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File Cache.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| Cache | 244 | 472 | 216 | ||
| Cache.VersionChecker | 561 | 20 | 5 |
Contributing tests
This file is covered by 406 tests.
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| 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[|<separator>] 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 |  public static void enableSessionProperties() |
| 336 | { | |
| 337 | 10 | bypassSessionProperties = false; |
| 338 | } | |
| 339 | ||
| 340 | 10 | 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 | @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 | public static boolean isPropsAreReadOnly() |
| 367 | { | |
| 368 | 0 | return propsAreReadOnly; |
| 369 | } | |
| 370 | ||
| 371 | 32 | 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 | 325 | public static void loadProperties(String propsFile) |
| 383 | { | |
| 384 | 325 | propertiesFile = propsFile; |
| 385 | 325 | String releasePropertiesFile = null; |
| 386 | 325 | boolean defaultProperties = false; |
| 387 | 325 | 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 | 283 | propsAreReadOnly = true; |
| 402 | } | |
| 403 | ||
| 404 | 325 | if (propertiesFile == null) |
| 405 | { // BH 2019 | |
| 406 | 59 | Platform.readInfoProperties(JS_PROPERTY_PREFIX, |
| 407 | applicationProperties); | |
| 408 | } | |
| 409 | else | |
| 410 | { | |
| 411 | 266 | try |
| 412 | { | |
| 413 | 266 | InputStream fis; |
| 414 | 266 | try |
| 415 | { | |
| 416 | // props file provided as URL | |
| 417 | 266 | 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 | 266 | fis = null; |
| 429 | } | |
| 430 | 266 | if (fis == null) |
| 431 | { | |
| 432 | 266 | 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 | 266 | if (defaultProperties && (!new File(propertiesFile).exists()) |
| 437 | && (new File(releasePropertiesFile).exists())) | |
| 438 | { | |
| 439 | 0 | readPropertiesFile = releasePropertiesFile; |
| 440 | } | |
| 441 | 266 | fis = new FileInputStream(readPropertiesFile); |
| 442 | } | |
| 443 | 265 | applicationProperties.clear(); |
| 444 | 265 | applicationProperties.load(fis); |
| 445 | ||
| 446 | // remove any old build properties | |
| 447 | ||
| 448 | 265 | deleteBuildProperties(); |
| 449 | 265 | 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 | 325 | String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM); |
| 469 | // default to upgrading old settings | |
| 470 | 325 | switch (proxyType) |
| 471 | { | |
| 472 | 0 | case PROXYTYPE_NONE: |
| 473 | 0 | clearProxyProperties(); |
| 474 | 0 | break; |
| 475 | 325 | case PROXYTYPE_SYSTEM: // use system settings |
| 476 | 325 | resetProxyProperties(); |
| 477 | 325 | 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 | 325 | String authorDetails = resolveResourceURLFor("/authors.props"); |
| 498 | ||
| 499 | 325 | try |
| 500 | { | |
| 501 | 325 | if (authorDetails != null) |
| 502 | { | |
| 503 | 325 | URL localJarFileURL = new URL(authorDetails); |
| 504 | 325 | InputStream in = localJarFileURL.openStream(); |
| 505 | 325 | applicationProperties.load(in); |
| 506 | 325 | 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 | 325 | if (authorDetails == null) |
| 516 | { | |
| 517 | 0 | applicationProperties.remove("AUTHORS"); |
| 518 | 0 | applicationProperties.remove("AUTHORFNAMES"); |
| 519 | 0 | applicationProperties.remove("YEAR"); |
| 520 | } | |
| 521 | ||
| 522 | 325 | loadBuildProperties(false); |
| 523 | ||
| 524 | 325 | SiftsSettings |
| 525 | .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); | |
| 526 | ||
| 527 | 325 | SiftsSettings.setSiftDownloadDirectory(Cache |
| 528 | .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); | |
| 529 | ||
| 530 | 325 | SiftsSettings.setFailSafePIDThreshold( |
| 531 | Cache.getDefault("sifts_fail_safe_pid_threshold", | |
| 532 | DEFAULT_FAIL_SAFE_PID_THRESHOLD)); | |
| 533 | ||
| 534 | 325 | SiftsSettings.setCacheThresholdInDays( |
| 535 | Cache.getDefault("sifts_cache_threshold_in_days", | |
| 536 | DEFAULT_CACHE_THRESHOLD_IN_DAYS)); | |
| 537 | ||
| 538 | 325 | IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", |
| 539 | "https://www.jalview.org/services/identifiers")); | |
| 540 | 325 | IdOrgSettings.setDownloadLocation(ID_ORG_FILE); |
| 541 | ||
| 542 | 325 | StructureImportSettings.setDefaultStructureFileFormat( |
| 543 | Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); | |
| 544 | 325 | StructureImportSettings |
| 545 | .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); | |
| 546 | // StructureImportSettings | |
| 547 | // .setDefaultPDBFileParser(Cache.getDefault( | |
| 548 | // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); | |
| 549 | ||
| 550 | 325 | 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 | 325 | 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 | 126 | @Override |
| 565 | public void run() | |
| 566 | { | |
| 567 | 126 | String remoteBuildPropertiesUrl = Cache |
| 568 | .getAppbaseBuildProperties(); | |
| 569 | ||
| 570 | 126 | String orgtimeout = System |
| 571 | .getProperty("sun.net.client.defaultConnectTimeout"); | |
| 572 | 126 | if (orgtimeout == null) |
| 573 | { | |
| 574 | 18 | orgtimeout = "30"; |
| 575 | 18 | Console.debug("Setting default net timeout to " + orgtimeout |
| 576 | + " seconds."); | |
| 577 | } | |
| 578 | 126 | String remoteVersion = null; |
