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[galaxyproject/usegalaxy-playbook] 3088f2: Job conf updates for Rodeo.
by GitHub 13 Oct '14

13 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3088f2a4163a7c00ea95a2b79fddb13140514c53 https://github.com/galaxyproject/usegalaxy-playbook/commit/3088f2a4163a7c00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M files/galaxy/usegalaxy.org/dynamic_rules/reserved.py M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Job conf updates for Rodeo. Commit: 1425812883a708f6b5db52424877131d778057c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/1425812883a708f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test. Commit: 288841a0899cd5840877343c2236658352a61160 https://github.com/galaxyproject/usegalaxy-playbook/commit/288841a0899cd584… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Fix job conf (there were some unfinished changes in there). Commit: bf815e533408071a72c328b777d823f3eb9e0b67 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf815e533408071a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Fix concurrency. Commit: 563afb451eb64a90d303867434159534b16b88fb https://github.com/galaxyproject/usegalaxy-playbook/commit/563afb451eb64a90… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-13 (Mon, 13 Oct 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6f878bbac19e...…

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1744b7d8e9ab/ Changeset: 1744b7d8e9ab Branch: stable User: natefoo Date: 2014-10-14 00:48:30+00:00 Summary: Merge closed duplicate stable head with current stable. Affected #: 2 files diff -r 4a550ab8a4b2c0a45b48732edde703010a7c7509 -r 1744b7d8e9ab619d78c0516f9ccb093b0a814163 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -3,22 +3,19 @@ """ import logging, atexit -import os, os.path, sys +import os, os.path from inspect import isclass -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources from galaxy.util import asbool -import config import galaxy.model import galaxy.model.mapping -import galaxy.web.framework +import galaxy.web.framework.webapp log = logging.getLogger( __name__ ) @@ -31,7 +28,6 @@ them to the webapp. """ from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir( controller_dir ): https://bitbucket.org/galaxy/galaxy-central/commits/dbee027f7410/ Changeset: dbee027f7410 User: natefoo Date: 2014-10-14 00:49:02+00:00 Summary: Merge stable. Affected #: 2 files diff -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b -r dbee027f74101741533851ce2634b60adca4c454 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 +cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 diff -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b -r dbee027f74101741533851ce2634b60adca4c454 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -3,22 +3,19 @@ """ import logging, atexit -import os, os.path, sys +import os, os.path from inspect import isclass -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources from galaxy.util import asbool -import config import galaxy.model import galaxy.model.mapping -import galaxy.web.framework +import galaxy.web.framework.webapp log = logging.getLogger( __name__ ) @@ -31,7 +28,6 @@ them to the webapp. """ from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir( controller_dir ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Additional fixes for install and test framework.
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f42dfab2cee/ Changeset: 3f42dfab2cee User: davebgx Date: 2014-10-13 20:07:29+00:00 Summary: Additional fixes for install and test framework. Affected #: 2 files diff -r 67050bf7b3cff0e482bd6ed15b286864ffc77ae5 -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -118,7 +118,8 @@ tool_data_table_conf = None # Set up default tool data tables. If a non-sample version is in config/, use that. Otherwise iterate through lower # priority versions. -for conf in [ 'config/tool_data_table_conf.xml', +for conf in [ 'tool_data_table_conf.test.xml', + 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample', 'tool_data_table_conf.xml', 'tool_data_table_conf.xml.sample' ]: diff -r 67050bf7b3cff0e482bd6ed15b286864ffc77ae5 -r 3f42dfab2cee4706551c9ca0211e7cd08e35058b test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -332,13 +332,14 @@ template_path = "templates", tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ), tool_data_path = tool_data_path, - tool_data_table_config_path = galaxy_tool_data_table_conf_file, tool_dependency_dir = tool_dependency_dir, tool_path = tool_path, tool_parse_help = False, tool_sheds_config_file = galaxy_tool_sheds_conf_file, update_integrated_tool_panel = False, use_heartbeat = False ) + if os.path.exists( galaxy_tool_data_table_conf_file ): + kwargs[ 'tool_data_table_config_path' ] = galaxy_tool_data_table_conf_file galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None ) # If the user has passed in a path for the .ini file, do not overwrite it. if not galaxy_config_file: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset cb0c2ea402e4
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a550ab8a4b2/ Changeset: 4a550ab8a4b2 Branch: stable User: natefoo Date: 2014-10-13 19:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset cb0c2ea402e4 Affected #: 1 file diff -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 -r 4a550ab8a4b2c0a45b48732edde703010a7c7509 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 +cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in dannon/galaxy-central-prmaker/stable (pull request #527)
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/67050bf7b3cf/ Changeset: 67050bf7b3cf User: dannon Date: 2014-10-13 18:01:54+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #527) [STABLE] Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cb0c2ea402e4/ Changeset: cb0c2ea402e4 Branch: stable User: dannon Date: 2014-10-13 14:19:32+00:00 Summary: Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 4 files diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -53,7 +53,6 @@ """Start the job manager""" self.app = app self.dispatcher = dispatcher - self.job_lock = False self.sa_session = app.model.context self.track_jobs_in_database = self.app.config.track_jobs_in_database @@ -174,7 +173,7 @@ try: # If jobs are locked, there's nothing to monitor and we skip # to the sleep. - if not self.job_lock: + if not self.app.job_manager.job_lock: self.__monitor_step() except: log.exception( "Exception in monitor_step" ) diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -26,6 +26,7 @@ else: self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() + self.job_lock = False self.job_handler.start() def shutdown( self ): diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -110,7 +110,7 @@ job_lock = kwargs.get('job_lock', False) # job_queue is exposed in the root app, but this will be 'fixed' at some # point, so we're using the reference from the handler. - app.job_manager.job_handler.job_queue.job_lock = job_lock + app.job_manager.job_lock = job_lock log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")) diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r cb0c2ea402e4c82c7872177e874ce59de29c9c13 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1107,7 +1107,7 @@ kwargs={'job_lock': False } ) job_lock = False else: - job_lock = trans.app.job_manager.job_handler.job_queue.job_lock + job_lock = trans.app.job_manager.job_lock cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, https://bitbucket.org/galaxy/galaxy-central/commits/67050bf7b3cf/ Changeset: 67050bf7b3cf User: dannon Date: 2014-10-13 18:01:54+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #527) [STABLE] Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Close branch stable
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/85ca6ed4af00/ Changeset: 85ca6ed4af00 Branch: stable User: dan Date: 2014-10-13 17:54:05+00:00 Summary: Close branch stable Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: nsoranzo: Fix import bug for run_reports.sh . Remove unused imports.
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea936c90b939/ Changeset: ea936c90b939 Branch: stable User: nsoranzo Date: 2014-10-13 16:27:45+00:00 Summary: Fix import bug for run_reports.sh . Remove unused imports. Import bug: File "/opt/galaxy-central/lib/galaxy/webapps/reports/buildapp.py", line 25, in <module> class ReportsWebApplication( galaxy.web.framework.webapp.WebApplication ): AttributeError: 'module' object has no attribute 'webapp' The bug was introduced by commit d57655849ac4 . Affected #: 1 file diff -r 0215d23d79717f46e7715e209048606975693dd7 -r ea936c90b93933326dc3b163aaca361b5cafb5b7 lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -3,22 +3,19 @@ """ import logging, atexit -import os, os.path, sys +import os, os.path from inspect import isclass -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources from galaxy.util import asbool -import config import galaxy.model import galaxy.model.mapping -import galaxy.web.framework +import galaxy.web.framework.webapp log = logging.getLogger( __name__ ) @@ -31,7 +28,6 @@ them to the webapp. """ from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir( controller_dir ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix Xslx binary (bad merge?).
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/861fd5d6c459/ Changeset: 861fd5d6c459 User: dannon Date: 2014-10-13 16:55:31+00:00 Summary: Fix Xslx binary (bad merge?). Affected #: 1 file diff -r be638dd2f087e895bb611a132999ec8309db0c03 -r 861fd5d6c459284aed91a2c92a01e5cd09064c18 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -281,22 +281,6 @@ return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) -class Xlsx(Binary): - """Class for Excel 2007 (xlsx) files""" - file_ext="xlsx" - def sniff( self, filename ): - # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. - try: - if zipfile.is_zipfile( filename ): - tempzip = zipfile.ZipFile( filename ) - if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: - return True - return False - except: - return False - -Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) - # ------------- Dataproviders # pipe through samtools view @@ -639,3 +623,19 @@ Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) +class Xlsx(Binary): + """Class for Excel 2007 (xlsx) files""" + file_ext="xlsx" + def sniff( self, filename ): + # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. + try: + if zipfile.is_zipfile( filename ): + tempzip = zipfile.ZipFile( filename ) + if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: + return True + return False + except: + return False + +Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/701c01f794e2/ Changeset: 701c01f794e2 User: dannon Date: 2014-10-13 14:44:11+00:00 Summary: Simplify to_json_string/from_json_string; without the extra logging there's no reason to wrap the functions and pass args Affected #: 1 file diff -r 738cdb119ce34e570224eb87ee7a270caa53f39b -r 701c01f794e2fc6cf5586fde68a0d7a33a161790 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -15,13 +15,8 @@ log = logging.getLogger( __name__ ) - -def to_json_string(*args, **kwargs): - return json.dumps(*args, **kwargs) - - -def from_json_string(*args, **kwargs): - return json.loads(*args, **kwargs) +to_json_string = dumps +from_json_string = loads def json_fix( val ): https://bitbucket.org/galaxy/galaxy-central/commits/cce814e5b0fe/ Changeset: cce814e5b0fe Branch: docker-work User: dannon Date: 2014-10-13 15:24:21+00:00 Summary: Branch prune. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/be638dd2f087/ Changeset: be638dd2f087 User: dannon Date: 2014-10-13 15:24:36+00:00 Summary: Merge. Affected #: 1 file diff -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 -r be638dd2f087e895bb611a132999ec8309db0c03 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -15,13 +15,8 @@ log = logging.getLogger( __name__ ) - -def to_json_string(*args, **kwargs): - return json.dumps(*args, **kwargs) - - -def from_json_string(*args, **kwargs): - return json.loads(*args, **kwargs) +to_json_string = dumps +from_json_string = loads def json_fix( val ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in kellrott/galaxy-farm/docker-work (pull request #525)
