From: soares Date: Tue, 3 Sep 2019 17:07:46 +0000 (+0100) Subject: JAL-3210 gradle jalviewjsServer now working. Up to date src and swingjs from Jalview... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8dc18dd90300a9046aa8ca5b7fc135bb18fffe7d;p=jalview.git JAL-3210 gradle jalviewjsServer now working. Up to date src and swingjs from Jalview-JS/...applet branch. Transpiles and launches. --- diff --git a/README b/README index 43ffa63..72628ed 100644 --- a/README +++ b/README @@ -1,12 +1,22 @@ Download and install a clean eclipse-jee-2019-06 -In gradle.properties edit `jalviewjs_eclipse_root` to point to the root dir. DO NOT include the Eclipse.app folder in the path (up to this point, but not the .app folder) if it's the macOS version. +In gradle.properties edit `jalviewjs_eclipse_root` to point to the root dir. +If you're on a mac, DO NOT include the Eclipse.app folder in the path (use the path up to this point, but not the .app folder). +You can use a '~' as the first character which will get replaced with System.getProperty("user.home"). + +Note that the gradle tasks will take care of copying net.sf.j2s.core.jar and the com.seeq.eclipse.importprojects.jar into the dropins and plugins dir (on either unix or mac -- not tested on windows yet). gradle tasks of interest: -`jalviewjs` (should do everything) -jalviewjsTranspile (should run a new eclipse compile+transpile) + +gradle jalviewjs # (should build the .../site dir) + +gradle jalviewjsSiteTar # will produce build/distribution/site.tar.gz + +gradle jalviewjsTranspile # should run a new eclipse compile+transpile + +gradle jalviewjsServer # will run a localhost http server to allow you to test the site in a browser. Just use the URL given in the output. diff --git a/build.gradle b/build.gradle index 184e71e..f6d211a 100644 --- a/build.gradle +++ b/build.gradle @@ -3,6 +3,7 @@ import org.gradle.internal.os.OperatingSystem import org.gradle.plugins.ide.eclipse.model.* import groovy.transform.ExternalizeMethods + plugins { id 'java' id 'application' @@ -346,10 +347,12 @@ task jalviewjsCopySiteResources (type: Copy) { } task cleanJalviewjs { + /* delete jalviewDir+"/"+jalviewjs_site_dir delete jalviewDir+"/"+eclipse_bin_dir delete file(tempEclipseWorkspace.getAbsolutePath()+"/.metadata") delete jalviewDir+"/"+jalviewjs_j2s_settings + */ } task jalviewjsProjectImport(type: Exec) { @@ -413,18 +416,19 @@ task jalviewjsServer { doLast { SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory() def port = Integer.valueOf(jalviewjs_server_port) - def add = 0 + def start = port def running = false - while(add < 1000) { + HttpFileServer server +println "server wait = ${jalviewjs_server_wait}" + while(port < start+100 && !running) { try { - HttpFileServer server = factory.start(new File(jalviewDirAbsolutePath+"/"+jalviewjs_site_dir), port) + server = factory.start(new File(jalviewDirAbsolutePath+"/"+jalviewjs_site_dir), port) running = true + println("SERVER STARTED on "+server.getResourceUrl(jalviewjs_server_resource)+" for ${jalviewjs_server_wait} seconds. Ctrc+C to kill it.") + java.lang.Thread.sleep(Integer.valueOf(jalviewjs_server_wait)*1000); } catch (Exception e) { port++; - add++; } } - println("SERVER STARTED on http://localhost:"+port+"/ . Ctrc+C to kill it") - java.lang.Thread.sleep(Integer.valueOf(jalviewjs_server_wait)*1000); } } diff --git a/gradle.properties b/gradle.properties index 4f3a34b..b465af2 100644 --- a/gradle.properties +++ b/gradle.properties @@ -52,8 +52,8 @@ jalviewjs_eclipse_workspace = ../tmp/eclipse-workspace #jalviewjs_eclipseBuildArg = build jalviewjs_eclipseBuildArg = cleanBuild jalviewjs_server_port = 9001 -jalviewjs_server_wait = 10 - +jalviewjs_server_wait = 30 +jalviewjs_server_resource = /jalview_bin_Jalview.html j2s.compiler.status = enable #j2s.site.directory = null diff --git a/resources/images/jalview_logo_background_fade-640x480.png b/resources/images/jalview_logo_background_fade-640x480.png deleted file mode 100644 index 4b65200..0000000 Binary files a/resources/images/jalview_logo_background_fade-640x480.png and /dev/null differ diff --git a/resources/images/jalview_logo_background_getdown-640x480.png b/resources/images/jalview_logo_background_getdown-640x480.png deleted file mode 100644 index 20d972a..0000000 Binary files a/resources/images/jalview_logo_background_getdown-640x480.png and /dev/null differ diff --git a/resources/images/jalview_logo_background_getdown-progress-TEST2.png b/resources/images/jalview_logo_background_getdown-progress-TEST2.png deleted file mode 100755 index 1a9bf34..0000000 Binary files a/resources/images/jalview_logo_background_getdown-progress-TEST2.png and /dev/null differ diff --git a/resources/images/jalview_logo_background_getdown-progress.png b/resources/images/jalview_logo_background_getdown-progress.png deleted file mode 100644 index fb87750..0000000 Binary files a/resources/images/jalview_logo_background_getdown-progress.png and /dev/null differ diff --git a/resources/images/jalview_logo_background_getdown-progress1.png b/resources/images/jalview_logo_background_getdown-progress1.png deleted file mode 