| 579 | 126 | if (remoteBuildPropertiesUrl.startsWith("http")) |
| 580 | { | |
| 581 | 126 | try |
| 582 | { | |
| 583 | 126 | System.setProperty("sun.net.client.defaultConnectTimeout", |
| 584 | "5000"); | |
| 585 | ||
| 586 | 126 | URL url = new URL(remoteBuildPropertiesUrl); |
| 587 | ||
| 588 | 126 | BufferedReader in = new BufferedReader( |
| 589 | new InputStreamReader(HttpUtils.openStream(url))); | |
| 590 | ||
| 591 | 125 | Properties remoteBuildProperties = new Properties(); |
| 592 | 125 | remoteBuildProperties.load(in); |
| 593 | 125 | 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 | 125 | System.setProperty("sun.net.client.defaultConnectTimeout", |
| 607 | orgtimeout); | |
| 608 | ||
| 609 | 125 | setProperty("LATEST_VERSION", remoteVersion); |
| 610 | } | |
| 611 | } | |
| 612 | ||
| 613 | 126 | VersionChecker vc = new VersionChecker(); |
| 614 | 126 | vc.start(); |
| 615 | } | |
| 616 | else | |
| 617 | { | |
| 618 | 199 | if (jnlpVersion != null) |
| 619 | { | |
| 620 | 0 | setProperty("LATEST_VERSION", jnlpVersion); |
| 621 | } | |
| 622 | else | |
| 623 | { | |
| 624 | 199 | applicationProperties.remove("LATEST_VERSION"); |
| 625 | } | |
| 626 | } | |
| 627 | ||
| 628 | // LOAD USERDEFINED COLOURS | |
| 629 | 325 | Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); |
| 630 | 325 | 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 | 799 | private static String resolveResourceURLFor(String resourcePath) |
| 641 | { | |
| 642 | 799 | String url = null; |
| 643 | 799 | if (Platform.isJS() || !Cache.class.getProtectionDomain() |
| 644 | .getCodeSource().getLocation().toString().endsWith(".jar")) | |
| 645 | { | |
| 646 | 799 | try |
| 647 | { | |
| 648 | 799 | 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 | 799 | return url; |
| 661 | } | |
| 662 | ||
| 663 | 474 | public static void loadBuildProperties(boolean reportVersion) |
| 664 | { | |
| 665 | 474 | String codeInstallation = getProperty("INSTALLATION"); |
| 666 | 474 | 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 | 474 | try |
| 673 | { | |
| 674 | 474 | String buildDetails = resolveResourceURLFor("/.build_properties"); |
| 675 | 474 | URL localJarFileURL = new URL(buildDetails); |
| 676 | 474 | InputStream in = localJarFileURL.openStream(); |
| 677 | 474 | buildProperties.load(in); |
| 678 | 474 | in.close(); |
| 679 | 474 | if (buildProperties.getProperty("BUILD_DATE", null) != null) |
| 680 | { | |
| 681 | 474 | applicationProperties.put("BUILD_DATE", |
| 682 | buildProperties.getProperty("BUILD_DATE")); | |
| 683 | } | |
| 684 | 474 | if (buildProperties.getProperty("INSTALLATION", null) != null) |
| 685 | { | |
| 686 | 474 | applicationProperties.put("INSTALLATION", |
| 687 | buildProperties.getProperty("INSTALLATION")); | |
| 688 | } | |
| 689 | 474 | if (buildProperties.getProperty("VERSION", null) != null) |
| 690 | { | |
| 691 | 474 | applicationProperties.put("VERSION", |
| 692 | buildProperties.getProperty("VERSION")); | |
| 693 | } | |
| 694 | 474 | if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null) |
| 695 | { | |
| 696 | 474 | 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 | 474 | String codeVersion = getProperty("VERSION"); |
| 707 | 474 | codeInstallation = getProperty("INSTALLATION"); |
| 708 | ||
| 709 | 474 | 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 | 474 | codeInstallation = " (" + codeInstallation + ")"; |
| 718 | } | |
| 719 | 474 | setProperty("VERSION", codeVersion); |
| 720 | 474 | new BuildDetails(codeVersion, null, codeInstallation); |
| 721 | 474 | if (printVersion && reportVersion) |
| 722 | { | |
| 723 | 51 | jalview.bin.Console |
| 724 | .outPrintln(ChannelProperties.getProperty("app_name") | |
| 725 | + " version: " + codeVersion + codeInstallation); | |
| 726 | } | |
| 727 | } | |
| 728 | ||
| 729 | 265 | private static void deleteBuildProperties() |
| 730 | { | |
| 731 | 265 | applicationProperties.remove("LATEST_VERSION"); |
| 732 | 265 | applicationProperties.remove("VERSION"); |
| 733 | 265 | applicationProperties.remove("AUTHORS"); |
| 734 | 265 | applicationProperties.remove("AUTHORFNAMES"); |
| 735 | 265 | applicationProperties.remove("YEAR"); |
| 736 | 265 | applicationProperties.remove("BUILD_DATE"); |
| 737 | 265 | 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 | 464556 | public static String getProperty(String key) |
| 750 | { | |
| 751 | 464557 | return getProperty(key, false); |
| 752 | } | |
| 753 | ||
| 754 | 464557 | public static String getProperty(String key, |
| 755 | boolean skipSessionProperties) | |
| 756 | { | |
| 757 | 464558 | String prop = null; |
| 758 | 464562 | if (!(skipSessionProperties || bypassSessionProperties)) |
| 759 | { | |
| 760 | 464463 | prop = getSessionProperty(key); |
| 761 | } | |
| 762 | 464564 | if (prop == null) |
| 763 | { | |
| 764 | 464565 | prop = applicationProperties.getProperty(key); |
| 765 | } | |
| 766 | 464566 | if (prop == null && Platform.isJS()) |
| 767 | { | |
| 768 | 0 | prop = applicationProperties.getProperty(Platform.getUniqueAppletID() |
| 769 | + "_" + JS_PROPERTY_PREFIX + key); | |
| 770 | } | |
| 771 | 464566 | 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 | 445199 | public static boolean getDefault(String property, boolean def) |
| 780 | { | |
| 781 | 445199 | String string = getProperty(property); |
| 782 | 445207 | if (string != null) |
| 783 | { | |
| 784 | 350785 | def = Boolean.valueOf(string).booleanValue(); |