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82ce88b096ff/ Changeset: 82ce88b096ff User: dannon Date: 2014-10-13 15:23:42+00:00 Summary: Merged in kellrott/galaxy-farm/docker-work (pull request #525) Adding 'set user' flag to docker calls Affected #: 3 files diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -196,7 +196,8 @@ adding the '\-\-rm' flag to the command line, the container will be removed automatically after the program is complete. --> -  +  + <!-- Following can be used to connect to docke server in different diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -243,7 +243,8 @@ env_directives=env_directives, working_directory=working_directory, net=prop("net", "none"), # By default, docker instance has networking disabled - auto_rm=prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE), + auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), + set_user=asbool(prop("set_user", docker_util.DEFAULT_SET_USER)), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -10,6 +10,7 @@ DEFAULT_MEMORY = None DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True +DEFAULT_SET_USER = True class DockerVolume(object): @@ -119,6 +120,7 @@ sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, auto_rm=DEFAULT_AUTO_REMOVE, + set_user=DEFAULT_SET_USER, host=DEFAULT_HOST, ): command_parts = __docker_prefix( @@ -146,6 +148,8 @@ command_parts.extend(["--net", net]) if auto_rm: command_parts.append("--rm") + if set_user: + command_parts.extend(["-u", str(os.geteuid())]) full_image = image if tag: full_image = "%s:%s" % (full_image, tag) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7fa4a243b126/ Changeset: 7fa4a243b126 Branch: docker-work User: kell...(a)gmail.com Date: 2014-10-12 04:40:15+00:00 Summary: Adding docker_set_user option so that docker jobs will be run with the '-u <current user>' flag so docker container commands don't run as root. Affected #: 3 files diff -r db93990f8def9e20c979337dbca0ef1e7e06f400 -r 7fa4a243b126c4a1d5dbbfc600899763b55a6d82 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -196,7 +196,8 @@ adding the '--rm' flag to the command line, the container will be removed automatically after the program is complete. --> -  +  +  -  +  + <!-- Following can be used to connect to docke server in different diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -243,7 +243,8 @@ env_directives=env_directives, working_directory=working_directory, net=prop("net", "none"), # By default, docker instance has networking disabled - auto_rm=prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE), + auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), + set_user=asbool(prop("set_user", docker_util.DEFAULT_SET_USER)), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r 16425b81c25e3d806a9e5594773612599e68b785 -r 82ce88b096ffb95246e2b6832454ef64b1b2f477 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -10,6 +10,7 @@ DEFAULT_MEMORY = None DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True +DEFAULT_SET_USER = True class DockerVolume(object): @@ -119,6 +120,7 @@ sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, auto_rm=DEFAULT_AUTO_REMOVE, + set_user=DEFAULT_SET_USER, host=DEFAULT_HOST, ): command_parts = __docker_prefix( @@ -146,6 +148,8 @@ command_parts.extend(["--net", net]) if auto_rm: command_parts.append("--rm") + if set_user: + command_parts.extend(["-u", str(os.geteuid())]) full_image = image if tag: full_image = "%s:%s" % (full_image, tag) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in hunter_moseley/galaxy-central (pull request #526)
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16425b81c25e/ Changeset: 16425b81c25e User: dannon Date: 2014-10-13 15:23:01+00:00 Summary: Merged in hunter_moseley/galaxy-central (pull request #526) Added an Xlsx(Binary) datatype that allows Upload File to properly detect the file and upload it. Affected #: 2 files diff -r 738cdb119ce34e570224eb87ee7a270caa53f39b -r 16425b81c25e3d806a9e5594773612599e68b785 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -253,6 +253,8 @@ <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/><datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/><datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> +  + <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" /></registration><sniffers><!-- diff -r 738cdb119ce34e570224eb87ee7a270caa53f39b -r 16425b81c25e3d806a9e5594773612599e68b785 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -12,6 +12,7 @@ import subprocess import tempfile import re +import zipfile from galaxy import eggs eggs.require( "bx-python" ) @@ -279,6 +280,24 @@ except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) + +class Xlsx(Binary): + """Class for Excel 2007 (xlsx) files""" + file_ext="xlsx" + def sniff( self, filename ): + # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. + try: + if zipfile.is_zipfile( filename ): + tempzip = zipfile.ZipFile( filename ) + if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: + return True + return False + except: + return False + +Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) + + # ------------- Dataproviders # pipe through samtools view #ALSO: (as Sam) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7111e4f6a3d1/ Changeset: 7111e4f6a3d1 User: Hunter Moseley Date: 2014-10-12 15:34:05+00:00 Summary: Added an Xlsx(Binary) datatype that properly sniffs the file and allows Upload File to properly detect the file and upload it. Affected #: 2 files diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 7111e4f6a3d1d95dac9f5f0e194c020e22ca4dbc config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -253,6 +253,8 @@ <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/><datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/><datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/> +  + <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" /></registration><sniffers> + <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" /></registration><sniffers><!-- diff -r 738cdb119ce34e570224eb87ee7a270caa53f39b -r 16425b81c25e3d806a9e5594773612599e68b785 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -12,6 +12,7 @@ import subprocess import tempfile import re +import zipfile from galaxy import eggs eggs.require( "bx-python" ) @@ -279,6 +280,24 @@ except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) + +class Xlsx(Binary): + """Class for Excel 2007 (xlsx) files""" + file_ext="xlsx" + def sniff( self, filename ): + # Xlsx is compressed in zip format and must not be uncompressed in Galaxy. + try: + if zipfile.is_zipfile( filename ): + tempzip = zipfile.ZipFile( filename ) + if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1: + return True + return False + except: + return False + +Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) + + # ------------- Dataproviders # pipe through samtools view #ALSO: (as Sam) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update comments in job handler to refer to the correct classes (historical, copied from JobQueue etc circa 2010) and functionality.
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/738cdb119ce3/ Changeset: 738cdb119ce3 User: dannon Date: 2014-10-13 14:34:44+00:00 Summary: Update comments in job handler to refer to the correct classes (historical, copied from JobQueue etc circa 2010) and functionality. Affected #: 1 file diff -r 5454f62f54df718c61ef4bf5f5446249f6525024 -r 738cdb119ce34e570224eb87ee7a270caa53f39b lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -44,13 +44,13 @@ class JobHandlerQueue( object ): """ - Job manager, waits for jobs to be runnable and then dispatches to - a JobRunner. + Job Handler's Internal Queue, this is what actually implements waiting for + jobs to be runnable and dispatching to a JobRunner. """ STOP_SIGNAL = object() def __init__( self, app, dispatcher ): - """Start the job manager""" + """Initializes the Job Handler Queue, creates (unstarted) monitoring thread""" self.app = app self.dispatcher = dispatcher @@ -77,7 +77,7 @@ def start( self ): """ - The JobManager should start, and then start its Handler, if it has one. + Starts the JobHandler's thread after checking for any unhandled jobs. """ # Recover jobs at startup self.__check_jobs_at_startup() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5454f62f54df/ Changeset: 5454f62f54df User: dannon Date: 2014-10-13 14:19:32+00:00 Summary: Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs Affected #: 4 files diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 5454f62f54df718c61ef4bf5f5446249f6525024 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -53,7 +53,6 @@ """Start the job manager""" self.app = app self.dispatcher = dispatcher - self.job_lock = False self.sa_session = app.model.context self.track_jobs_in_database = self.app.config.track_jobs_in_database @@ -174,7 +173,7 @@ try: # If jobs are locked, there's nothing to monitor and we skip # to the sleep. - if not self.job_lock: + if not self.app.job_manager.job_lock: self.__monitor_step() except: log.exception( "Exception in monitor_step" ) diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 5454f62f54df718c61ef4bf5f5446249f6525024 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -26,6 +26,7 @@ else: self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() + self.job_lock = False self.job_handler.start() def shutdown( self ): diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 5454f62f54df718c61ef4bf5f5446249f6525024 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -110,7 +110,7 @@ job_lock = kwargs.get('job_lock', False) # job_queue is exposed in the root app, but this will be 'fixed' at some # point, so we're using the reference from the handler. - app.job_manager.job_handler.job_queue.job_lock = job_lock + app.job_manager.job_lock = job_lock log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")) diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 5454f62f54df718c61ef4bf5f5446249f6525024 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1107,7 +1107,7 @@ kwargs={'job_lock': False } ) job_lock = False else: - job_lock = trans.app.job_manager.job_handler.job_queue.job_lock + job_lock = trans.app.job_manager.job_lock cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 7436bde1f785
by commits-noreply＠bitbucket.org 13 Oct '14

13 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0215d23d7971/ Changeset: 0215d23d7971 Branch: stable User: natefoo Date: 2014-10-13 14:00:19+00:00 Summary: Update tag latest_2014.10.06 for changeset 7436bde1f785 Affected #: 1 file diff -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 -r 0215d23d79717f46e7715e209048606975693dd7 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 +7436bde1f7850762bcceb3a30fb4a3eceac42523 latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Small fixes to advanced job_conf.xml sample.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04015a2bc737/ Changeset: 04015a2bc737 User: jmchilton Date: 2014-10-10 21:07:09+00:00 Summary: Small fixes to advanced job_conf.xml sample. Thanks to Eric for the catch. Affected #: 1 file diff -r 2811a26c5446706b27699fabb48a6ba3e60667d2 -r 04015a2bc7375f1179950a3f698353d033fc3a5d config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -193,7 +193,7 @@ --> @@ -344,7 +344,7 @@ --></destination> - <destination id="pulsar_mq_dest" runner="amqp_pulsar" > + <destination id="pulsar_mq_dest" runner="pulsar_mq" ><!-- The RESTful Pulsar client sends a request to Pulsar to populate various system properties. This extra step can be disabled and these calculated here Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: added tooltip for changing the number of items per page link
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2811a26c5446/ Changeset: 2811a26c5446 User: martenson Date: 2014-10-10 20:38:06+00:00 Summary: added tooltip for changing the number of items per page link Affected #: 3 files diff -r c86a489a597657c769848d2781af631ca668a279 -r 2811a26c5446706b27699fabb48a6ba3e60667d2 client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js @@ -194,7 +194,7 @@ tmpl_array.push(' <% } %>'); tmpl_array.push(' </ul>'); tmpl_array.push(' <span>'); - tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); + tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); tmpl_array.push(' </span>'); return _.template(tmpl_array.join('')); diff -r c86a489a597657c769848d2781af631ca668a279 -r 2811a26c5446706b27699fabb48a6ba3e60667d2 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -194,7 +194,7 @@ tmpl_array.push(' <% } %>'); tmpl_array.push(' </ul>'); tmpl_array.push(' <span>'); - tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); + tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); tmpl_array.push(' </span>'); return _.template(tmpl_array.join('')); diff -r c86a489a597657c769848d2781af631ca668a279 -r 2811a26c5446706b27699fabb48a6ba3e60667d2 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render()}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render()}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: first version of data libraries pagination, including some bugfixes and docs