100644 index 804063a..0000000 Binary files a/resources/images/jalview_logo_background_getdown-progress1.png and /dev/null differ diff --git a/resources/images/jalview_logo_background_getdown-progress2.png b/resources/images/jalview_logo_background_getdown-progress2.png deleted file mode 100644 index fb87750..0000000 Binary files a/resources/images/jalview_logo_background_getdown-progress2.png and /dev/null differ diff --git a/resources/images/jalview_logos.icns b/resources/images/jalview_logos.icns deleted file mode 100755 index 6c2ee9a..0000000 Binary files a/resources/images/jalview_logos.icns and /dev/null differ diff --git a/resources/images/jalview_logos.ico b/resources/images/jalview_logos.ico deleted file mode 100644 index ba2ca82..0000000 Binary files a/resources/images/jalview_logos.ico and /dev/null differ diff --git a/resources/images/jetset_jalview_splash.gif b/resources/images/jetset_jalview_splash.gif deleted file mode 100644 index cc144b1..0000000 Binary files a/resources/images/jetset_jalview_splash.gif and /dev/null differ diff --git a/resources/images/jetset_jalview_splash.png b/resources/images/jetset_jalview_splash.png deleted file mode 100644 index 3ce1f46..0000000 Binary files a/resources/images/jetset_jalview_splash.png and /dev/null differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 17bf14a..ebbbeeb 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -32,7 +32,6 @@ action.load_project = Load Project action.save_project = Save Project action.save_project_as = Save Project as... action.quit = Quit -label.quit_jalview = Quit Jalview? action.expand_views = Expand Views action.gather_views = Gather Views action.page_setup = Page Setup... @@ -264,6 +263,7 @@ label.use_rnaview = Use RNAView for secondary structure label.autoadd_secstr = Add secondary structure annotation to alignment label.autoadd_temp = Add Temperature Factor annotation to alignment label.structure_viewer = Default structure viewer +label.structure_dimensions = Default dimensions label.double_click_to_browse = Double-click to browse for file label.chimera_path = Path to Chimera program label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.
Double-click to browse for file. @@ -955,8 +955,6 @@ error.implementation_error_maplist_is_null = Implementation error. MapList is nu error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document. -error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null' -exception.ssm_context_is_null = SSM context is null error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence error.cannot_have_mixed_length_replacement_vectors = Cannot have mixed length replacement vectors. Replacement vector for {0} is {1} strings long, and have already seen a {2} length vector. error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero length vector of replacement strings - either 1 value or n values. @@ -995,8 +993,7 @@ label.toggled = Toggled label.marked = Marked label.containing = containing label.not_containing = not containing -label.no_feature_of_type_found = No features of type {0} found -label.no_feature_found_selection = No features of type {0} found in selection +label.no_feature_of_type_found = No features of type {0} found. label.submission_params = Submission {0} label.empty_alignment_job = Empty Alignment Job label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service @@ -1308,7 +1305,6 @@ label.numeric_required = The value should be numeric label.filter = Filter label.filters = Filters label.join_conditions = Join conditions with -label.delete_condition = Delete this condition label.score = Score label.colour_by_label = Colour by label label.variable_colour = Variable colour... @@ -1355,13 +1351,12 @@ label.append_to_filename = Append to filename (%n is replaced by the backup numb label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above. label.index_digits = Number of digits to use for the backup number (%n) label.summary_of_backups_scheme = Summary of backup scheme -label.scheme_examples = Scheme examples label.increment_index = Increase appended text numbers - newest file has largest number. label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1. label.keep_files = Deleting old backup files label.keep_all_backup_files = Do not delete old backup files label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files -label.autodelete_old_backup_files = Auto-delete old backup files: +label.autodelete_old_backup_files = Autodelete old backup files: label.always_ask = Always ask label.auto_delete = Automatically delete label.filename = filename @@ -1371,18 +1366,10 @@ label.configuration = Configuration label.configure_feature_tooltip = Click to configure variable colour or filters label.schemes = Schemes label.customise = Customise -label.custom = Custom label.default = Default label.single_file = Single backup label.keep_all_versions = Keep all versions label.rolled_backups = Rolled backup files -label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme -label.custom_description = Your own saved scheme -label.default_description = Keep the last three versions of the file -label.single_file_description = Keep the last version of the file -label.keep_all_versions_description = Keep all previous versions of the file -label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest) -label.cancel_changes_description = Cancel changes made to your last saved Custom scheme label.previously_saved_scheme = Previously saved scheme label.no_backup_files = NO BACKUP FILES label.include_backup_files = Include backup files diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index f233763..baeb5af 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -32,7 +32,6 @@ action.load_project = Cargar proyecto action.save_project = Guardar proyecto action.save_project_as = Guardar proyecto como... action.quit = Salir -label.quit_jalview = Salir de Jalview? action.expand_views = Expandir vistas action.gather_views = Capturar vistas action.page_setup = Configuración de la página @@ -880,8 +879,6 @@ error.implementation_error_maplist_is_null = Error de implementaci error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia error.implementation_error_cannot_map_alignment_sequences = Error de implementación: no es posible maper un alineamiento de secuencias desde distintos conjuntos de datos en un único alineamiento en el documento VAMSAS. -error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo -exception.ssm_context_is_null = El contexto SSM es nulo error.idstring_seqstrings_only_one_per_sequence = idstrings y seqstrings contienen una cadena por cada secuencia error.cannot_have_mixed_length_replacement_vectors = No es posible tener vectores de reemplazo de distinta longitud. El vector de reemplazo para {0} es de {1} cadenas de largo, pero se ha considerado ya como un vector de longitud {2}. error.cannot_have_zero_length_vector_replacement_strings = No es posible tener un vector de cadenas de reemplazo de longitud cero - debe ser uno o n. @@ -920,8 +917,7 @@ label.toggled = Invertida label.marked = Marcada label.containing = conteniendo label.not_containing = no conteniendo -label.no_feature_of_type_found = No se han encontrado características del tipo {0} -label.no_feature_found_selection = No se han encontrado características del tipo {0} en la región seleccionada +label.no_feature_of_type_found = No se han encontrado características del tipo {0}. label.submission_params = Envío {0} label.empty_alignment_job = Trabajo de alineamiento vacío label.add_new_sbrs_service = Añadir un nuevo SBRS @@ -1206,6 +1202,7 @@ label.alpha_helix=H label.chimera_help=Ayuda para Chimera label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos) label.structure_viewer=Visualizador por defecto +label.structure_dimensions=Dimensiones por defecto label.embbed_biojson=Incrustar BioJSON al exportar HTML label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características. label.choose_annotations=Escoja anotaciones @@ -1308,7 +1305,6 @@ label.matchCondition_ge = >= label.numeric_required = Valor numérico requerido label.filter = Filtro label.filters = Filtros -label.delete_condition = Borrar esta condición label.join_conditions = Combinar condiciones con label.score = Puntuación label.colour_by_label = Colorear por texto @@ -1356,7 +1352,6 @@ label.append_to_filename = Adjuntar texto (%n es reemplazado por el n label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba. label.index_digits = Número de dígitos a utilizar para el número de respaldo. label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad -label.scheme_examples = Ejemplos de esquema label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1 label.keep_files = Borrando los respaldos antiguos @@ -1371,19 +1366,11 @@ label.braced_newest = (mas nuevo) label.configuration = Configuración label.configure_feature_tooltip = Haga clic para configurar el color o los filtros label.schemes = Esquemas -label.customise = Personalizar -label.custom = Personal +label.customise = Personalizado label.default = Defecto label.single_file = Solo uno respaldo label.keep_all_versions = Mantener todas las versiones label.rolled_backups = Ciclos respaldos -label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado -label.custom_description = Tu propio esquema guardado -label.default_description = Conserve las últimas tres versiones del archivo -label.single_file_description = Conserve la última versión del archivo -label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo -label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua) -label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado label.previously_saved_scheme = Esquema previamente guardado label.no_backup_files = NO ARCHIVOS DE RESPALDOS label.include_backup_files = Incluir archivos de respaldos diff --git a/utils/jalviewjs/libjs/VARNA-site.zip b/utils/jalviewjs/libjs/VARNA-site.zip index cf1c44c..36610bd 100644 Binary files a/utils/jalviewjs/libjs/VARNA-site.zip and b/utils/jalviewjs/libjs/VARNA-site.zip differ diff --git a/utils/jalviewjs/libjs/jmol-app.zip b/utils/jalviewjs/libjs/jmol-app.zip index 27b48de..3f8aaa8 100644 Binary files a/utils/jalviewjs/libjs/jmol-app.zip and b/utils/jalviewjs/libjs/jmol-app.zip differ