| 785 | } | |
| 786 | ||
| 787 | 445206 | return def; |
| 788 | } | |
| 789 | ||
| 790 | 302 | 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 | 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 | 12516 | public static String getDefault(String property, String def) |
| 833 | { | |
| 834 | 12516 | String value = getProperty(property); |
| 835 | 12516 | 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 | 2774 | public static Object setProperty(String key, String obj) |
| 849 | { | |
| 850 | 2774 | Object oldValue = null; |
| 851 | 2774 | try |
| 852 | { | |
| 853 | 2774 | oldValue = applicationProperties.setProperty(key, obj); |
| 854 | 2774 | 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 | 2774 | return oldValue; |
| 875 | } | |
| 876 | ||
| 877 | /** | |
| 878 | * remove the specified property from the jalview properties file | |
| 879 | * | |
| 880 | * @param string | |
| 881 | */ | |
| 882 | 27 | 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 | 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 | 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 | 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 | 1 | public static void initAnalytics() |
| 994 | { | |
| 995 | 1 | Plausible.setEnabled(true); |
| 996 | ||
| 997 | 1 | String appName = ChannelProperties.getProperty("app_name") + " Desktop"; |
| 998 | 1 | String version = Cache.getProperty("VERSION") + "_" |
| 999 | + Cache.getDefault("BUILD_DATE", "unknown"); | |
| 1000 | 1 | 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 | 1 | List<String> pathParts = new ArrayList<>(); |
| 1011 | 1 | pathParts.add(appName); |
| 1012 | 1 | pathParts.add(version); |
| 1013 | 1 | pathParts.add(APPLICATION_STARTED); |
| 1014 | 1 | path = ("/" + String.join("/", pathParts)).replace(' ', '+'); |
| 1015 | /* | |
| 1016 | } | |
| 1017 | */ | |
| 1018 | 1 | 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, and also | |
| 1022 | // add the JSON string values to the querystring for logging reasons. | |
| 1023 | 1 | plausible.sendEvent("application_launch", path, true, true); |
| 1024 | } | |
| 1025 | ||
| 1026 | private static final String APPLICATION_STARTED = "Application Started"; | |
| 1027 | ||
| 1028 | /** | |
| 1029 | * get the user's default colour if available | |
| 1030 | * | |
| 1031 | * @param property | |
| 1032 | * @param defcolour | |
| 1033 | * @return | |
| 1034 | */ | |
| 1035 | 86 | public static Color getDefaultColour(String property, Color defcolour) |
| 1036 | { | |
| 1037 | 86 | String colprop = getProperty(property); |
| 1038 | 86 | if (colprop == null) |
| 1039 | { | |
| 1040 | 12 | return defcolour; |
| 1041 | } | |
| 1042 | 74 | Color col = ColorUtils.parseColourString(colprop); |
| 1043 | 74 | if (col == null) |
| 1044 | { | |
| 1045 | 0 | Console.warn("Couldn't parse '" + colprop + "' as a colour for " |
| 1046 | + property); | |
| 1047 | } | |
| 1048 | 74 | return (col == null) ? defcolour : col; |
| 1049 | } | |
| 1050 | ||
| 1051 | /** | |
| 1052 | * store a colour as a Jalview user default property | |
| 1053 | * | |
| 1054 | * @param property | |
| 1055 | * @param colour | |
| 1056 | */ | |
| 1057 | 4 | public static void setColourProperty(String property, Color colour) |
| 1058 | { | |
| 1059 | 4 | setProperty(property, jalview.util.Format.getHexString(colour)); |
| 1060 | } | |
| 1061 | ||
| 1062 | /** | |
| 1063 | * Stores a formatted date in a jalview property, using a fixed locale. | |
| 1064 | * | |
| 1065 | * @param propertyName | |
| 1066 | * @param date | |
| 1067 | * @return the formatted date string | |
| 1068 | */ | |
| 1069 | 132 | public static String setDateProperty(String propertyName, Date date) |
| 1070 | { | |
| 1071 | 132 | String formatted = date_format.format(date); |
| 1072 | 132 | setProperty(propertyName, formatted); |
| 1073 | 132 | return formatted; |
| 1074 | } | |
| 1075 | ||
| 1076 | /** | |
| 1077 | * Reads a date stored in a Jalview property, parses it (using a fixed locale | |
| 1078 | * format) and returns as a Date, or null if parsing fails | |
| 1079 | * | |
| 1080 | * @param propertyName | |
| 1081 | * @return | |
| 1082 | * | |
| 1083 | */ | |
| 1084 | 42 | public static Date getDateProperty(String propertyName) |
| 1085 | { | |
| 1086 | 42 | String val = getProperty(propertyName); |
| 1087 | 42 | if (val != null) |
| 1088 | { | |
| 1089 | 42 | try |
| 1090 | { | |
| 1091 | 42 | return date_format.parse(val); |
| 1092 | } catch (Exception ex) | |
| 1093 | { | |
| 1094 | 8 | jalview.bin.Console |
| 1095 | .errPrintln("Invalid or corrupt date in property '" | |
| 1096 | + propertyName + "' : value was '" + val + "'"); | |
| 1097 | } | |
| 1098 | } | |
| 1099 | 8 | return null; |
| 1100 | } | |
| 1101 | ||
| 1102 | /** | |
| 1103 | * get and parse a property as an integer. send any parsing problems to | |
| 1104 | * System.err | |
| 1105 | * | |
| 1106 | * @param property | |
| 1107 | * @return null or Integer | |
| 1108 | */ | |
| 1109 | 90 | public static Integer getIntegerProperty(String property) |
| 1110 | { | |
| 1111 | 90 | String val = getProperty(property); |
| 1112 | ? | if (val != null && (val = val.trim()).length() > 0) |
| 1113 | { | |
| 1114 | 0 | try |
| 1115 | { | |
| 1116 | 0 | return Integer.valueOf(val); |
| 1117 | } catch (NumberFormatException x) | |
| 1118 | { | |
| 1119 | 0 | jalview.bin.Console.errPrintln("Invalid integer in property '" |