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c86a489a5976/ Changeset: c86a489a5976 User: martenson Date: 2014-10-10 20:33:51+00:00 Summary: first version of data libraries pagination, including some bugfixes and docs Affected #: 17 files diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 client/galaxy/scripts/galaxy.library.js --- a/client/galaxy/scripts/galaxy.library.js +++ b/client/galaxy/scripts/galaxy.library.js @@ -16,19 +16,19 @@ "mvc/library/library-library-view", "mvc/library/library-folder-view" ], -function(mod_masthead, - mod_utils, - mod_toastr, - mod_baseMVC, - mod_library_model, - mod_folderlist_view, - mod_librarylist_view, - mod_librarytoolbar_view, - mod_foldertoolbar_view, - mod_library_dataset_view, - mod_library_library_view, - mod_library_folder_view - ) { + function(mod_masthead, + mod_utils, + mod_toastr, + mod_baseMVC, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view, + mod_foldertoolbar_view, + mod_library_dataset_view, + mod_library_library_view, + mod_library_folder_view + ) { // ============================================================================ // ROUTER @@ -37,10 +37,11 @@ this.routesHit = 0; //keep count of number of routes handled by the application Backbone.history.on('route', function() { this.routesHit++; }, this); - }, +}, - routes: { +routes: { "" : "libraries", + "page/:show_page" : "libraries_page", "library/:library_id/permissions" : "library_permissions", "folders/:folder_id/permissions" : "folder_permissions", "folders/:id" : "folder_content", @@ -49,27 +50,28 @@ "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", "folders/:folder_id/download/:format" : "download", "folders/:folder_id/import/:source" : "import_datasets" - }, +}, - back: function() { +back: function() { if(this.routesHit > 1) { //more than one route hit -> user did not land to current page directly window.history.back(); - } else { + } else { //otherwise go to the home page. Use replaceState if available so //the navigation doesn't create an extra history entry this.navigate('#', {trigger:true, replace:true}); - } } +} }); // ============================================================================ /** session storage for library preferences */ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({ defaults : { - with_deleted : false, - sort_order : 'asc', - sort_by : 'name' + with_deleted : false, + sort_order : 'asc', + sort_by : 'name', + library_page_size : 20 } }); @@ -88,77 +90,86 @@ initialize : function(){ Galaxy.libraries = this; - this.preferences = new LibraryPrefs( {id: 'global-lib-prefs'} ); + this.preferences = new LibraryPrefs( { id: 'global-lib-prefs' } ); this.library_router = new LibraryRouter(); this.library_router.on('route:libraries', function() { Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); + + this.library_router.on('route:libraries_page', function( show_page ) { + if ( Galaxy.libraries.libraryToolbarView === null ){ + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView( { show_page: show_page } ); + } else { + Galaxy.libraries.libraryListView.render( { show_page: show_page } ) + } }); this.library_router.on('route:folder_content', function(id) { if (Galaxy.libraries.folderToolbarView){ Galaxy.libraries.folderToolbarView.$el.unbind('click'); - } - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); - }); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); + }); - this.library_router.on('route:download', function(folder_id, format) { + this.library_router.on('route:download', function(folder_id, format) { if ($('#folder_list_body').find(':checked').length === 0) { mod_toastr.info( 'You must select at least one dataset to download' ); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); - } else { + } else { Galaxy.libraries.folderToolbarView.download(folder_id, format); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); - } - }); + } + }); - this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); - }); - this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); - }); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); - this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); - }); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); - this.library_router.on('route:library_permissions', function(library_id){ + this.library_router.on('route:library_permissions', function(library_id){ if (Galaxy.libraries.libraryView){ Galaxy.libraries.libraryView.$el.unbind('click'); - } - Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); - }); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); - this.library_router.on('route:folder_permissions', function(folder_id){ + this.library_router.on('route:folder_permissions', function(folder_id){ if (Galaxy.libraries.folderView){ Galaxy.libraries.folderView.$el.unbind('click'); - } - Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); - }); - this.library_router.on('route:import_datasets', function(folder_id, source){ + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + this.library_router.on('route:import_datasets', function(folder_id, source){ if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){ Galaxy.libraries.folderToolbarView.showImportModal({source:source}); - } else { + } else { Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id}); Galaxy.libraries.folderToolbarView.showImportModal({source: source}); - } - }); + } + }); - Backbone.history.start({pushState: false}); + Backbone.history.start({pushState: false}); } }); diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -72,7 +72,7 @@ }, render: function(options){ - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); var toolbar_template = this.templateToolBar(); var template_defaults = { id: this.options.id, @@ -346,18 +346,18 @@ this.modal = Galaxy.modal; var template_modal = this.templateImportPathModal(); this.modal.show({ - closing_events : true, - title : 'Please enter paths to import', - body : template_modal({}), - buttons : { - 'Import' : function() {that.importFromPathsClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} - }, - closing_callback: function(){ - // TODO: should not trigger routes outside of the router - Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true}); - } - }); + closing_events : true, + title : 'Please enter paths to import', + body : template_modal({}), + buttons : { + 'Import' : function() { that.importFromPathsClicked(that); }, + 'Close' : function() { Galaxy.modal.hide(); } + }, + closing_callback: function(){ + // TODO: should not trigger routes outside of the router + Galaxy.libraries.library_router.navigate( 'folders/' + that.id, { trigger: true } ); + } + }); this.renderSelectBoxes(); }, @@ -367,34 +367,37 @@ */ fetchExtAndGenomes: function(){ var that = this; - mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False", - function(datatypes) { - for (key in datatypes) { - that.list_extensions.push({ - id : datatypes[key].extension, - text : datatypes[key].extension, - description : datatypes[key].description, - description_url : datatypes[key].description_url - }); - } - that.list_extensions.sort(function(a, b) { - return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; - }); - that.list_extensions.unshift(that.auto); - - }); - mod_utils.get(galaxy_config.root + "api/genomes", - function(genomes) { - for (key in genomes) { - that.list_genomes.push({ - id : genomes[key][1], - text : genomes[key][0] - }); - } - that.list_genomes.sort(function(a, b) { - return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; - }); - }); + mod_utils.get({ + url : galaxy_config.root + "api/datatypes?extension_only=False", + success : function( datatypes ) { + for (key in datatypes) { + that.list_extensions.push({ + id : datatypes[key].extension, + text : datatypes[key].extension, + description : datatypes[key].description, + description_url : datatypes[key].description_url + }); + } + that.list_extensions.sort(function(a, b) { + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; + }); + that.list_extensions.unshift(that.auto); + } + }); + mod_utils.get({ + url: galaxy_config.root + "api/genomes", + success: function( genomes ) { + for ( key in genomes ) { + that.list_genomes.push({ + id : genomes[key][1], + text : genomes[key][0] + }); + } + that.list_genomes.sort(function(a, b) { + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; + }); + } + }); }, renderSelectBoxes: function(){ @@ -1027,7 +1030,7 @@ tmpl_array.push(' </div>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'); tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); - tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); tmpl_array.push(' </div>'); // TOOLBAR END diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 client/galaxy/scripts/mvc/library/library-librarylist-view.js --- a/client/galaxy/scripts/mvc/library/library-librarylist-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarylist-view.js @@ -4,13 +4,15 @@ "utils/utils", "libs/toastr", "mvc/library/library-model", - "mvc/library/library-libraryrow-view"], -function(mod_masthead, - mod_baseMVC, - mod_utils, - mod_toastr, - mod_library_model, - mod_library_libraryrow_view) { + "mvc/library/library-libraryrow-view" +], function( + mod_masthead, + mod_baseMVC, + mod_utils, + mod_toastr, + mod_library_model, + mod_library_libraryrow_view +){ var LibraryListView = Backbone.View.extend({ el: '#libraries_element', @@ -19,104 +21,135 @@ 'click .sort-libraries-link' : 'sort_clicked' }, - modal: null, + /** + * Initialize and fetch the libraries from server. + * Async render afterwards. + * @param {object} options an options object + */ + defaults: { + page_count: null, + show_page: null + }, - // collection of {Item}s - collection: null, + initialize : function( options ){ + this.options = _.defaults( this.options || {}, this.defaults, options ); - // map of library model ids to library views = cache - rowViews: {}, - - initialize : function(options){ - this.options = _.defaults(this.options || {}, options); - var that = this; + var that = this; + this.modal = null; + // map of library model ids to library views = cache this.rowViews = {}; + // collection of {Item}s this.collection = new mod_library_model.Libraries(); this.collection.fetch({ success: function(){ that.render(); }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg); + error: function( model, response ){ + if ( typeof response.responseJSON !== "undefined" ){ + mod_toastr.error( response.responseJSON.err_msg ); } else { - mod_toastr.error('An error ocurred.'); + mod_toastr.error( 'An error ocurred.' ); } } }); }, - /** Renders the libraries table either from the object's own collection, - * or from a given array of library models, - * or renders an empty list in case no data is given. */ - render: function (options) { - $(".tooltip").hide(); + /** + * Render the libraries table either from the object's own collection, + * or from a given array of library models, + * or render an empty list in case no data is given. + */ + render: function ( options ) { + this.options = _.extend( this.options, options ); + + if ( ( this.options.page_size != null ) && ( this.options.page_size == parseInt( this.options.page_size ) ) ) { + Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( this.options.page_size ) } ); + } + + $( ".tooltip" ).hide(); + // this.options.show_page = this.options.show_page || 1; var template = this.templateLibraryList(); var libraries_to_render = null; - var include_deleted = Galaxy.libraries.preferences.get('with_deleted'); var models = null; - if (typeof options !== 'undefined'){ - include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false; + if ( this.options.show_page === null || this.options.show_page < 1 ){ + this.options.show_page = 1; + } + if ( typeof options !== 'undefined' ){ models = typeof options.models !== 'undefined' ? options.models : null; } - - if (this.collection !== null && models === null){ + if ( this.collection !== null && models === null ){ this.sortLibraries(); - if (include_deleted){ // show all the libraries + if ( Galaxy.libraries.preferences.get( 'with_deleted' ) ){ libraries_to_render = this.collection.models; - } else{ // show only undeleted libraries - libraries_to_render = this.collection.where({deleted: false}); + } else { + libraries_to_render = this.collection.where( { deleted: false } ); } - } else if (models !== null){ + } else if ( models !== null ){ libraries_to_render = models; } else { libraries_to_render = []; + } + this.options.total_libraries_count = libraries_to_render.length + var page_start = ( Galaxy.libraries.preferences.get( 'library_page_size' ) * ( this.options.show_page - 1 ) ); + this.options.page_count = Math.ceil( this.options.total_libraries_count / Galaxy.libraries.preferences.get( 'library_page_size' ) ); + if ( this.options.total_libraries_count > 0 && ( page_start < this.options.total_libraries_count ) ){ + libraries_to_render = libraries_to_render.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'library_page_size' ) ); + this.options.libraries_shown = libraries_to_render.length; + // User requests page with no libraries + if ( Galaxy.libraries.preferences.get( 'library_page_size' ) * this.options.show_page > ( this.options.total_libraries_count + Galaxy.libraries.preferences.get( 'library_page_size' ) ) ){ + libraries_to_render = []; } - - this.$el.html(template({length: libraries_to_render.length, order: Galaxy.libraries.preferences.get('sort_order') })); - - if (libraries_to_render.length > 0){ - this.renderRows(libraries_to_render); + this.$el.html( template({ + length: 1, + order: Galaxy.libraries.preferences.get( 'sort_order' ) + })); + Galaxy.libraries.libraryToolbarView.renderPaginator( this.options ); + this.renderRows( libraries_to_render ); + } else { + this.$el.html( template({ + length: 0, + order: Galaxy.libraries.preferences.get( 'sort_order' ) + })); + Galaxy.libraries.libraryToolbarView.renderPaginator( this.options ); } - // initialize the library tooltips - $("#center [data-toggle]").tooltip(); - // modification of upper DOM element to show scrollbars due - // to the #center element inheritance - $("#center").css('overflow','auto'); + $( "#center [data-toggle]" ).tooltip(); + $( "#center" ).css( 'overflow','auto' ); }, - /** Renders all given models as rows in the library list */ - renderRows: function(libraries_to_render){ - for (var i = 0; i < libraries_to_render.length; i++) { + /** + * Render all given models as rows in the library list + * @param {array} libraries_to_render array of library models to render + */ + renderRows: function( libraries_to_render ){ + for ( var i = 0; i < libraries_to_render.length; i++ ) { var library = libraries_to_render[i]; - var cachedView = _.findWhere(this.rowViews, {id: library.get('id')}); - if (cachedView !