "(non-canonical) " + installerAppdir;
1300  0 Console.warn(
1301    "Could not get canonical path for installer appdir, leaving as is.");
1302    }
1303    }
1304  206 appendIfNotNull(sb, "Installer template version: ",
1305    System.getProperty("installer.template_version"), "\n", null);
1306  206 appendIfNotNull(sb, "Installer appdir: ", installerAppdir, "\n",
1307    null);
1308  206 appendIfNotNull(sb, "Installer extrainfo: ",
1309    System.getProperty("installer.extrainfo"), "\n", null);
1310    }
1311  206 appendIfNotNull(sb, "Launcher version: ",
1312    System.getProperty("launcher.version"), "\n", null);
1313  206 if (extra)
1314    {
1315  206 appendIfNotNull(sb, "Launcher appdir: ",
1316    System.getProperty("launcher.appdir"), "\n", null);
1317  206 appendIfNotNull(sb, "Launcher distdir: ",
1318    System.getProperty("launcher.distdir"), "\n", null);
1319  206 appendIfNotNull(sb, "Launcher appbase: ",
1320    System.getProperty("launcher.appbase"), "\n", null);
1321  206 appendIfNotNull(sb, "Launcher script: ",
1322    System.getProperty("launcher.script"), "\n", null);
1323    }
1324  206 return sb.toString();
1325    }
1326   
1327    /**
1328    *
1329    * @return build details as reported in splashscreen
1330    */
 
1331  553 toggle public static String getBuildDetailsForSplash()
1332    {
1333    // consider returning more human friendly info
1334    // eg 'built from Source' or update channel
1335  553 return Cache.getDefault("INSTALLATION", "unknown");
1336    }
1337   
 
1338  0 toggle public static String getStackTraceString(Throwable t)
1339    {
1340  0 StringWriter sw = new StringWriter();
1341  0 PrintWriter pw = new PrintWriter(sw);
1342  0 t.printStackTrace(pw);
1343  0 return sw.toString();
1344    }
1345   
1346    // proxy properties methods
 
1347  0 toggle public static void clearProxyProperties()
1348    {
1349  0 setProxyProperties(null, null, null, null, null, null, null, null,
1350    null);
1351    }
1352   
 
1353  307 toggle public static void resetProxyProperties()
1354    {
1355  307 setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
1356    startupProxyProperties[2], startupProxyProperties[3],
1357    startupProxyProperties[4],
1358  307 startupProxyProperties[5] == null ? null
1359    : startupProxyProperties[5].toCharArray(),
1360    startupProxyProperties[6],
1361  307 startupProxyProperties[7] == null ? null
1362    : startupProxyProperties[7].toCharArray(),
1363    startupProxyProperties[8]);
1364  307 StringBuilder sb = new StringBuilder();
1365  307 sb.append("Setting proxy properties to: http.proxyHost=")
1366    .append(startupProxyProperties[0]).append(", http.proxyPort=")
1367    .append(startupProxyProperties[1])
1368  307 .append(startupProxyProperties[4] != null
1369    && !startupProxyProperties[4].isEmpty()
1370    ? " [" + startupProxyProperties[4] + "]"
1371    : "")
1372    .append(", https.proxyHost=").append(startupProxyProperties[2])
1373    .append(", https.proxyPort=").append(startupProxyProperties[3])
1374  307 .append(startupProxyProperties[6] != null
1375    && !startupProxyProperties[6].isEmpty()
1376    ? " [" + startupProxyProperties[6] + "]"
1377    : "");
1378   
1379  307 Console.debug(sb.toString());
1380    }
1381   
 
1382  75 toggle public static void setProxyPropertiesFromPreferences()
1383    {
1384  75 setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
1385    }
1386   
 
1387  75 toggle public static void setProxyPropertiesFromPreferences(
1388    String previousProxyType)
1389    {
1390  75 String proxyType = Cache.getDefault("USE_PROXY",
1391    Cache.PROXYTYPE_SYSTEM);
1392  75 if (previousProxyType != null
1393    && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
1394    // customProxy
1395    && proxyType.equals(previousProxyType))
1396    {
1397    // no change
1398  75 return;
1399    }
1400  0 switch (proxyType)
1401    {
1402  0 case Cache.PROXYTYPE_NONE:
1403  0 if (!previousProxyType.equals(proxyType))
1404    {
1405  0 Console.info("Setting no proxy settings");
1406  0 Cache.setProxyProperties(null, null, null, null, null, null, null,
1407    null, null);
1408    }
1409  0 break;
1410  0 case Cache.PROXYTYPE_CUSTOM:
1411    // always re-set a custom proxy -- it might have changed, particularly
1412    // password
1413  0 Console.info("Setting custom proxy settings");
1414  0 boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
1415  0 Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
1416    Cache.getDefault("PROXY_PORT", null),
1417    Cache.getDefault("PROXY_SERVER_HTTPS", null),
1418    Cache.getDefault("PROXY_PORT_HTTPS", null),
1419  0 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1420    : null,
1421  0 proxyAuthSet ? Cache.proxyAuthPassword : null,
1422  0 proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
1423    : null,
1424  0 proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
1425  0 break;
1426  0 default: // system proxy settings by default
1427  0 Console.info("Setting system proxy settings");
1428  0 Cache.resetProxyProperties();
1429    }
1430    }
1431   
 