| 1120 | + property + "' (value was '" + val + "')"); | |
| 1121 | } | |
| 1122 | } | |
| 1123 | 90 | return null; |
| 1124 | } | |
| 1125 | ||
| 1126 | /** | |
| 1127 | * Set the specified value, or remove it if null or empty. Does not save the | |
| 1128 | * properties file. | |
| 1129 | * | |
| 1130 | * @param propName | |
| 1131 | * @param value | |
| 1132 | */ | |
| 1133 | 0 | public static void setOrRemove(String propName, String value) |
| 1134 | { | |
| 1135 | 0 | if (propName == null) |
| 1136 | { | |
| 1137 | 0 | return; |
| 1138 | } | |
| 1139 | 0 | if (value == null || value.trim().length() < 1) |
| 1140 | { | |
| 1141 | 0 | Cache.applicationProperties.remove(propName); |
| 1142 | } | |
| 1143 | else | |
| 1144 | { | |
| 1145 | 0 | Cache.applicationProperties.setProperty(propName, value); |
| 1146 | } | |
| 1147 | } | |
| 1148 | ||
| 1149 | /** | |
| 1150 | * Loads in user colour schemes from files. | |
| 1151 | * | |
| 1152 | * @param files | |
| 1153 | * a '|'-delimited list of file paths | |
| 1154 | */ | |
| 1155 | 325 | public static void initUserColourSchemes(String files) |
| 1156 | { | |
| 1157 | 325 | if (files == null || files.length() == 0) |
| 1158 | { | |
| 1159 | 325 | return; |
| 1160 | } | |
| 1161 | ||
| 1162 | // In case colours can't be loaded, we'll remove them | |
| 1163 | // from the default list here. | |
| 1164 | 0 | StringBuffer coloursFound = new StringBuffer(); |
| 1165 | 0 | StringTokenizer st = new StringTokenizer(files, "|"); |
| 1166 | 0 | while (st.hasMoreElements()) |
| 1167 | { | |
| 1168 | 0 | String file = st.nextToken(); |
| 1169 | 0 | try |
| 1170 | { | |
| 1171 | 0 | UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file); |
| 1172 | 0 | if (ucs != null) |
| 1173 | { | |
| 1174 | 0 | if (coloursFound.length() > 0) |
| 1175 | { | |
| 1176 | 0 | coloursFound.append("|"); |
| 1177 | } | |
| 1178 | 0 | coloursFound.append(file); |
| 1179 | 0 | ColourSchemes.getInstance().registerColourScheme(ucs); |
| 1180 | } | |
| 1181 | } catch (Exception ex) | |
| 1182 | { | |
| 1183 | 0 | if (!Jalview.quiet()) |
| 1184 | 0 | jalview.bin.Console |
| 1185 | .outPrintln("Error loading User ColourFile\n" + ex); | |
| 1186 | } | |
| 1187 | } | |
| 1188 | 0 | if (!files.equals(coloursFound.toString())) |
| 1189 | { | |
| 1190 | 0 | if (coloursFound.toString().length() > 1) |
| 1191 | { | |
| 1192 | 0 | setProperty(UserDefinedColours.USER_DEFINED_COLOURS, |
| 1193 | coloursFound.toString()); | |
| 1194 | } | |
| 1195 | else | |
| 1196 | { | |
| 1197 | 0 | applicationProperties |
| 1198 | .remove(UserDefinedColours.USER_DEFINED_COLOURS); | |
| 1199 | } | |
| 1200 | } | |
| 1201 | } | |
| 1202 | ||
| 1203 | /** | |
| 1204 | * Initial logging information helper for various versions output | |
| 1205 | * | |
| 1206 | * @param prefix | |
| 1207 | * @param value | |
| 1208 | * @param defaultValue | |
| 1209 | */ | |
| 1210 | 3388 | private static void appendIfNotNull(StringBuilder sb, String prefix, |
| 1211 | String value, String suffix, String defaultValue) | |
| 1212 | { | |
| 1213 | 3388 | if (value == null && defaultValue == null) |
| 1214 | { | |
| 1215 | 2178 | return; |
| 1216 | } | |
| 1217 | 1210 | if (prefix != null) |
| 1218 | 1210 | sb.append(prefix); |
| 1219 | 1210 | sb.append(value == null ? defaultValue : value); |
| 1220 | 1210 | if (suffix != null) |
| 1221 | 1210 | sb.append(suffix); |
| 1222 | } | |
| 1223 | ||
| 1224 | /** | |
| 1225 | * | |
| 1226 | * @return Jalview version, build details and JVM platform version for console | |
| 1227 | */ | |
| 1228 | 242 | public static String getVersionDetailsForConsole() |
| 1229 | { | |
| 1230 | 242 | boolean extra = Console.isDebugEnabled() |
| 1231 | || !"release".equals(ChannelProperties.getProperty("channel")); | |
| 1232 | 242 | StringBuilder sb = new StringBuilder(); |
| 1233 | 242 | sb.append(ChannelProperties.getProperty("app_name")) |
| 1234 | .append(" Version: "); | |
| 1235 | 242 | sb.append(Cache.getDefault("VERSION", "TEST")); |
| 1236 | 242 | sb.append("\n"); |
| 1237 | 242 | sb.append(ChannelProperties.getProperty("app_name")) |
| 1238 | .append(" Installation: "); | |
| 1239 | 242 | sb.append(Cache.getDefault("INSTALLATION", "unknown")); |
| 1240 | 242 | sb.append("\n"); |
| 1241 | 242 | appendIfNotNull(sb, "Channel: ", |
| 1242 | ChannelProperties.getProperty("channel"), "\n", null); | |
| 1243 | 242 | sb.append("Build Date: "); |
| 1244 | 242 | sb.append(Cache.getDefault("BUILD_DATE", "unknown")); |
| 1245 | 242 | sb.append("\n"); |
| 1246 | 242 | if (extra) |
| 1247 | { | |
| 1248 | 242 | appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n", |
| 1249 | "unknown"); | |
| 1250 | 242 | appendIfNotNull(sb, "Log file: ", |
| 1251 | System.getProperty("installer.logfile"), "\n", "unknown"); | |
| 1252 | } | |
| 1253 | 242 | sb.append("Java version: "); |
| 1254 | 242 | sb.append(System.getProperty("java.version")); |
| 1255 | 242 | sb.append("\n"); |
| 1256 | 242 | if (extra) |
| 1257 | { | |
| 1258 | 242 | appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), |
| 1259 | "\n", "unknown"); | |
| 1260 | 242 | appendIfNotNull(sb, "Java launch class: ", |
| 1261 | System.getProperty("sun.java.command"), "\n", "unknown"); | |
| 1262 | 242 | sb.append("Java platform: "); |
| 1263 | 242 | sb.append(System.getProperty("os.name")); |
| 1264 | 242 | sb.append(" "); |
| 1265 | 242 | sb.append(System.getProperty("os.version")); |