== undefined && this instanceof Backbone.View){ + // search whether we have the item cached + var cachedView = _.findWhere( this.rowViews, { id: library.get( 'id' ) } ); + if ( cachedView !== undefined && this instanceof Backbone.View ){ cachedView.delegateEvents(); - this.$el.find('#library_list_body').append(cachedView.el); + this.$el.find( '#library_list_body' ).append( cachedView.el ); } else { - this.renderOne({library:library}) + this.renderOne( { library: library } ) } } }, /** - * Creates a view for the given model and adds it to the libraries view. + * Create a view for the given model and add it to the libraries view. * @param {Library} model of the view that will be rendered */ - renderOne: function(options){ + renderOne: function( options ){ var library = options.library; - var rowView = new mod_library_libraryrow_view.LibraryRowView(library); - // we want to prepend new item - if (options.prepend){ - this.$el.find('#library_list_body').prepend(rowView.el); - } else { - this.$el.find('#library_list_body').append(rowView.el); - } + var rowView = new mod_library_libraryrow_view.LibraryRowView( library ); + this.$el.find( '#library_list_body' ).append( rowView.el ); // save new rowView to cache - this.rowViews[library.get('id')] = rowView; + this.rowViews[ library.get( 'id' ) ] = rowView; }, - /** Table heading was clicked, update sorting preferences and re-render */ + /** + * Table heading was clicked, update sorting preferences and re-render. + * @return {[type]} [description] + */ sort_clicked : function(){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ Galaxy.libraries.preferences.set({'sort_order': 'desc'}); @@ -126,8 +159,10 @@ this.render(); }, - /** Sorts the underlying collection according to the parameters received. - Currently supports only sorting by name. */ + /** + * Sort the underlying collection according to the parameters received. + * Currently supports only sorting by name. + */ sortLibraries: function(){ if (Galaxy.libraries.preferences.get('sort_by') === 'name'){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ @@ -138,6 +173,13 @@ } }, + redirectToHome: function(){ + window.location = '../'; + }, + redirectToLogin: function(){ + window.location = '/user/login'; + }, + // MMMMMMMMMMMMMMMMMM // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM @@ -147,14 +189,14 @@ tmpl_array.push('<div class="library_container table-responsive">'); tmpl_array.push('<% if(length === 0) { %>'); - tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>'); + tmpl_array.push('<div>There are no libraries visible to you here. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>'); tmpl_array.push('<% } else{ %>'); tmpl_array.push('<table class="grid table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th style="width:22%;">description</th>'); tmpl_array.push(' <th style="width:22%;">synopsis</th> '); - tmpl_array.push(' <th style="width:26%;"></th> '); + tmpl_array.push(' <th style="width:26%;"></th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody id="library_list_body">'); // library item views will attach here @@ -166,14 +208,6 @@ return _.template(tmpl_array.join('')); }, - - redirectToHome: function(){ - window.location = '../'; - }, - redirectToLogin: function(){ - window.location = '/user/login'; - }, - }); return { diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js @@ -11,11 +11,13 @@ el: '#center', events: { - 'click #create_new_library_btn' : 'show_library_modal', - 'click #include_deleted_chk' : 'check_include_deleted' + 'click #create_new_library_btn' : 'showLibraryModal', + 'click #include_deleted_chk' : 'includeDeletedChecked', + 'click #page_size_prompt' : 'showPageSizePrompt' }, - initialize: function(){ + initialize: function( options ){ + this.options = _.defaults( this.options || {}, options ); this.render(); }, @@ -23,21 +25,34 @@ var toolbar_template = this.templateToolBar(); var is_admin = false; var is_anonym = true; - if (Galaxy.currUser){ + if ( Galaxy.currUser ){ is_admin = Galaxy.currUser.isAdmin(); is_anonym = Galaxy.currUser.isAnonymous(); } - this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym})); - if (is_admin){ - this.$el.find('#include_deleted_chk')[0].checked = Galaxy.libraries.preferences.get('with_deleted'); + this.$el.html(toolbar_template( { admin_user: is_admin, anon_user: is_anonym } ) ); + if ( is_admin ){ + this.$el.find( '#include_deleted_chk' )[0].checked = Galaxy.libraries.preferences.get( 'with_deleted' ); } }, - show_library_modal : function (event){ + /** + * Called from LibraryListView when needed. + * @param {object} options common options + */ + renderPaginator: function( options ){ + this.options = _.extend( this.options, options ); + var paginator_template = this.templatePaginator(); + this.$el.find( '#library_paginator' ).html( paginator_template({ + show_page: parseInt( this.options.show_page ), + page_count: parseInt( this.options.page_count ), + total_libraries_count: this.options.total_libraries_count, + libraries_shown: this.options.libraries_shown + })); + }, + + showLibraryModal : function (event){ event.preventDefault(); event.stopPropagation(); - - // create modal var self = this; this.modal = Galaxy.modal; this.modal.show({ @@ -45,22 +60,22 @@ title : 'Create New Library', body : this.templateNewLibraryInModal(), buttons : { - 'Create' : function() {self.create_new_library_event();}, - 'Close' : function() {self.modal.hide();} + 'Create' : function() { self.createNewLibrary(); }, + 'Close' : function() { self.modal.hide(); } } }); }, - create_new_library_event: function(){ - var libraryDetails = this.serialize_new_library(); - if (this.validate_new_library(libraryDetails)){ + createNewLibrary: function(){ + var libraryDetails = this.serializeNewLibrary(); + if (this.valdiateNewLibrary(libraryDetails)){ var library = new mod_library_model.Library(); var self = this; library.save(libraryDetails, { success: function (library) { Galaxy.libraries.libraryListView.collection.add(library); self.modal.hide(); - self.clear_library_modal(); + self.clearLibraryModal(); Galaxy.libraries.libraryListView.render(); mod_toastr.success('Library created.'); }, @@ -78,15 +93,22 @@ return false; }, + showPageSizePrompt: function(){ + var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); + if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { + Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); + Galaxy.libraries.libraryListView.render(); + } + }, + // clear the library modal once saved - clear_library_modal : function(){ + clearLibraryModal : function(){ $("input[name='Name']").val(''); $("input[name='Description']").val(''); $("input[name='Synopsis']").val(''); }, - // serialize data from the new library form - serialize_new_library : function(){ + serializeNewLibrary : function(){ return { name: $("input[name='Name']").val(), description: $("input[name='Description']").val(), @@ -94,18 +116,20 @@ }; }, - // validate new library info - validate_new_library: function(libraryDetails){ + valdiateNewLibrary: function( libraryDetails ){ return libraryDetails.name !== ''; }, - // include or exclude deleted libraries from the view - check_include_deleted: function(event){ + /** + * Include or exclude deleted libraries in the view. + * @param {object} event common event + */ + includeDeletedChecked: function( event ){ if (event.target.checked){ - Galaxy.libraries.preferences.set({'with_deleted': true}); + Galaxy.libraries.preferences.set( { 'with_deleted': true } ); Galaxy.libraries.libraryListView.render(); } else{ - Galaxy.libraries.preferences.set({'with_deleted': false}); + Galaxy.libraries.preferences.set( { 'with_deleted': false } ); Galaxy.libraries.libraryListView.render(); } }, @@ -113,22 +137,26 @@ templateToolBar: function(){ tmpl_array = []; + tmpl_array.push('<div class="library_style_container">'); - // TOOLBAR tmpl_array.push(' <div id="toolbar_form">'); tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>'); - tmpl_array.push(' <% if(admin_user === true) { %>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"> | <input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted |</input></span>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); - tmpl_array.push(' </div>'); - - tmpl_array.push(' <div>'); - tmpl_array.push(' '); - tmpl_array.push(' </div>'); - + tmpl_array.push(' <form class="form-inline" role="form">'); + tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>'); + tmpl_array.push(' <% if(admin_user === true) { %>'); + tmpl_array.push(' <div class="checkbox" style="height: 20px;">'); + tmpl_array.push(' <label>'); + tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>'); + tmpl_array.push(' </label>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' <span id="library_paginator" class="library-paginator">'); + // paginator will append here + tmpl_array.push(' </span>'); + tmpl_array.push(' </form>'); + tmpl_array.push(' </div>'); tmpl_array.push(' </div>'); tmpl_array.push(' <div id="libraries_element">'); // table with libraries will append here @@ -138,6 +166,39 @@ return _.template(tmpl_array.join('')); }, + templatePaginator: function(){ + tmpl_array = []; + + tmpl_array.push(' <ul class="pagination pagination-sm">'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count + tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); // we are on the first page + tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <li class="active">'); + tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>'); + tmpl_array.push(' </li>'); + tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>'); + tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' <span>'); + tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); + tmpl_array.push(' </span>'); + + return _.template(tmpl_array.join('')); + }, templateNewLibraryInModal: function(){ tmpl_array = []; diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 lib/galaxy/managers/libraries.py --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -103,6 +103,9 @@ :param deleted: if True, show only ``deleted`` libraries, if False show only ``non-deleted`` :type deleted: boolean (optional) + + :returns: query that will emit all accessible libraries + :rtype: sqlalchemy query """ is_admin = trans.user_is_admin() query = trans.sa_session.query( trans.app.model.Library ) diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -16,19 +16,19 @@ "mvc/library/library-library-view", "mvc/library/library-folder-view" ], -function(mod_masthead, - mod_utils, - mod_toastr, - mod_baseMVC, - mod_library_model, - mod_folderlist_view, - mod_librarylist_view, - mod_librarytoolbar_view, - mod_foldertoolbar_view, - mod_library_dataset_view, - mod_library_library_view, - mod_library_folder_view - ) { + function(mod_masthead, + mod_utils, + mod_toastr, + mod_baseMVC, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view, + mod_foldertoolbar_view, + mod_library_dataset_view, + mod_library_library_view, + mod_library_folder_view + ) { // ============================================================================ // ROUTER @@ -37,10 +37,11 @@ this.routesHit = 0; //keep count of number of routes handled by the application Backbone.history.on('route', function() { this.routesHit++; }, this); - }, +}, - routes: { +routes: { "" : "libraries", + "page/:show_page" : "libraries_page", "library/:library_id/permissions" : "library_permissions", "folders/:folder_id/permissions" : "folder_permissions", "folders/:id" : "folder_content", @@ -49,27 +50,28 @@ "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", "folders/:folder_id/download/:format" : "download", "folders/:folder_id/import/:source" : "import_datasets" - }, +}, - back: function() { +back: function() { if(this.routesHit > 1) { //more than one route hit -> user did not land to current page directly window.history.back(); - } else { + } else { //otherwise go to the home page. Use replaceState if available so //the navigation doesn't create an extra history entry this.navigate('#', {trigger:true, replace:true}); - } } +} }); // ============================================================================ /** session storage for library preferences */ var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({ defaults : { - with_deleted : false, - sort_order : 'asc', - sort_by : 'name' + with_deleted : false, + sort_order : 'asc', + sort_by : 'name', + library_page_size : 20 } }); @@ -88,77 +90,86 @@ initialize : function(){ Galaxy.libraries = this; - this.preferences = new LibraryPrefs( {id: 'global-lib-prefs'} ); + this.preferences = new LibraryPrefs( { id: 'global-lib-prefs' } ); this.library_router = new LibraryRouter(); this.library_router.on('route:libraries', function() { Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); + + this.library_router.on('route:libraries_page', function( show_page ) { + if ( Galaxy.libraries.libraryToolbarView === null ){ + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView( { show_page: show_page } ); + } else { + Galaxy.libraries.libraryListView.render( { show_page: show_page } ) + } }); this.library_router.on('route:folder_content', function(id) { if (Galaxy.libraries.folderToolbarView){ Galaxy.libraries.folderToolbarView.