1432  307 toggle public static void setProxyProperties(String httpHost, String httpPort,
1433    String httpsHost, String httpsPort, String httpUser,
1434    char[] httpPassword, String httpsUser, char[] httpsPassword,
1435    String nonProxyHosts)
1436    {
1437  307 setOrClearSystemProperty("http.proxyHost", httpHost);
1438  307 setOrClearSystemProperty("http.proxyPort", httpPort);
1439  307 setOrClearSystemProperty("https.proxyHost", httpsHost);
1440  307 setOrClearSystemProperty("https.proxyPort", httpsPort);
1441  307 setOrClearSystemProperty("http.proxyUser", httpUser);
1442  307 setOrClearSystemProperty("https.proxyUser", httpsUser);
1443    // note: passwords for http.proxyPassword and https.proxyPassword are sent
1444    // via the Authenticator, properties do not need to be set
1445   
1446    // are we using a custom proxy (password prompt might be required)?
1447  307 boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
1448    .equals(PROXYTYPE_CUSTOM);
1449   
1450    /*
1451    * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
1452    * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
1453    * is not re-called).
1454    * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
1455    * the AuthCache.
1456    * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
1457    * ...
1458    * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
1459    */
1460    /*
1461    try
1462    {
1463    sun.net.www.protocol.http.AuthCacheValue
1464    .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
1465    } catch (Throwable t)
1466    {
1467    Cache.error(t.getMessage());
1468    Cache.debug(getStackTraceString(t));
1469    }
1470    */
1471   
1472  307 if (httpUser != null || httpsUser != null)
1473    {
1474  0 try
1475    {
1476  0 char[] displayHttpPw = new char[httpPassword == null ? 0
1477    : httpPassword.length];
1478  0 Arrays.fill(displayHttpPw, '*');
1479  0 Console.debug(
1480    "CACHE Proxy: setting new Authenticator with httpUser='"
1481    + httpUser + "' httpPassword='" + displayHttpPw
1482    + "'");
1483  0 if (!Platform.isJS())
1484    /* *
1485    * java.net.Authenticator not implemented in SwingJS yet
1486    *
1487    * @j2sIgnore
1488    *
1489    */
1490    {
1491  0 Authenticator.setDefault(new Authenticator()
1492    {
 