| 1266 | 242 | sb.append(" ("); |
| 1267 | 242 | sb.append(System.getProperty("os.arch")); |
| 1268 | 242 | sb.append(")"); |
| 1269 | 242 | sb.append("\n"); |
| 1270 | 242 | LookAndFeel laf = UIManager.getLookAndFeel(); |
| 1271 | 242 | String lafName = laf == null ? "Not obtained" : laf.getName(); |
| 1272 | 242 | String lafClass = laf == null ? "unknown" : laf.getClass().getName(); |
| 1273 | 242 | sb.append("Java LAF: "); |
| 1274 | 242 | sb.append(lafName); |
| 1275 | 242 | sb.append(" ("); |
| 1276 | 242 | sb.append(lafClass); |
| 1277 | 242 | sb.append(")\n"); |
| 1278 | // pid() only available in Java 9+ | |
| 1279 | 242 | if (LaunchUtils.getJavaVersion() > 8) |
| 1280 | { | |
| 1281 | 242 | sb.append("Java Virtual Machine PID: "); |
| 1282 | 242 | sb.append(ProcessHandle.current().pid()); |
| 1283 | 242 | sb.append("\n"); |
| 1284 | } | |
| 1285 | ||
| 1286 | } | |
| 1287 | 242 | appendIfNotNull(sb, "Installer version: ", |
| 1288 | System.getProperty("sys.install4jVersion"), "\n", null); | |
| 1289 | 242 | if (extra) |
| 1290 | { | |
| 1291 | 242 | String installerAppdir = System.getProperty("installer.appdir"); |
| 1292 | 242 | if (installerAppdir != null) |
| 1293 | { | |
| 1294 | 0 | try |
| 1295 | { | |
| 1296 | 0 | String temp = new File(installerAppdir).getCanonicalPath(); |
| 1297 | 0 | installerAppdir = temp; |
| 1298 | } catch (IOException e) | |
| 1299 | { | |
| 1300 | 0 | installerAppdir = "(non-canonical) " + installerAppdir; |
| 1301 | 0 | Console.warn( |
| 1302 | "Could not get canonical path for installer appdir, leaving as is."); | |
| 1303 | } | |
| 1304 | } | |
| 1305 | 242 | appendIfNotNull(sb, "Installer template version: ", |
| 1306 | System.getProperty("installer.template_version"), "\n", null); | |
| 1307 | 242 | appendIfNotNull(sb, "Installer appdir: ", installerAppdir, "\n", |
| 1308 | null); | |
| 1309 | 242 | appendIfNotNull(sb, "Installer extrainfo: ", |
| 1310 | System.getProperty("installer.extrainfo"), "\n", null); | |
| 1311 | } | |
| 1312 | 242 | appendIfNotNull(sb, "Launcher version: ", |
| 1313 | System.getProperty("launcher.version"), "\n", null); | |
| 1314 | 242 | if (extra) |
| 1315 | { | |
| 1316 | 242 | appendIfNotNull(sb, "Launcher appdir: ", |
| 1317 | System.getProperty("launcher.appdir"), "\n", null); | |
| 1318 | 242 | appendIfNotNull(sb, "Launcher distdir: ", |
| 1319 | System.getProperty("launcher.distdir"), "\n", null); | |
| 1320 | 242 | appendIfNotNull(sb, "Launcher appbase: ", |
| 1321 | System.getProperty("launcher.appbase"), "\n", null); | |
| 1322 | 242 | appendIfNotNull(sb, "Launcher script: ", |
| 1323 | System.getProperty("launcher.script"), "\n", null); | |
| 1324 | } | |
| 1325 | 242 | return sb.toString(); |
| 1326 | } | |
| 1327 | ||
| 1328 | /** | |
| 1329 | * | |
| 1330 | * @return build details as reported in splashscreen | |
| 1331 | */ | |
| 1332 | 547 | public static String getBuildDetailsForSplash() |
| 1333 | { | |
| 1334 | // consider returning more human friendly info | |
| 1335 | // eg 'built from Source' or update channel | |
| 1336 | 547 | return Cache.getDefault("INSTALLATION", "unknown"); |
| 1337 | } | |
| 1338 | ||
| 1339 | 0 | public static String getStackTraceString(Throwable t) |
| 1340 | { | |
| 1341 | 0 | StringWriter sw = new StringWriter(); |
| 1342 | 0 | PrintWriter pw = new PrintWriter(sw); |
| 1343 | 0 | t.printStackTrace(pw); |
| 1344 | 0 | return sw.toString(); |
| 1345 | } | |
| 1346 | ||
| 1347 | // proxy properties methods | |
| 1348 | 0 | public static void clearProxyProperties() |
| 1349 | { | |
| 1350 | 0 | setProxyProperties(null, null, null, null, null, null, null, null, |
| 1351 | null); | |
| 1352 | } | |
| 1353 | ||
| 1354 | 325 | public static void resetProxyProperties() |
| 1355 | { | |
| 1356 | 325 | setProxyProperties(startupProxyProperties[0], startupProxyProperties[1], |
| 1357 | startupProxyProperties[2], startupProxyProperties[3], | |
| 1358 | startupProxyProperties[4], | |
| 1359 | 325 | startupProxyProperties[5] == null ? null |
| 1360 | : startupProxyProperties[5].toCharArray(), | |
| 1361 | startupProxyProperties[6], | |
| 1362 | 325 | startupProxyProperties[7] == null ? null |
| 1363 | : startupProxyProperties[7].toCharArray(), | |
| 1364 | startupProxyProperties[8]); | |
| 1365 | 325 | StringBuilder sb = new StringBuilder(); |
| 1366 | 325 | sb.append("Setting proxy properties to: http.proxyHost=") |
| 1367 | .append(startupProxyProperties[0]).append(", http.proxyPort=") | |
| 1368 | .append(startupProxyProperties[1]) | |
| 1369 | 325 | .append(startupProxyProperties[4] != null |
| 1370 | && !startupProxyProperties[4].isEmpty() | |
| 1371 | ? " [" + startupProxyProperties[4] + "]" | |
| 1372 | : "") | |
| 1373 | .append(", https.proxyHost=").append(startupProxyProperties[2]) | |
| 1374 | .append(", https.proxyPort=").append(startupProxyProperties[3]) | |
| 1375 | 325 | .append(startupProxyProperties[6] != null |
| 1376 | && !startupProxyProperties[6].isEmpty() | |
| 1377 | ? " [" + startupProxyProperties[6] + "]" | |
| 1378 | : ""); | |
| 1379 | ||
| 1380 | 325 | Console.debug(sb.toString()); |
| 1381 | } | |
| 1382 | ||
| 1383 | 93 | public static void setProxyPropertiesFromPreferences() |
| 1384 | { | |
| 1385 | 93 | setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM); |
| 1386 | } | |
| 1387 | ||
| 1388 | 93 | public static void setProxyPropertiesFromPreferences( |