$el.unbind('click'); - } - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); - }); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); + }); - this.library_router.on('route:download', function(folder_id, format) { + this.library_router.on('route:download', function(folder_id, format) { if ($('#folder_list_body').find(':checked').length === 0) { mod_toastr.info( 'You must select at least one dataset to download' ); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); - } else { + } else { Galaxy.libraries.folderToolbarView.download(folder_id, format); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); - } - }); + } + }); - this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); - }); - this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); - }); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); - this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ if (Galaxy.libraries.datasetView){ Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); - }); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); - this.library_router.on('route:library_permissions', function(library_id){ + this.library_router.on('route:library_permissions', function(library_id){ if (Galaxy.libraries.libraryView){ Galaxy.libraries.libraryView.$el.unbind('click'); - } - Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); - }); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); - this.library_router.on('route:folder_permissions', function(folder_id){ + this.library_router.on('route:folder_permissions', function(folder_id){ if (Galaxy.libraries.folderView){ Galaxy.libraries.folderView.$el.unbind('click'); - } - Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); - }); - this.library_router.on('route:import_datasets', function(folder_id, source){ + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + this.library_router.on('route:import_datasets', function(folder_id, source){ if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){ Galaxy.libraries.folderToolbarView.showImportModal({source:source}); - } else { + } else { Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id}); Galaxy.libraries.folderToolbarView.showImportModal({source: source}); - } - }); + } + }); - Backbone.history.start({pushState: false}); + Backbone.history.start({pushState: false}); } }); diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -72,7 +72,7 @@ }, render: function(options){ - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); var toolbar_template = this.templateToolBar(); var template_defaults = { id: this.options.id, @@ -346,18 +346,18 @@ this.modal = Galaxy.modal; var template_modal = this.templateImportPathModal(); this.modal.show({ - closing_events : true, - title : 'Please enter paths to import', - body : template_modal({}), - buttons : { - 'Import' : function() {that.importFromPathsClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} - }, - closing_callback: function(){ - // TODO: should not trigger routes outside of the router - Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true}); - } - }); + closing_events : true, + title : 'Please enter paths to import', + body : template_modal({}), + buttons : { + 'Import' : function() { that.importFromPathsClicked(that); }, + 'Close' : function() { Galaxy.modal.hide(); } + }, + closing_callback: function(){ + // TODO: should not trigger routes outside of the router + Galaxy.libraries.library_router.navigate( 'folders/' + that.id, { trigger: true } ); + } + }); this.renderSelectBoxes(); }, @@ -367,34 +367,37 @@ */ fetchExtAndGenomes: function(){ var that = this; - mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False", - function(datatypes) { - for (key in datatypes) { - that.list_extensions.push({ - id : datatypes[key].extension, - text : datatypes[key].extension, - description : datatypes[key].description, - description_url : datatypes[key].description_url - }); - } - that.list_extensions.sort(function(a, b) { - return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; - }); - that.list_extensions.unshift(that.auto); - - }); - mod_utils.get(galaxy_config.root + "api/genomes", - function(genomes) { - for (key in genomes) { - that.list_genomes.push({ - id : genomes[key][1], - text : genomes[key][0] - }); - } - that.list_genomes.sort(function(a, b) { - return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; - }); - }); + mod_utils.get({ + url : galaxy_config.root + "api/datatypes?extension_only=False", + success : function( datatypes ) { + for (key in datatypes) { + that.list_extensions.push({ + id : datatypes[key].extension, + text : datatypes[key].extension, + description : datatypes[key].description, + description_url : datatypes[key].description_url + }); + } + that.list_extensions.sort(function(a, b) { + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; + }); + that.list_extensions.unshift(that.auto); + } + }); + mod_utils.get({ + url: galaxy_config.root + "api/genomes", + success: function( genomes ) { + for ( key in genomes ) { + that.list_genomes.push({ + id : genomes[key][1], + text : genomes[key][0] + }); + } + that.list_genomes.sort(function(a, b) { + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; + }); + } + }); }, renderSelectBoxes: function(){ @@ -1027,7 +1030,7 @@ tmpl_array.push(' </div>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'); tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); - tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); tmpl_array.push(' </div>'); // TOOLBAR END diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -4,13 +4,15 @@ "utils/utils", "libs/toastr", "mvc/library/library-model", - "mvc/library/library-libraryrow-view"], -function(mod_masthead, - mod_baseMVC, - mod_utils, - mod_toastr, - mod_library_model, - mod_library_libraryrow_view) { + "mvc/library/library-libraryrow-view" +], function( + mod_masthead, + mod_baseMVC, + mod_utils, + mod_toastr, + mod_library_model, + mod_library_libraryrow_view +){ var LibraryListView = Backbone.View.extend({ el: '#libraries_element', @@ -19,104 +21,135 @@ 'click .sort-libraries-link' : 'sort_clicked' }, - modal: null, + /** + * Initialize and fetch the libraries from server. + * Async render afterwards. + * @param {object} options an options object + */ + defaults: { + page_count: null, + show_page: null + }, - // collection of {Item}s - collection: null, + initialize : function( options ){ + this.options = _.defaults( this.options || {}, this.defaults, options ); - // map of library model ids to library views = cache - rowViews: {}, - - initialize : function(options){ - this.options = _.defaults(this.options || {}, options); - var that = this; + var that = this; + this.modal = null; + // map of library model ids to library views = cache this.rowViews = {}; + // collection of {Item}s this.collection = new mod_library_model.Libraries(); this.collection.fetch({ success: function(){ that.render(); }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg); + error: function( model, response ){ + if ( typeof response.responseJSON !== "undefined" ){ + mod_toastr.error( response.responseJSON.err_msg ); } else { - mod_toastr.error('An error ocurred.'); + mod_toastr.error( 'An error ocurred.' ); } } }); }, - /** Renders the libraries table either from the object's own collection, - * or from a given array of library models, - * or renders an empty list in case no data is given. */ - render: function (options) { - $(".tooltip").hide(); + /** + * Render the libraries table either from the object's own collection, + * or from a given array of library models, + * or render an empty list in case no data is given. + */ + render: function ( options ) { + this.options = _.extend( this.options, options ); + + if ( ( this.options.page_size != null ) && ( this.options.page_size == parseInt( this.options.page_size ) ) ) { + Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( this.options.page_size ) } ); + } + + $( ".tooltip" ).hide(); + // this.options.show_page = this.options.show_page || 1; var template = this.templateLibraryList(); var libraries_to_render = null; - var include_deleted = Galaxy.libraries.preferences.get('with_deleted'); var models = null; - if (typeof options !== 'undefined'){ - include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false; + if ( this.options.show_page === null || this.options.show_page < 1 ){ + this.options.show_page = 1; + } + if ( typeof options !== 'undefined' ){ models = typeof options.models !== 'undefined' ? options.models : null; } - - if (this.collection !== null && models === null){ + if ( this.collection !== null && models === null ){ this.sortLibraries(); - if (include_deleted){ // show all the libraries + if ( Galaxy.libraries.preferences.get( 'with_deleted' ) ){ libraries_to_render = this.collection.models; - } else{ // show only undeleted libraries - libraries_to_render = this.collection.where({deleted: false}); + } else { + libraries_to_render = this.collection.where( { deleted: false } ); } - } else if (models !== null){ + } else if ( models !== null ){ libraries_to_render = models; } else { libraries_to_render = []; + } + this.options.total_libraries_count = libraries_to_render.length + var page_start = ( Galaxy.libraries.preferences.get( 'library_page_size' ) * ( this.options.show_page - 1 ) ); + this.options.page_count = Math.ceil( this.options.total_libraries_count / Galaxy.libraries.preferences.get( 'library_page_size' ) ); + if ( this.options.total_libraries_count > 0 && ( page_start < this.options.total_libraries_count ) ){ + libraries_to_render = libraries_to_render.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'library_page_size' ) ); + this.options.libraries_shown = libraries_to_render.length; + // User requests page with no libraries + if ( Galaxy.libraries.preferences.get( 'library_page_size' ) * this.options.show_page > ( this.options.total_libraries_count + Galaxy.libraries.preferences.get( 'library_page_size' ) ) ){ + libraries_to_render = []; } - - this.$el.html(template({length: libraries_to_render.length, order: Galaxy.libraries.preferences.get('sort_order') })); - - if (libraries_to_render.length > 0){ - this.renderRows(libraries_to_render); + this.$el.html( template({ + length: 1, + order: Galaxy.libraries.preferences.get( 'sort_order' ) + })); + Galaxy.libraries.libraryToolbarView.renderPaginator( this.options ); + this.renderRows( libraries_to_render ); + } else { + this.$el.html( template({ + length: 0, + order: Galaxy.libraries.preferences.get( 'sort_order' ) + })); + Galaxy.libraries.libraryToolbarView.renderPaginator( this.options ); } - // initialize the library tooltips - $("#center [data-toggle]").tooltip(); - // modification of upper DOM element to show scrollbars due - // to the #center element inheritance - $("#center").css('overflow','auto'); + $( "#center [data-toggle]" ).tooltip(); + $( "#center" ).css( 'overflow','auto' ); }, - /** Renders all given models as rows in the library list */ - renderRows: function(libraries_to_render){ - for (var i = 0; i < libraries_to_render.length; i++) { + /** + * Render all given models as rows in the library list + * @param {array} libraries_to_render array of library models to render + */ + renderRows: function( libraries_to_render ){ + for ( var i = 0; i < libraries_to_render.length; i++ ) { var library = libraries_to_render[i]; - var cachedView = _.findWhere(this.rowViews, {id: library.get('id')}); - if (cachedView !== undefined && this instanceof Backbone.View){ + // search whether we have the item cached + var cachedView = _.findWhere( this.rowViews, { id: library.get( 'id' ) } ); + if ( cachedView !== undefined && this instanceof Backbone.View ){ cachedView.delegateEvents(); - this.$el.find('#library_list_body').append(cachedView.el); + this.$el.find( '#library_list_body' ).append( cachedView.el ); } else { - this.renderOne({library:library}) + this.renderOne( { library: library } ) } } }, /** - * Creates a view for the given model and adds it to the libraries view. + * Create a view for the given model and add it to the libraries view. * @param {Library} model of the view that will be rendered */ - renderOne: function(options){ + renderOne: function( options ){ var library = options.library; - var rowView = new mod_library_libraryrow_view.LibraryRowView(library); - // we want to prepend new item - if (options.prepend){ - this.$el.find('#library_list_body').prepend(rowView.el); - } else { - this.$el.find('#library_list_body').append(rowView.el); - } + var rowView = new mod_library_libraryrow_view.LibraryRowView( library ); + this.