1493  0 toggle @Override
1494    protected PasswordAuthentication getPasswordAuthentication()
1495    {
1496  0 if (getRequestorType() == RequestorType.PROXY)
1497    {
1498  0 String protocol = getRequestingProtocol();
1499  0 boolean needProxyPasswordSet = false;
1500  0 if (customProxySet &&
1501    // we have a username but no password for the scheme being
1502    // requested
1503    (protocol.equalsIgnoreCase("http")
1504    && (httpUser != null && httpUser.length() > 0
1505    && (httpPassword == null
1506    || httpPassword.length == 0)))
1507    || (protocol.equalsIgnoreCase("https")
1508    && (httpsUser != null
1509    && httpsUser.length() > 0
1510    && (httpsPassword == null
1511    || httpsPassword.length == 0))))
1512    {
1513    // open Preferences -> Connections
1514  0 String message = MessageManager
1515    .getString("label.proxy_password_required");
1516  0 Preferences.openPreferences(
1517    Preferences.TabRef.CONNECTIONS_TAB, message);
1518  0 Preferences.getInstance()
1519    .proxyAuthPasswordCheckHighlight(true, true);
1520    }
1521    else
1522    {
1523  0 try
1524    {
1525  0 if (protocol.equalsIgnoreCase("http")
1526    && getRequestingHost()
1527    .equalsIgnoreCase(httpHost)
1528    && getRequestingPort() == Integer
1529    .valueOf(httpPort))
1530    {
1531  0 Console.debug(
1532    "AUTHENTICATOR returning PasswordAuthentication(\""
1533    + httpUser + "\", '"
1534    + new String(displayHttpPw) + "')");
1535  0 return new PasswordAuthentication(httpUser,
1536    httpPassword);
1537    }
1538  0 if (protocol.equalsIgnoreCase("https")
1539    && getRequestingHost()
1540    .equalsIgnoreCase(httpsHost)
1541    && getRequestingPort() == Integer
1542    .valueOf(httpsPort))
1543    {
1544  0 char[] displayHttpsPw = new char[httpPassword.length];
1545  0 Arrays.fill(displayHttpsPw, '*');
1546  0 Console.debug(
1547    "AUTHENTICATOR returning PasswordAuthentication(\""
1548    + httpsUser + "\", '" + displayHttpsPw
1549    + "'");
1550  0 return new PasswordAuthentication(httpsUser,
1551    httpsPassword);
1552    }
1553    } catch (NumberFormatException e)
1554    {
1555  0 Console.error("Problem with proxy port values [http:"
1556    + httpPort + ", https:" + httpsPort + "]");
1557    }
1558  0 Console.debug(
1559    "AUTHENTICATOR after trying to get PasswordAuthentication");
1560    }
1561    }
1562    // non proxy request
1563  0 Console.debug("AUTHENTICATOR returning null");
1564  0 return null;
1565    }
1566    });
1567    } // end of j2sIgnore for java.net.Authenticator
1568   
1569    // required to re-enable basic authentication (should be okay for a
1570    // local proxy)
1571  0 Console.debug(
1572    "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
1573  0 System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
1574    } catch (SecurityException e)
1575    {
1576  0 Console.error("Could not set default Authenticator");
1577  0 Console.debug(getStackTraceString(e));
1578    }
1579    }
1580    else
1581    {
1582    // reset the Authenticator to protect http.proxyUser and
1583    // http.proxyPassword Just In Case
1584    /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
1585    * has working credentials. No workaround for Java 11.
1586    */
1587  307 if (!Platform.isJS())
1588    /* *
1589    * java.net.Authenticator not implemented in SwingJS yet
1590    *
1591    * @j2sIgnore
1592    *
1593    */
1594    {
1595  307 Console.debug(
1596    "AUTHENTICATOR setting default Authenticator to null");
1597  307 Authenticator.setDefault(null);
1598    }
1599    }
1600   
1601    // nonProxyHosts not currently configurable in Preferences
1602  307 Console.debug(
1603    "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
1604    + nonProxyHosts + "\"");
1605  307 setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
1606    }
1607   
 
1608  0 toggle public static void setOrClearSystemProperty(String key, char[] value)
1609    {
1610  0 setOrClearSystemProperty(key,
1611  0 (value == null) ? null : new String(value));
1612    }
1613   
 
1614  2149 toggle public static void setOrClearSystemProperty(String key, String value)
1615    {
1616  2149 if (key == null)
1617    {
1618  0 return;
1619    }
1620  2149 if (value == null)
1621    {
1622  2149 System.clearProperty(key);
1623    }
1624    else
1625    {
1626  0 System.setProperty(key, value);
1627    }
1628    }
1629   
1630    /**
1631    * Getdown appbase methods
1632    */
1633   
1634    private static final String releaseAppbase;
1635   
1636    private static String getdownAppbase;
1637   
1638    private static String getdownDistDir;
1639   
 
1640  55 toggle static
1641    {
1642  55 if (!Platform.isJS())
1643    {
1644  55 Float specversion = Float
1645    .parseFloat(System.getProperty("java.specification.version"));
1646  55 releaseAppbase = (specversion < 9)
1647    ? "https://www.jalview.org/getdown/release/1.8"
1648    : "https://www.jalview.org/getdown/release/11";
1649    }
1650    else
1651    {
1652    // this value currenly made up, can be changed to URL that will be
1653    // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
1654  0 releaseAppbase = "https://www.jalview.org/jalview-js";
1655  0 getdownAppbase = releaseAppbase;
1656  0 getdownDistDir = "/swingjs/j2s";
1657    }
1658    }
1659   
1660    // look for properties (passed in by getdown) otherwise default to release
 