| 1389 | String previousProxyType) | |
| 1390 | { | |
| 1391 | 93 | String proxyType = Cache.getDefault("USE_PROXY", |
| 1392 | Cache.PROXYTYPE_SYSTEM); | |
| 1393 | 93 | if (previousProxyType != null |
| 1394 | && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply | |
| 1395 | // customProxy | |
| 1396 | && proxyType.equals(previousProxyType)) | |
| 1397 | { | |
| 1398 | // no change | |
| 1399 | 93 | return; |
| 1400 | } | |
| 1401 | 0 | switch (proxyType) |
| 1402 | { | |
| 1403 | 0 | case Cache.PROXYTYPE_NONE: |
| 1404 | 0 | if (!previousProxyType.equals(proxyType)) |
| 1405 | { | |
| 1406 | 0 | Console.info("Setting no proxy settings"); |
| 1407 | 0 | Cache.setProxyProperties(null, null, null, null, null, null, null, |
| 1408 | null, null); | |
| 1409 | } | |
| 1410 | 0 | break; |
| 1411 | 0 | case Cache.PROXYTYPE_CUSTOM: |
| 1412 | // always re-set a custom proxy -- it might have changed, particularly | |
| 1413 | // password | |
| 1414 | 0 | Console.info("Setting custom proxy settings"); |
| 1415 | 0 | boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false); |
| 1416 | 0 | Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null), |
| 1417 | Cache.getDefault("PROXY_PORT", null), | |
| 1418 | Cache.getDefault("PROXY_SERVER_HTTPS", null), | |
| 1419 | Cache.getDefault("PROXY_PORT_HTTPS", null), | |
| 1420 | 0 | proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") |
| 1421 | : null, | |
| 1422 | 0 | proxyAuthSet ? Cache.proxyAuthPassword : null, |
| 1423 | 0 | proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") |
| 1424 | : null, | |
| 1425 | 0 | proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost"); |
| 1426 | 0 | break; |
| 1427 | 0 | default: // system proxy settings by default |
| 1428 | 0 | Console.info("Setting system proxy settings"); |
| 1429 | 0 | Cache.resetProxyProperties(); |
| 1430 | } | |
| 1431 | } | |
| 1432 | ||
| 1433 | 325 | public static void setProxyProperties(String httpHost, String httpPort, |
| 1434 | String httpsHost, String httpsPort, String httpUser, | |
| 1435 | char[] httpPassword, String httpsUser, char[] httpsPassword, | |
| 1436 | String nonProxyHosts) | |
| 1437 | { | |
| 1438 | 325 | setOrClearSystemProperty("http.proxyHost", httpHost); |
| 1439 | 325 | setOrClearSystemProperty("http.proxyPort", httpPort); |
| 1440 | 325 | setOrClearSystemProperty("https.proxyHost", httpsHost); |
| 1441 | 325 | setOrClearSystemProperty("https.proxyPort", httpsPort); |
| 1442 | 325 | setOrClearSystemProperty("http.proxyUser", httpUser); |
| 1443 | 325 | setOrClearSystemProperty("https.proxyUser", httpsUser); |
| 1444 | // note: passwords for http.proxyPassword and https.proxyPassword are sent | |
| 1445 | // via the Authenticator, properties do not need to be set | |
| 1446 | ||
| 1447 | // are we using a custom proxy (password prompt might be required)? | |
| 1448 | 325 | boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM) |
| 1449 | .equals(PROXYTYPE_CUSTOM); | |
| 1450 | ||
| 1451 | /* | |
| 1452 | * A bug in Java means the AuthCache does not get reset, so once it has working credentials, | |
| 1453 | * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication() | |
| 1454 | * is not re-called). | |
| 1455 | * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear | |
| 1456 | * the AuthCache. | |
| 1457 | * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials | |
| 1458 | * ... | |
| 1459 | * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out | |
| 1460 | */ | |
| 1461 | /* | |
| 1462 | try | |
| 1463 | { | |
| 1464 | sun.net.www.protocol.http.AuthCacheValue | |
| 1465 | .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl()); | |
| 1466 | } catch (Throwable t) | |
| 1467 | { | |
| 1468 | Cache.error(t.getMessage()); | |
| 1469 | Cache.debug(getStackTraceString(t)); | |
| 1470 | } | |
| 1471 | */ | |
| 1472 | ||
| 1473 | 325 | if (httpUser != null || httpsUser != null) |
| 1474 | { | |
| 1475 | 0 | try |
| 1476 | { | |
| 1477 | 0 | char[] displayHttpPw = new char[httpPassword == null ? 0 |
| 1478 | : httpPassword.length]; | |
| 1479 | 0 | Arrays.fill(displayHttpPw, '*'); |
| 1480 | 0 | Console.debug( |
| 1481 | "CACHE Proxy: setting new Authenticator with httpUser='" | |
| 1482 | + httpUser + "' httpPassword='" + displayHttpPw | |
| 1483 | + "'"); | |
| 1484 | 0 | if (!Platform.isJS()) |
| 1485 | /* * | |
| 1486 | * java.net.Authenticator not implemented in SwingJS yet | |
| 1487 | * | |
| 1488 | * @j2sIgnore | |
| 1489 | * | |
| 1490 | */ | |
| 1491 | { | |
| 1492 | 0 | Authenticator.setDefault(new Authenticator() |
| 1493 | { | |
| 1494 | 0 | @Override |
| 1495 | protected PasswordAuthentication getPasswordAuthentication() | |
| 1496 | { | |
| 1497 | 0 | if (getRequestorType() == RequestorType.PROXY) |
| 1498 | { | |
| 1499 | 0 | String protocol = getRequestingProtocol(); |
| 1500 | 0 | boolean needProxyPasswordSet = false; |
| 1501 | 0 | if (customProxySet && |
| 1502 | // we have a username but no password for the scheme being | |
| 1503 | // requested | |
| 1504 | (protocol.equalsIgnoreCase("http") | |
| 1505 | && (httpUser != null | |
| 1506 | && httpUser.length() > 0 | |
| 1507 | && (httpPassword == null | |
| 1508 | || httpPassword.length == 0))) | |
| 1509 | || (protocol.equalsIgnoreCase("https") | |
| 1510 | && (httpsUser != null | |
| 1511 | && httpsUser.length() > 0 | |
| 1512 | && (httpsPassword == null | |
| 1513 | || httpsPassword.length == 0)))) | |