$el.find( '#library_list_body' ).append( rowView.el ); // save new rowView to cache - this.rowViews[library.get('id')] = rowView; + this.rowViews[ library.get( 'id' ) ] = rowView; }, - /** Table heading was clicked, update sorting preferences and re-render */ + /** + * Table heading was clicked, update sorting preferences and re-render. + * @return {[type]} [description] + */ sort_clicked : function(){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ Galaxy.libraries.preferences.set({'sort_order': 'desc'}); @@ -126,8 +159,10 @@ this.render(); }, - /** Sorts the underlying collection according to the parameters received. - Currently supports only sorting by name. */ + /** + * Sort the underlying collection according to the parameters received. + * Currently supports only sorting by name. + */ sortLibraries: function(){ if (Galaxy.libraries.preferences.get('sort_by') === 'name'){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ @@ -138,6 +173,13 @@ } }, + redirectToHome: function(){ + window.location = '../'; + }, + redirectToLogin: function(){ + window.location = '/user/login'; + }, + // MMMMMMMMMMMMMMMMMM // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM @@ -147,14 +189,14 @@ tmpl_array.push('<div class="library_container table-responsive">'); tmpl_array.push('<% if(length === 0) { %>'); - tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>'); + tmpl_array.push('<div>There are no libraries visible to you here. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>'); tmpl_array.push('<% } else{ %>'); tmpl_array.push('<table class="grid table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th style="width:22%;">description</th>'); tmpl_array.push(' <th style="width:22%;">synopsis</th> '); - tmpl_array.push(' <th style="width:26%;"></th> '); + tmpl_array.push(' <th style="width:26%;"></th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody id="library_list_body">'); // library item views will attach here @@ -166,14 +208,6 @@ return _.template(tmpl_array.join('')); }, - - redirectToHome: function(){ - window.location = '../'; - }, - redirectToLogin: function(){ - window.location = '/user/login'; - }, - }); return { diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -11,11 +11,13 @@ el: '#center', events: { - 'click #create_new_library_btn' : 'show_library_modal', - 'click #include_deleted_chk' : 'check_include_deleted' + 'click #create_new_library_btn' : 'showLibraryModal', + 'click #include_deleted_chk' : 'includeDeletedChecked', + 'click #page_size_prompt' : 'showPageSizePrompt' }, - initialize: function(){ + initialize: function( options ){ + this.options = _.defaults( this.options || {}, options ); this.render(); }, @@ -23,21 +25,34 @@ var toolbar_template = this.templateToolBar(); var is_admin = false; var is_anonym = true; - if (Galaxy.currUser){ + if ( Galaxy.currUser ){ is_admin = Galaxy.currUser.isAdmin(); is_anonym = Galaxy.currUser.isAnonymous(); } - this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym})); - if (is_admin){ - this.$el.find('#include_deleted_chk')[0].checked = Galaxy.libraries.preferences.get('with_deleted'); + this.$el.html(toolbar_template( { admin_user: is_admin, anon_user: is_anonym } ) ); + if ( is_admin ){ + this.$el.find( '#include_deleted_chk' )[0].checked = Galaxy.libraries.preferences.get( 'with_deleted' ); } }, - show_library_modal : function (event){ + /** + * Called from LibraryListView when needed. + * @param {object} options common options + */ + renderPaginator: function( options ){ + this.options = _.extend( this.options, options ); + var paginator_template = this.templatePaginator(); + this.$el.find( '#library_paginator' ).html( paginator_template({ + show_page: parseInt( this.options.show_page ), + page_count: parseInt( this.options.page_count ), + total_libraries_count: this.options.total_libraries_count, + libraries_shown: this.options.libraries_shown + })); + }, + + showLibraryModal : function (event){ event.preventDefault(); event.stopPropagation(); - - // create modal var self = this; this.modal = Galaxy.modal; this.modal.show({ @@ -45,22 +60,22 @@ title : 'Create New Library', body : this.templateNewLibraryInModal(), buttons : { - 'Create' : function() {self.create_new_library_event();}, - 'Close' : function() {self.modal.hide();} + 'Create' : function() { self.createNewLibrary(); }, + 'Close' : function() { self.modal.hide(); } } }); }, - create_new_library_event: function(){ - var libraryDetails = this.serialize_new_library(); - if (this.validate_new_library(libraryDetails)){ + createNewLibrary: function(){ + var libraryDetails = this.serializeNewLibrary(); + if (this.valdiateNewLibrary(libraryDetails)){ var library = new mod_library_model.Library(); var self = this; library.save(libraryDetails, { success: function (library) { Galaxy.libraries.libraryListView.collection.add(library); self.modal.hide(); - self.clear_library_modal(); + self.clearLibraryModal(); Galaxy.libraries.libraryListView.render(); mod_toastr.success('Library created.'); }, @@ -78,15 +93,22 @@ return false; }, + showPageSizePrompt: function(){ + var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); + if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { + Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); + Galaxy.libraries.libraryListView.render(); + } + }, + // clear the library modal once saved - clear_library_modal : function(){ + clearLibraryModal : function(){ $("input[name='Name']").val(''); $("input[name='Description']").val(''); $("input[name='Synopsis']").val(''); }, - // serialize data from the new library form - serialize_new_library : function(){ + serializeNewLibrary : function(){ return { name: $("input[name='Name']").val(), description: $("input[name='Description']").val(), @@ -94,18 +116,20 @@ }; }, - // validate new library info - validate_new_library: function(libraryDetails){ + valdiateNewLibrary: function( libraryDetails ){ return libraryDetails.name !== ''; }, - // include or exclude deleted libraries from the view - check_include_deleted: function(event){ + /** + * Include or exclude deleted libraries in the view. + * @param {object} event common event + */ + includeDeletedChecked: function( event ){ if (event.target.checked){ - Galaxy.libraries.preferences.set({'with_deleted': true}); + Galaxy.libraries.preferences.set( { 'with_deleted': true } ); Galaxy.libraries.libraryListView.render(); } else{ - Galaxy.libraries.preferences.set({'with_deleted': false}); + Galaxy.libraries.preferences.set( { 'with_deleted': false } ); Galaxy.libraries.libraryListView.render(); } }, @@ -113,22 +137,26 @@ templateToolBar: function(){ tmpl_array = []; + tmpl_array.push('<div class="library_style_container">'); - // TOOLBAR tmpl_array.push(' <div id="toolbar_form">'); tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>'); - tmpl_array.push(' <% if(admin_user === true) { %>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"> | <input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted |</input></span>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); - tmpl_array.push(' </div>'); - - tmpl_array.push(' <div>'); - tmpl_array.push(' '); - tmpl_array.push(' </div>'); - + tmpl_array.push(' <form class="form-inline" role="form">'); + tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>'); + tmpl_array.push(' <% if(admin_user === true) { %>'); + tmpl_array.push(' <div class="checkbox" style="height: 20px;">'); + tmpl_array.push(' <label>'); + tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>'); + tmpl_array.push(' </label>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' <span id="library_paginator" class="library-paginator">'); + // paginator will append here + tmpl_array.push(' </span>'); + tmpl_array.push(' </form>'); + tmpl_array.push(' </div>'); tmpl_array.push(' </div>'); tmpl_array.push(' <div id="libraries_element">'); // table with libraries will append here @@ -138,6 +166,39 @@ return _.template(tmpl_array.join('')); }, + templatePaginator: function(){ + tmpl_array = []; + + tmpl_array.push(' <ul class="pagination pagination-sm">'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count + tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); // we are on the first page + tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <li class="active">'); + tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>'); + tmpl_array.push(' </li>'); + tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>'); + tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' <span>'); + tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries'); + tmpl_array.push(' </span>'); + + return _.template(tmpl_array.join('')); + }, templateNewLibraryInModal: function(){ tmpl_array = []; diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You must select at least one dataset to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});this.library_router.on("route:import_datasets",function(p,q){if(Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView){Galaxy.libraries.folderToolbarView.showImportModal({source:q})}else{Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p});Galaxy.libraries.folderToolbarView.showImportModal({source:q})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","page/:show_page":"libraries_page","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name",library_page_size:20}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:libraries_page",function(p){if(Galaxy.libraries.libraryToolbarView===null){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView({show_page:p})}else{Galaxy.libraries.libraryListView.render({show_page:p})}});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You must select at least one dataset to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});this.library_router.on("route:import_datasets",function(p,q){if(Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView){Galaxy.libraries.folderToolbarView.showImportModal({source:q})}else{Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p});Galaxy.libraries.folderToolbarView.showImportModal({source:q})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)}});e.get({url:galaxy_config.root+"api/genomes",success:function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})}})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);var i=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){i.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},render:function(i){$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null},initialize:function(h){this.options=_.defaults(this.options||{},this.defaults,h);var i=this;this.modal=null;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){i.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},render:function(i){this.options=_.extend(this.options,i);if((this.options.page_size!=null)&&(this.options.page_size==parseInt(this.options.page_size))){Galaxy.libraries.preferences.set({library_page_size:parseInt(this.options.page_size)})}$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var l=null;if(this.options.show_page===null||this.options.show_page<1){this.options.show_page=1}if(typeof i!=="undefined"){l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(Galaxy.libraries.preferences.get("with_deleted")){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.options.total_libraries_count=k.length;var h=(Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1));this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size"));if(this.options.total_libraries_count>0&&(h<this.options.total_libraries_count)){k=k.slice(h,h+Galaxy.libraries.preferences.get("library_page_size"));this.options.libraries_shown=k.length;if(Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>(this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size"))){k=[]}this.$el.html(j({length:1,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options);this.renderRows(k)}else{this.$el.html(j({length:0,order:Galaxy.libraries.preferences.get("sort_order")}));Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);this.$el.find("#library_list_body").append(h.el);this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you here. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th>');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},});return{LibraryListView:f}}); \ No newline at end of file diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"> | <input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted |</input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(" <div>");tmpl_array.push(" ");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render()}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -757,6 +757,7 @@ .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} .modal-dialog{width:690px} +.pagination>.active>a{background-color:#ebd9b2;color:black}.pagination>.active>a:hover{color:black;background-color:#ebd9b2} .modal-body{overflow:auto} .nav-tabs{margin-bottom:15px} a{text-decoration:underline} @@ -1360,6 +1361,8 @@ .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #bfbfbf;background:#eee} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #aa6;background:#ffc} .libraryItem-upload{margin-right:2px;padding:0 2px 0 2px;border:1px solid #1197c0;background:#a6e4f7} +.pagination-sm{height:15px} +.library-paginator{margin-left:2em} .toast-title{font-weight:bold} .toast-message{-ms-word-wrap:break-word;word-wrap:break-word}.toast-message a,.toast-message label{color:#fff} .toast-message a:hover{color:#ccc;text-decoration:none} diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -42,3 +42,5 @@ .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #bfbfbf;background:#eee} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #aa6;background:#ffc} .libraryItem-upload{margin-right:2px;padding:0 2px 0 2px;border:1px solid #1197c0;background:#a6e4f7} +.pagination-sm{height:15px} +.library-paginator{margin-left:2em} diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -35,6 +35,16 @@ width: 690px; } +.pagination { + > .active > a { + background-color: #ebd9b2; + color: black; + &:hover { + color: black; + background-color: #ebd9b2; + } + } +} /* NOTE: these styles do not currently work. @@ -70,4 +80,4 @@ .nav-tabs { margin-bottom: 15px; -} \ No newline at end of file +} diff -r 905bcdb0f1191e9e5150330d210953d10af682a8 -r c86a489a597657c769848d2781af631ca668a279 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -98,8 +98,7 @@ } } -th.button_heading -{ +th.button_heading{ width: 2em; } @@ -209,3 +208,9 @@ border: 1px solid @state-upload-border; background: @state-upload-bg; } +.pagination-sm { + height: 15px; +} +.library-paginator { + margin-left: 2em; +} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Merge stable.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/905bcdb0f119/ Changeset: 905bcdb0f119 User: dannon Date: 2014-10-10 18:40:58+00:00 Summary: Merge stable. Affected #: 1 file diff -r bfd407dbdd22a07a73eda40a359db6ab1e9acef3 -r 905bcdb0f1191e9e5150330d210953d10af682a8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06 +0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Merge.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7436bde1f785/ Changeset: 7436bde1f785 Branch: stable User: dannon Date: 2014-10-10 18:40:07+00:00 Summary: Merge. Affected #: 1 file diff -r c28c30887d37f3ea8fd2fb57276bab1c3b5d49f0 -r 7436bde1f7850762bcceb3a30fb4a3eceac42523 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06 +0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Merged in dannon/galaxy-central-prmaker/stable (pull request #524)