1661  123 toggle private static void setGetdownAppbase()
1662    {
1663  123 if (getdownAppbase != null)
1664    {
1665  105 return;
1666    }
1667  18 String appbase = System.getProperty("launcher.appbase");
1668  18 if (appbase == null)
1669    {
1670  18 appbase = System.getProperty("getdownappbase"); // old name
1671    }
1672  18 String distDir = System.getProperty("launcher.distdir");
1673  18 if (distDir == null)
1674    {
1675  18 distDir = System.getProperty("getdowndistdir"); // old name
1676    }
1677  18 if (appbase == null)
1678    {
1679  18 appbase = buildProperties.getProperty("GETDOWNAPPBASE");
1680  18 distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
1681    }
1682  18 if (appbase == null)
1683    {
1684  18 appbase = releaseAppbase;
1685  18 distDir = "release";
1686    }
1687  18 if (appbase.endsWith("/"))
1688    {
1689  0 appbase = appbase.substring(0, appbase.length() - 1);
1690    }
1691  18 if (distDir == null)
1692    {
1693  0 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1694    }
1695  18 getdownAppbase = appbase;
1696  18 getdownDistDir = distDir;
1697    }
1698   
 
1699  123 toggle public static String getGetdownAppbase()
1700    {
1701  123 setGetdownAppbase();
1702  123 return getdownAppbase;
1703    }
1704   
 
1705  123 toggle public static String getAppbaseBuildProperties()
1706    {
1707  123 String appbase = getGetdownAppbase();
1708  123 return appbase + "/" + getdownDistDir + "/build_properties";
1709    }
1710   
1711    private static final Collection<String> bootstrapProperties = new ArrayList<>(
1712    Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
1713   
 
1714  132 toggle public static Properties bootstrapProperties(String filename)
1715    {
1716  132 Properties bootstrapProps = new Properties();
1717  132 File file = null;
1718  132 if (filename != null)
1719    {
1720  30 file = new File(filename);
1721    }
1722  132 if (file == null || !file.exists())
1723    {
1724  102 if (file != null)
1725    {
1726  0 jalview.bin.Console
1727    .errPrintln("Could not load bootstrap preferences file '"
1728    + file.getPath() + "'");
1729    }
1730  102 String channelPrefsFilename = ChannelProperties
1731    .getProperty("preferences.filename");
1732  102 String propertiesFilename = System.getProperty("user.home")
1733    + File.separatorChar + channelPrefsFilename;
1734  102 jalview.bin.Console.errPrintln(
1735    "Using default properties file '" + propertiesFilename + "'");
1736  102 file = new File(propertiesFilename);
1737    }
1738  132 if (file == null || !file.exists())
1739   
1740    {
1741  0 String releasePrefsFilename = fallbackPropertiesFile;
1742  0 String releasePropertiesFilename = System.getProperty("user.home")
1743    + File.separatorChar + releasePrefsFilename;
1744  0 jalview.bin.Console.errPrintln("Falling back to properties file '"
1745    + releasePropertiesFilename + "'");
1746  0 file = new File(releasePropertiesFilename);
1747    }
1748   
1749  132 if (!file.exists())
1750    {
1751  0 jalview.bin.Console
1752    .errPrintln("Could not load bootstrap preferences file '"
1753    + file.getPath() + "'");
1754  0 return null;
1755    }
1756   
1757  132 try
1758    {
1759  132 FileInputStream in = new FileInputStream(file.getAbsoluteFile());
1760  132 Properties props = new Properties();
1761  132 props.load(in);
1762  132 for (String prop : bootstrapProperties)
1763    {
1764  264 if (props.containsKey(prop))
1765  9 bootstrapProps.put(prop, props.getProperty(prop));
1766    }
1767    } catch (FileNotFoundException e)
1768    {
1769  0 jalview.bin.Console
1770    .errPrintln("Could not find bootstrap preferences file '"
1771    + file.getAbsolutePath() + "'");
1772    } catch (IOException e)
1773    {
1774  0 jalview.bin.Console.errPrintln(
1775    "IOException when loading bootstrap preferences file '"
1776    + file.getAbsolutePath() + "'");
1777    }
1778  132 return bootstrapProps;
1779    }
1780   
 
1781  0 toggle public static void setSessionProperty(String key, String val)
1782    {
1783  0 if (key != null)
1784    {
1785  0 sessionProperties.put(key, val);
1786    }
1787    }
1788   
 
1789  315106 toggle public static String getSessionProperty(String key)
1790    {
1791  315105 return key == null ? null : sessionProperties.get(key);
1792    }
1793   
 
1794  75 toggle public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
1795    {
1796  75 ArgParser ap = Jalview.getInstance().getArgParser();
1797  75 return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
1798    }
1799    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 28 2024 18:14:23 GMT using coverage data from Thu Nov 28 2024 18:14:06 GMT.
  • OpenClover is free and open-source software.