| 1514 | { | |
| 1515 | // open Preferences -> Connections | |
| 1516 | 0 | String message = MessageManager |
| 1517 | .getString("label.proxy_password_required"); | |
| 1518 | 0 | Preferences.openPreferences( |
| 1519 | Preferences.TabRef.CONNECTIONS_TAB, message); | |
| 1520 | 0 | Preferences.getInstance() |
| 1521 | .proxyAuthPasswordCheckHighlight(true, true); | |
| 1522 | } | |
| 1523 | else | |
| 1524 | { | |
| 1525 | 0 | try |
| 1526 | { | |
| 1527 | 0 | if (protocol.equalsIgnoreCase("http") |
| 1528 | && getRequestingHost() | |
| 1529 | .equalsIgnoreCase(httpHost) | |
| 1530 | && getRequestingPort() == Integer | |
| 1531 | .valueOf(httpPort)) | |
| 1532 | { | |
| 1533 | 0 | Console.debug( |
| 1534 | "AUTHENTICATOR returning PasswordAuthentication(\"" | |
| 1535 | + httpUser + "\", '" | |
| 1536 | + new String(displayHttpPw) + "')"); | |
| 1537 | 0 | return new PasswordAuthentication(httpUser, |
| 1538 | httpPassword); | |
| 1539 | } | |
| 1540 | 0 | if (protocol.equalsIgnoreCase("https") |
| 1541 | && getRequestingHost() | |
| 1542 | .equalsIgnoreCase(httpsHost) | |
| 1543 | && getRequestingPort() == Integer | |
| 1544 | .valueOf(httpsPort)) | |
| 1545 | { | |
| 1546 | 0 | char[] displayHttpsPw = new char[httpPassword.length]; |
| 1547 | 0 | Arrays.fill(displayHttpsPw, '*'); |
| 1548 | 0 | Console.debug( |
| 1549 | "AUTHENTICATOR returning PasswordAuthentication(\"" | |
| 1550 | + httpsUser + "\", '" + displayHttpsPw | |
| 1551 | + "'"); | |
| 1552 | 0 | return new PasswordAuthentication(httpsUser, |
| 1553 | httpsPassword); | |
| 1554 | } | |
| 1555 | } catch (NumberFormatException e) | |
| 1556 | { | |
| 1557 | 0 | Console.error("Problem with proxy port values [http:" |
| 1558 | + httpPort + ", https:" + httpsPort + "]"); | |
| 1559 | } | |
| 1560 | 0 | Console.debug( |
| 1561 | "AUTHENTICATOR after trying to get PasswordAuthentication"); | |
| 1562 | } | |
| 1563 | } | |
| 1564 | // non proxy request | |
| 1565 | 0 | Console.debug("AUTHENTICATOR returning null"); |
| 1566 | 0 | return null; |
| 1567 | } | |
| 1568 | }); | |
| 1569 | } // end of j2sIgnore for java.net.Authenticator | |
| 1570 | ||
| 1571 | // required to re-enable basic authentication (should be okay for a | |
| 1572 | // local proxy) | |
| 1573 | 0 | Console.debug( |
| 1574 | "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\""); | |
| 1575 | 0 | System.setProperty("jdk.http.auth.tunneling.disabledSchemes", ""); |
| 1576 | } catch (SecurityException e) | |
| 1577 | { | |
| 1578 | 0 | Console.error("Could not set default Authenticator"); |
| 1579 | 0 | Console.debug(getStackTraceString(e)); |
| 1580 | } | |
| 1581 | } | |
| 1582 | else | |
| 1583 | { | |
| 1584 | // reset the Authenticator to protect http.proxyUser and | |
| 1585 | // http.proxyPassword Just In Case | |
| 1586 | /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache | |
| 1587 | * has working credentials. No workaround for Java 11. | |
| 1588 | */ | |
| 1589 | 325 | if (!Platform.isJS()) |
| 1590 | /* * | |
| 1591 | * java.net.Authenticator not implemented in SwingJS yet | |
| 1592 | * | |
| 1593 | * @j2sIgnore | |
| 1594 | * | |
| 1595 | */ | |
| 1596 | { | |
| 1597 | 325 | Console.debug( |
| 1598 | "AUTHENTICATOR setting default Authenticator to null"); | |
| 1599 | 325 | Authenticator.setDefault(null); |
| 1600 | } | |
| 1601 | } | |
| 1602 | ||
| 1603 | // nonProxyHosts not currently configurable in Preferences | |
| 1604 | 325 | Console.debug( |
| 1605 | "AUTHENTICATOR setting property 'http.nonProxyHosts' to \"" | |
| 1606 | + nonProxyHosts + "\""); | |
| 1607 | 325 | setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts); |
| 1608 | } | |
| 1609 | ||
| 1610 | 0 | public static void setOrClearSystemProperty(String key, char[] value) |
| 1611 | { | |
| 1612 | 0 | setOrClearSystemProperty(key, |
| 1613 | 0 | (value == null) ? null : new String(value)); |
| 1614 | } | |
| 1615 | ||
| 1616 | 2275 | public static void setOrClearSystemProperty(String key, String value) |
| 1617 | { | |
| 1618 | 2275 | if (key == null) |
| 1619 | { | |
| 1620 | 0 | return; |
| 1621 | } | |
| 1622 | 2275 | if (value == null) |
| 1623 | { | |
| 1624 | 2275 | System.clearProperty(key); |
| 1625 | } | |
| 1626 | else | |
| 1627 | { | |
| 1628 | 0 | System.setProperty(key, value); |
| 1629 | } | |
| 1630 | } | |
| 1631 | ||
| 1632 | /** | |
| 1633 | * Getdown appbase methods | |
| 1634 | */ | |
| 1635 | ||
| 1636 | private static final String releaseAppbase; | |
| 1637 | ||
| 1638 | private static String getdownAppbase; | |
| 1639 | ||
| 1640 | private static String getdownDistDir; | |
| 1641 | ||
| 1642 | 55 | static |
| 1643 | { | |
| 1644 | 55 | if (!Platform.isJS()) |
| 1645 | { | |
| 1646 | 55 | Float specversion = Float |
| 1647 | .parseFloat(System.getProperty("java.specification.version")); | |
| 1648 | 55 | releaseAppbase = (specversion < 9) |
| 1649 | ? "https://www.jalview.org/getdown/release/1.8" | |
| 1650 | : "https://www.jalview.org/getdown/release/11"; | |
| 1651 | } | |
| 1652 | else | |
| 1653 | { | |
| 1654 | // this value currenly made up, can be changed to URL that will be | |
| 1655 | // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties" | |
| 1656 | 0 | releaseAppbase = "https://www.jalview.org/jalview-js"; |
| 1657 | 0 | getdownAppbase = releaseAppbase; |
| 1658 | 0 | getdownDistDir = "/swingjs/j2s"; |
| 1659 | } | |
| 1660 | } | |
| 1661 | ||