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bfd407dbdd22/ Changeset: bfd407dbdd22 User: dan Date: 2014-10-10 18:36:55+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #524) [STABLE] Strip r3 instance types for now; hvm virtualization required, which causes launch failures. Affected #: 1 file diff -r a575533ed283363e8e754a68ade04569c4e481f0 -r bfd407dbdd22a07a73eda40a359db6ab1e9acef3 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -36,9 +36,6 @@ ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"), ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"), ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"), - ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"), - ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"), - ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c28c30887d37/ Changeset: c28c30887d37 Branch: stable User: dannon Date: 2014-10-10 18:13:46+00:00 Summary: Strip r3 instance types for now; hvm virtualization required, which causes launch failures. Affected #: 1 file diff -r 0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac -r c28c30887d37f3ea8fd2fb57276bab1c3b5d49f0 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -35,9 +35,6 @@ ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"), ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"), ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"), - ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"), - ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"), - ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), ] https://bitbucket.org/galaxy/galaxy-central/commits/bfd407dbdd22/ Changeset: bfd407dbdd22 User: dan Date: 2014-10-10 18:36:55+00:00 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #524) [STABLE] Strip r3 instance types for now; hvm virtualization required, which causes launch failures. Affected #: 1 file diff -r a575533ed283363e8e754a68ade04569c4e481f0 -r bfd407dbdd22a07a73eda40a359db6ab1e9acef3 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -36,9 +36,6 @@ ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"), ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"), ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"), - ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"), - ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"), - ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Unit makos
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a575533ed283/ Changeset: a575533ed283 User: guerler Date: 2014-10-10 16:51:40+00:00 Summary: ToolForm: Unit makos Affected #: 3 files diff -r 8ce690c0910c1f6a11f90fe91b51ca964e879d1f -r a575533ed283363e8e754a68ade04569c4e481f0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1235,7 +1235,7 @@ requires_setting_metadata = True default_tool_action = DefaultToolAction dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) - default_template = 'tool_form.api.mako' + default_template = 'tool_form.mako' def __init__( self, config_file, root, app, guid=None, repository_id=None ): """Load a tool from the config named by `config_file`""" diff -r 8ce690c0910c1f6a11f90fe91b51ca964e879d1f -r a575533ed283363e8e754a68ade04569c4e481f0 templates/webapps/galaxy/tool_form.api.mako --- a/templates/webapps/galaxy/tool_form.api.mako +++ /dev/null @@ -1,47 +0,0 @@ -<%inherit file="/base.mako"/> -<% - # load tool help - tool_help = '' - if tool.help: - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - endif - - # check if citations exist - tool_citations = False - if tool.citations: - tool_citations = True - - # form configuration - self.form_config = { - 'id' : tool.id, - 'help' : tool_help, - 'citations' : tool_citations, - 'biostar_url' : trans.app.config.biostar_url, - 'history_id' : trans.security.encode_id( trans.history.id ), - 'job_id' : trans.security.encode_id( job.id ) if job else None - } -%> -${h.js("libs/bibtex", "libs/jquery/jquery-ui")} -${h.css('base', 'jquery-ui/smoothness/jquery-ui')} -<script> - require(['mvc/tools/tools-form'], function(ToolsForm){ - $(function(){ - var form = new ToolsForm.View(${ h.dumps(self.form_config) }); - }); - }); -</script> - -## classic tool form -<div id="tool-form-classic" style="display: none;"> - <%include file="tool_form.mako"/> -</div> \ No newline at end of file diff -r 8ce690c0910c1f6a11f90fe91b51ca964e879d1f -r a575533ed283363e8e754a68ade04569c4e481f0 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,412 +1,456 @@ -##<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/base_panels.mako" import="overlay" /> +<%inherit file="/base.mako"/> +<% + # load tool help + tool_help = '' + if tool.help: + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help -<% import galaxy.util %> + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) -<%def name="stylesheets()"> - ${h.css( "autocomplete_tagging", "base", "library" )} - <style type="text/css"> - html, body { - background-color: #fff; - } - </style> -</%def> + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + endif -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/jquery/jstorage" )} - ${h.js( "libs/bibtex" )} - <script type="text/javascript"> - require( [ "galaxy.tools" ] ); - window.enhanced_galaxy_tools = true; - </script> - <script type="text/javascript"> - $(function() { - $(window).bind("refresh_on_change", function() { - $(':file').each( function() { - var file = $(this); - var file_value = file.val(); - if (file_value) { - // disable file input, since we don't want to upload the file on refresh - var file_name = $(this).attr("name"); - file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); - // create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); - file.after(new_file_input); - } + # check if citations exist + tool_citations = False + if tool.citations: + tool_citations = True + + # form configuration + self.form_config = { + 'id' : tool.id, + 'help' : tool_help, + 'citations' : tool_citations, + 'biostar_url' : trans.app.config.biostar_url, + 'history_id' : trans.security.encode_id( trans.history.id ), + 'job_id' : trans.security.encode_id( job.id ) if job else None + } +%> +${h.js("libs/bibtex", "libs/jquery/jquery-ui")} +${h.css('base', 'jquery-ui/smoothness/jquery-ui')} +<script> + require(['mvc/tools/tools-form'], function(ToolsForm){ + $(function(){ + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + }); + }); +</script> + +## classic tool form +<div id="tool-form-classic" style="display: none;"> + <%namespace file="/message.mako" import="render_msg" /> + <%namespace file="/base_panels.mako" import="overlay" /> + + <% import galaxy.util %> + + <%def name="stylesheets()"> + ${h.css( "autocomplete_tagging", "base", "library" )} + <style type="text/css"> + html, body { + background-color: #fff; + } + </style> + </%def> + + <%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/jquery/jstorage" )} + ${h.js( "libs/bibtex" )} + <script type="text/javascript"> + require( [ "galaxy.tools" ] ); + window.enhanced_galaxy_tools = true; + </script> + <script type="text/javascript"> + $(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $(document.createElement('input')); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); + file.after(new_file_input); + } + }); }); - }); - // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements - $( 'div.drilldown-container' ).each( function() { - $(this).find('span.form-toggle' ).each( function() { - var show_hide_click_elt = $(this); - var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); - $('#' + group_id + '-container').each( function() { - var show_hide_elt = $(this); - if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { - show_hide_elt.hide(); + // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements + $( 'div.drilldown-container' ).each( function() { + $(this).find('span.form-toggle' ).each( function() { + var show_hide_click_elt = $(this); + var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); + $('#' + group_id + '-container').each( function() { + var show_hide_elt = $(this); + if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { + show_hide_elt.hide(); + } + show_hide_click_elt.click( function() { + if ( show_hide_click_elt.hasClass("toggle") ){ + show_hide_click_elt.addClass("toggle-expand"); + show_hide_click_elt.removeClass("toggle"); + show_hide_elt.slideUp( 'fast' ); + } + else { + show_hide_click_elt.addClass("toggle"); + show_hide_click_elt.removeClass("toggle-expand"); + show_hide_elt.slideDown( 'fast' ); + } + }); + }); + }); + }); + + $(".add-librarydataset").click(function() { + var link = $(this); + $.ajax({ + url: "/visualization/list_libraries", + error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, + success: function(table_html) { + show_modal( + "Select Library Dataset", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Select": function() { + var names = []; + var ids = []; + counter = 1; + $('input[name=ldda_ids]:checked').each(function() { + var name = $.trim( $(this).siblings("label").text() ); + var id = $(this).val(); + names.push( counter + ". " + name ); + counter += 1; + ids.push(id); + }); + link.html( names.join("<br/>") ); + link.siblings("input[type=hidden]").val( ids.join("||") ); + hide_modal(); + } + } + ); } - show_hide_click_elt.click( function() { - if ( show_hide_click_elt.hasClass("toggle") ){ - show_hide_click_elt.addClass("toggle-expand"); - show_hide_click_elt.removeClass("toggle"); - show_hide_elt.slideUp( 'fast' ); - } - else { - show_hide_click_elt.addClass("toggle"); - show_hide_click_elt.removeClass("toggle-expand"); - show_hide_elt.slideDown( 'fast' ); - } - }); }); }); }); - $(".add-librarydataset").click(function() { - var link = $(this); - $.ajax({ - url: "/visualization/list_libraries", - error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, - success: function(table_html) { - show_modal( - "Select Library Dataset", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Select": function() { - var names = []; - var ids = []; - counter = 1; - $('input[name=ldda_ids]:checked').each(function() { - var name = $.trim( $(this).siblings("label").text() ); - var id = $(this).val(); - names.push( counter + ". " + name ); - counter += 1; - ids.push(id); - }); - link.html( names.join("<br/>") ); - link.siblings("input[type=hidden]").val( ids.join("||") ); - hide_modal(); - } - } - ); - } - }); - }); - }); + %if not add_frame.debug: + if( window.name != "galaxy_main" ) { + location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); + } + %endif - %if not add_frame.debug: - if( window.name != "galaxy_main" ) { - location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); - } + </script> + + </%def> + + <%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( tool_state, other_values ) + %> + %for input_index, input in enumerate( inputs.itervalues() ): + %if not input.visible: + <% pass %> + %elif input.type == "repeat": + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.title_plural}</strong> + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif + </div> + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + %if input.min < num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif + </div> + %if rep_errors.has_key( '__index__' ): + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> + %endif + %endfor + %if input.max > num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif + </div> + %elif input.type == "conditional": + <% + group_state = tool_state[input.name] + group_errors = errors.get( input.name, {} ) + current_case = group_state['__current_case__'] + group_prefix = prefix + input.name + "|" + %> + %if input.value_ref_in_group: + ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %endif + ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} + %else: + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %endif + %else: + ${row_for_param( prefix, input, tool_state, errors, other_values )} + %endif + %endfor + </%def> + + <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> + <% + if parent_errors.has_key( param.name ): + cls = "form-row form-row-error" + else: + cls = "form-row" + + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may + # be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if type( field_html ) is not unicode: + field_html = unicode( field_html, 'utf-8', 'replace' ) + + if param.type == "hidden": + return field_html + %> + <div class="${cls}"> + ${label_for_param( param )} + ${input_for_param( param, field_html )} + ${errors_for_param( param, parent_errors )} + ${help_for_param( param )} + <div style="clear: both;"></div> + </div> + </%def> + + <%def name="input_for_param( param, field_html )"> + <div class="form-row-input">${field_html}</div> + </%def> + + <%def name="label_for_param( param )"> + <% label = param.get_label()%> + %if label: + <label for="${param.name}">${label}:</label> + %endif + </%def> + + <%def name="errors_for_param( param, parent_errors )"> + %if parent_errors.has_key( param.name ): + <div class="form-row-error-message"> + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + </div> + %endif + </%def> + + <%def name="help_for_param( param )"> + %if param.help: + <div class="toolParamHelp" style="clear: both;"> + ${param.help} + </div> + %endif + </%def> + + <%def name="row_for_rerun()"> + %if trans.app.config.track_jobs_in_database and tool_state.rerun_remap_job_id is not None: + <div id="remap-row" class="form-row"> + <input type="checkbox" name="rerun_remap_job_id" value="${tool_state.rerun_remap_job_id}"> Resume dependencies from this job + <div class="toolParamHelp" style="clear: both;"> + The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run. + </div> + </div> + <div style="clear: both;"></div> + %endif + </%def> + + <% overlay(visible=False) %> + + %if add_frame.from_noframe: + <div class="warningmessage"> + <strong>Welcome to Galaxy</strong> + <hr/> + It appears that you found this tool from a link outside of Galaxy. + If you're not familiar with Galaxy, please consider visiting the + <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. + To learn more about what Galaxy is and what it can do for you, please visit + the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. + </div> + <br/> %endif - </script> + <% + # Render an error message if a dynamically generated select list is missing a required + # index file or entry in the tool_data_table_conf.xml file. + message = "" + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file -</%def> + # Handle calculating the redirect url for the special case where we have nginx proxy + # upload and need to do url_for on the redirect portion of the tool action. + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) + %> -<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"><% - from galaxy.util.expressions import ExpressionContext - other_values = ExpressionContext( tool_state, other_values ) + # Name of the tool in lower case + low_tool_name = tool.name.lower() %> - %for input_index, input in enumerate( inputs.itervalues() ): - %if not input.visible: - <% pass %> - %elif input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.title_plural}</strong> - %if input.help: - <div class="toolParamHelp" style="clear: both;"> - ${input.help} - </div> - %endif - </div> - <% - repeat_state = tool_state[input.name] - num_repeats = len( repeat_state ) - %> - %for i in range( num_repeats ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] + + %if tool_id_version_message: + ${render_msg( tool_id_version_message, 'warning' )} + %endif + + <div class="toolForm" id="${tool.id}"> + <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> + %if tool.has_multiple_pages: + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) + %elif not tool_version_select_field: + <div class="toolFormTitle">${tool.name} (version ${tool.version}) + %else: + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} + %endif + + <span class="pull-right"> + %if trans.app.config.biostar_url: + ## BioStar links + Help from Biostar + <div class="icon-btn-group"> + <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a> + <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a> + </div> + %endif + <div class="icon-btn-group"> + <a href="#" data-link="${h.url_for( controller='root', action='index', tool_id=tool.id, qualified=True )}" + class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> + </div> + </span> + </div> + <div class="toolFormBody"> + <input type="hidden" name="refresh" value="refresh"> + <input type="hidden" name="tool_id" value="${tool.id}"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + %if tool.display_by_page[tool_state.page]: + ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} + ${row_for_rerun()} + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} + %if tool_state.page == tool.last_page: + ${row_for_rerun()} + %endif + <div class="form-row form-actions"> + %if tool_state.page == tool.last_page: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> + %endif + </div> + %endif + </div> + </form> + </div> + %if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - %if input.min < num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - %endif - </div> - %if rep_errors.has_key( '__index__' ): - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> - %endif - %endfor - %if input.max > num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - %endif - </div> - %elif input.type == "conditional": - <% - group_state = tool_state[input.name] - group_errors = errors.get( input.name, {} ) - current_case = group_state['__current_case__'] - group_prefix = prefix + input.name + "|" - %> - %if input.value_ref_in_group: - ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} - %endif - ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} - %elif input.type == "upload_dataset": - %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before - <% - if input.name in errors: - rep_errors = errors[input.name][0] - else: - rep_errors = dict() + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') %> - ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} - %else: - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> - <% - repeat_state = tool_state[input.name] - %> - %for i in range( len( repeat_state ) ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - </div> - %endfor - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - </div> - %endif - %else: - ${row_for_param( prefix, input, tool_state, errors, other_values )} - %endif - %endfor -</%def> - -<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> - <% - if parent_errors.has_key( param.name ): - cls = "form-row form-row-error" - else: - cls = "form-row" - - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change - - # Field may contain characters submitted by user and these characters may - # be unicode; handle non-ascii characters gracefully. - field_html = field.get_html( prefix ) - if type( field_html ) is not unicode: - field_html = unicode( field_html, 'utf-8', 'replace' ) - - if param.type == "hidden": - return field_html - %> - <div class="${cls}"> - ${label_for_param( param )} - ${input_for_param( param, field_html )} - ${errors_for_param( param, parent_errors )} - ${help_for_param( param )} - <div style="clear: both;"></div> - </div> -</%def> - -<%def name="input_for_param( param, field_html )"> - <div class="form-row-input">${field_html}</div> -</%def> - -<%def name="label_for_param( param )"> - <% label = param.get_label()%> - %if label: - <label for="${param.name}">${label}:</label> - %endif -</%def> - -<%def name="errors_for_param( param, parent_errors )"> - %if parent_errors.has_key( param.name ): - <div class="form-row-error-message"> - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + ${tool_help} + </div></div> %endif -</%def> - -<%def name="help_for_param( param )"> - %if param.help: - <div class="toolParamHelp" style="clear: both;"> - ${param.help} + %if tool.tool_shed_repository: + <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %> + %if tool_url: + <br/> + ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) } + %endif + %endif + %if tool.citations: + <script> + require(["mvc/citation/citation-model", "mvc/citation/citation-view" + ], function( citationModel, citationView ){ + $(function() { + var citations = new citationModel.ToolCitationCollection(); + citations.tool_id = "${tool.id}"; + var citation_list_view = new citationView.CitationListView({ collection: citations } ); + citation_list_view.render(); + citations.fetch(); + } ); + } ); + </script> + <div id="citations"></div> %endif -</%def> - -<%def name="row_for_rerun()"> - %if trans.app.config.track_jobs_in_database and tool_state.rerun_remap_job_id is not None: - <div id="remap-row" class="form-row"> - <input type="checkbox" name="rerun_remap_job_id" value="${tool_state.rerun_remap_job_id}"> Resume dependencies from this job - <div class="toolParamHelp" style="clear: both;"> - The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run. - </div> - </div> - <div style="clear: both;"></div> - %endif -</%def> - -<% overlay(visible=False) %> - -%if add_frame.from_noframe: - <div class="warningmessage"> - <strong>Welcome to Galaxy</strong> - <hr/> - It appears that you found this tool from a link outside of Galaxy. - If you're not familiar with Galaxy, please consider visiting the - <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. - To learn more about what Galaxy is and what it can do for you, please visit - the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. - </div> - <br/> -%endif - -<% - # Render an error message if a dynamically generated select list is missing a required - # index file or entry in the tool_data_table_conf.xml file. - message = "" - params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry - params_with_missing_index_file = tool.params_with_missing_index_file - if params_with_missing_data_table_entry: - param = params_with_missing_data_table_entry[0] - message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name - if tool.params_with_missing_index_file: - param = params_with_missing_index_file[0] - message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file - - # Handle calculating the redirect url for the special case where we have nginx proxy - # upload and need to do url_for on the redirect portion of the tool action. - try: - tool_url = h.url_for(tool.action) - except AttributeError: - assert len(tool.action) == 2 - tool_url = tool.action[0] + h.url_for(tool.action[1]) -%> - -<% - # Name of the tool in lower case - low_tool_name = tool.name.lower() -%> - -%if tool_id_version_message: - ${render_msg( tool_id_version_message, 'warning' )} -%endif - -<div class="toolForm" id="${tool.id}"> - <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) - %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version}) - %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} - %endif - - <span class="pull-right"> - %if trans.app.config.biostar_url: - ## BioStar links - Help from Biostar - <div class="icon-btn-group"> - <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}" - target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a> - <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" - target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a> - </div> - %endif - <div class="icon-btn-group"> - <a href="#" data-link="${h.url_for( controller='root', action='index', tool_id=tool.id, qualified=True )}" - class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> - </div> - </span> - </div> - <div class="toolFormBody"> - <input type="hidden" name="refresh" value="refresh"> - <input type="hidden" name="tool_id" value="${tool.id}"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - %if tool.display_by_page[tool_state.page]: - ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} - ${row_for_rerun()} - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} - %if tool_state.page == tool.last_page: - ${row_for_rerun()} - %endif - <div class="form-row form-actions"> - %if tool_state.page == tool.last_page: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> - %endif - </div> - %endif - </div> - </form> -</div> -%if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - %> - ${tool_help} - </div> - </div> -%endif -%if tool.tool_shed_repository: - <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %> - %if tool_url: - <br/> - ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) } - %endif -%endif -%if tool.citations: - <script> - require(["mvc/citation/citation-model", "mvc/citation/citation-view" - ], function( citationModel, citationView ){ - $(function() { - var citations = new citationModel.ToolCitationCollection(); - citations.tool_id = "${tool.id}"; - var citation_list_view = new citationView.CitationListView({ collection: citations } ); - citation_list_view.render(); - citations.fetch(); - } ); - } ); - </script> - <div id="citations"> - </div> -%endif - +</div> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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