| 1662 | // look for properties (passed in by getdown) otherwise default to release | |
| 1663 | 126 | private static void setGetdownAppbase() |
| 1664 | { | |
| 1665 | 126 | if (getdownAppbase != null) |
| 1666 | { | |
| 1667 | 108 | return; |
| 1668 | } | |
| 1669 | 18 | String appbase = System.getProperty("launcher.appbase"); |
| 1670 | 18 | if (appbase == null) |
| 1671 | { | |
| 1672 | 18 | appbase = System.getProperty("getdownappbase"); // old name |
| 1673 | } | |
| 1674 | 18 | String distDir = System.getProperty("launcher.distdir"); |
| 1675 | 18 | if (distDir == null) |
| 1676 | { | |
| 1677 | 18 | distDir = System.getProperty("getdowndistdir"); // old name |
| 1678 | } | |
| 1679 | 18 | if (appbase == null) |
| 1680 | { | |
| 1681 | 18 | appbase = buildProperties.getProperty("GETDOWNAPPBASE"); |
| 1682 | 18 | distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR"); |
| 1683 | } | |
| 1684 | 18 | if (appbase == null) |
| 1685 | { | |
| 1686 | 18 | appbase = releaseAppbase; |
| 1687 | 18 | distDir = "release"; |
| 1688 | } | |
| 1689 | 18 | if (appbase.endsWith("/")) |
| 1690 | { | |
| 1691 | 0 | appbase = appbase.substring(0, appbase.length() - 1); |
| 1692 | } | |
| 1693 | 18 | if (distDir == null) |
| 1694 | { | |
| 1695 | 0 | distDir = appbase.equals(releaseAppbase) ? "release" : "alt"; |
| 1696 | } | |
| 1697 | 18 | getdownAppbase = appbase; |
| 1698 | 18 | getdownDistDir = distDir; |
| 1699 | } | |
| 1700 | ||
| 1701 | 126 | public static String getGetdownAppbase() |
| 1702 | { | |
| 1703 | 126 | setGetdownAppbase(); |
| 1704 | 126 | return getdownAppbase; |
| 1705 | } | |
| 1706 | ||
| 1707 | 126 | public static String getAppbaseBuildProperties() |
| 1708 | { | |
| 1709 | 126 | String appbase = getGetdownAppbase(); |
| 1710 | 126 | return appbase + "/" + getdownDistDir + "/build_properties"; |
| 1711 | } | |
| 1712 | ||
| 1713 | private static final Collection<String> bootstrapProperties = new ArrayList<>( | |
| 1714 | Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST)); | |
| 1715 | ||
| 1716 | 150 | public static Properties bootstrapProperties(String filename) |
| 1717 | { | |
| 1718 | 150 | Properties bootstrapProps = new Properties(); |
| 1719 | 150 | File file = null; |
| 1720 | 150 | if (filename != null) |
| 1721 | { | |
| 1722 | 48 | file = new File(filename); |
| 1723 | } | |
| 1724 | 150 | if (file == null || !file.exists()) |
| 1725 | { | |
| 1726 | 102 | if (file != null) |
| 1727 | { | |
| 1728 | 0 | jalview.bin.Console |
| 1729 | .errPrintln("Could not load bootstrap preferences file '" | |
| 1730 | + file.getPath() + "'"); | |
| 1731 | } | |
| 1732 | 102 | String channelPrefsFilename = ChannelProperties |
| 1733 | .getProperty("preferences.filename"); | |
| 1734 | 102 | String propertiesFilename = System.getProperty("user.home") |
| 1735 | + File.separatorChar + channelPrefsFilename; | |
| 1736 | 102 | jalview.bin.Console.errPrintln( |
| 1737 | "Using default properties file '" + propertiesFilename + "'"); | |
| 1738 | 102 | file = new File(propertiesFilename); |
| 1739 | } | |
| 1740 | 150 | if (file == null || !file.exists()) |
| 1741 | ||
| 1742 | { | |
| 1743 | 0 | String releasePrefsFilename = fallbackPropertiesFile; |
| 1744 | 0 | String releasePropertiesFilename = System.getProperty("user.home") |
| 1745 | + File.separatorChar + releasePrefsFilename; | |
| 1746 | 0 | jalview.bin.Console.errPrintln("Falling back to properties file '" |
| 1747 | + releasePropertiesFilename + "'"); | |
| 1748 | 0 | file = new File(releasePropertiesFilename); |
| 1749 | } | |
| 1750 | ||
| 1751 | 150 | if (!file.exists()) |
| 1752 | { | |
| 1753 | 0 | jalview.bin.Console |
| 1754 | .errPrintln("Could not load bootstrap preferences file '" | |
| 1755 | + file.getPath() + "'"); | |
| 1756 | 0 | return null; |
| 1757 | } | |
| 1758 | ||
| 1759 | 150 | try |
| 1760 | { | |
| 1761 | 150 | FileInputStream in = new FileInputStream(file.getAbsoluteFile()); |
| 1762 | 150 | Properties props = new Properties(); |
| 1763 | 150 | props.load(in); |
| 1764 | 150 | for (String prop : bootstrapProperties) |
| 1765 | { | |
| 1766 | 300 | if (props.containsKey(prop)) |
| 1767 | 9 | bootstrapProps.put(prop, props.getProperty(prop)); |
| 1768 | } | |
| 1769 | } catch (FileNotFoundException e) | |
| 1770 | { | |
| 1771 | 0 | jalview.bin.Console |
| 1772 | .errPrintln("Could not find bootstrap preferences file '" | |
| 1773 | + file.getAbsolutePath() + "'"); | |
| 1774 | } catch (IOException e) | |
| 1775 | { | |
| 1776 | 0 | jalview.bin.Console.errPrintln( |
| 1777 | "IOException when loading bootstrap preferences file '" | |
| 1778 | + file.getAbsolutePath() + "'"); | |
| 1779 | } | |
| 1780 | 150 | return bootstrapProps; |
| 1781 | } | |
| 1782 | ||
| 1783 | 0 | public static void setSessionProperty(String key, String val) |
| 1784 | { | |
| 1785 | 0 | if (key != null) |
| 1786 | { | |
| 1787 | 0 | sessionProperties.put(key, val); |
| 1788 | } | |
| 1789 | } | |
| 1790 | ||
| 1791 | 464461 | public static String getSessionProperty(String key) |
| 1792 | { | |
| 1793 | 464462 | return key == null ? null : sessionProperties.get(key); |
| 1794 | } | |
| 1795 | ||
| 1796 | 93 | public static boolean getArgCacheDefault(Arg a, String pref, boolean def) |
| 1797 | { | |
| 1798 | 93 | ArgParser ap = Jalview.getInstance().getArgParser(); |
| 1799 | 93 | return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def); |
| 1800 | } | |
| 1801 | } |