From e3b63e16d08fe08556bc690eaf5eec3e00b8aaae Mon Sep 17 00:00:00 2001 From: vjalili Date: Wed, 11 Apr 2018 12:09:13 -0700 Subject: [PATCH 001/352] Add migration script for cloudauthz table. --- .../versions/0142_add_cloudauthz_tables.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py diff --git a/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py b/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py new file mode 100644 index 00000000000..904850f3af0 --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py @@ -0,0 +1,44 @@ +""" +Migration script to add a new tables for CloudAuthz (tokens required to access cloud-based resources). +""" +from __future__ import print_function + +import logging + +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table + +from galaxy.model.custom_types import JSONType + +log = logging.getLogger(__name__) +metadata = MetaData() + +cloudauthz = Table( + "cloudauthz", metadata, + Column('id', Integer, primary_key=True), + Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True), + Column('provider', String(255)), + Column('config', JSONType), + Column('tokens', JSONType), + Column('last_update', DateTime), + Column('last_activity', DateTime)) + + +def upgrade(migrate_engine): + print(__doc__) + metadata.bind = migrate_engine + metadata.reflect() + + try: + cloudauthz.create() + except Exception as e: + log.exception("Failed to create cloudauthz table: {}".format(str(e))) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + + try: + cloudauthz.drop() + except Exception as e: + log.exception("Failed to drop cloudauthz table: {}".format(str(e))) From c25e69253f105b9f20ed1b114e5bfdeecad60310 Mon Sep 17 00:00:00 2001 From: vjalili Date: Wed, 11 Apr 2018 15:15:58 -0700 Subject: [PATCH 002/352] Add CloudAuthz class to model. --- lib/galaxy/model/__init__.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index daae3897dc4..a85a586cc3e 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -4687,6 +4687,16 @@ class UserAuthnzToken(UserMixin): return instance +class CloudAuthz(object): + def __init__(self, user, provider, config): + self.user = user + self.provider = provider + self.config = config + self.tokens = None + self.last_update = datetime.now() + self.last_activity = datetime.now() + + class Page(Dictifiable): dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted'] From dd9e8a5e6258ab14c7481691c3b5e6ef54c00836 Mon Sep 17 00:00:00 2001 From: vjalili Date: Wed, 11 Apr 2018 15:16:42 -0700 Subject: [PATCH 003/352] Add CloudAuthz to mapping. --- lib/galaxy/model/mapping.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index a46a0af3d6a..6f82ab225af 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -133,6 +133,16 @@ model.UserAuthnzToken.table = Table( Column('lifetime', Integer), Column('assoc_type', VARCHAR(64))) +model.CloudAuthz.table = Table( + "cloudauthz", metadata, + Column('id', Integer, primary_key=True), + Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True), + Column('provider', String(255)), + Column('config', JSONType), + Column('tokens', JSONType), + Column('last_update', DateTime), + Column('last_activity', DateTime)) + model.PasswordResetToken.table = Table( "password_reset_token", metadata, Column("token", String(32), primary_key=True, unique=True, index=True), @@ -1477,6 +1487,12 @@ mapper(model.UserAuthnzToken, model.UserAuthnzToken.table, properties=dict( backref='social_auth') )) +mapper(model.CloudAuthz, model.CloudAuthz.table, properties=dict( + user=relation(model.User, + primaryjoin=(model.CloudAuthz.table.c.user_id == model.User.table.c.id), + backref='cloudauthz') +)) + mapper(model.ValidationError, model.ValidationError.table) simple_mapping(model.HistoryDatasetAssociation, From 14288a2b150d49e46577c2e8238e93d927548202 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 13:55:51 -0700 Subject: [PATCH 004/352] Add authn_id and user_id to cloudauthz. --- lib/galaxy/model/__init__.py | 5 +++-- lib/galaxy/model/mapping.py | 6 +++++- .../model/migrate/versions/0142_add_cloudauthz_tables.py | 1 + 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index a85a586cc3e..fb6e176d234 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -4688,10 +4688,11 @@ class UserAuthnzToken(UserMixin): class CloudAuthz(object): - def __init__(self, user, provider, config): - self.user = user + def __init__(self, user_id, provider, config, authn_id): + self.user_id = user_id self.provider = provider self.config = config + self.authn_id = authn_id self.tokens = None self.last_update = datetime.now() self.last_activity = datetime.now() diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index 6f82ab225af..8550cc30022 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -139,6 +139,7 @@ model.CloudAuthz.table = Table( Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True), Column('provider', String(255)), Column('config', JSONType), + Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True), Column('tokens', JSONType), Column('last_update', DateTime), Column('last_activity', DateTime)) @@ -1490,7 +1491,10 @@ mapper(model.UserAuthnzToken, model.UserAuthnzToken.table, properties=dict( mapper(model.CloudAuthz, model.CloudAuthz.table, properties=dict( user=relation(model.User, primaryjoin=(model.CloudAuthz.table.c.user_id == model.User.table.c.id), - backref='cloudauthz') + backref='cloudauthz'), + authn=relation(model.UserAuthnzToken, + primaryjoin=(model.CloudAuthz.table.c.authn_id == model.UserAuthnzToken.table.c.id), + backref='cloudauthz') )) mapper(model.ValidationError, model.ValidationError.table) diff --git a/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py b/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py index 904850f3af0..7f47e083cb7 100644 --- a/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py +++ b/lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py @@ -18,6 +18,7 @@ cloudauthz = Table( Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True), Column('provider', String(255)), Column('config', JSONType), + Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True), Column('tokens', JSONType), Column('last_update', DateTime), Column('last_activity', DateTime)) From 7f5a59d1347af33285b7e6df5955cedf9d456221 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 14:00:07 -0700 Subject: [PATCH 005/352] Add cloudauthz api and manger, and define a route for API calls. --- lib/galaxy/managers/cloudauthzs.py | 20 ++++++ lib/galaxy/webapps/galaxy/api/cloudauthz.py | 80 +++++++++++++++++++++ lib/galaxy/webapps/galaxy/buildapp.py | 3 + 3 files changed, 103 insertions(+) create mode 100644 lib/galaxy/managers/cloudauthzs.py create mode 100644 lib/galaxy/webapps/galaxy/api/cloudauthz.py diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py new file mode 100644 index 00000000000..8be08f56a0c --- /dev/null +++ b/lib/galaxy/managers/cloudauthzs.py @@ -0,0 +1,20 @@ +""" +Manager and serializer for cloud authorizations (cloudauthzs). +""" + +import logging + +from galaxy import model +from galaxy.managers import sharable +from galaxy.managers import deletable + +og = logging.getLogger(__name__) + + +class CloudAuthzManager(sharable.SharableModelManager): + + model_class = model.CloudAuthz + foreign_key_name = 'cloudauthz' + + def __init__(self, app, *args, **kwargs): + super(CloudAuthzManager, self).__init__(app, *args, **kwargs) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py new file mode 100644 index 00000000000..002c3a0c866 --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -0,0 +1,80 @@ +""" +API operations on defining cloud authorizations. +""" + +import logging + +from galaxy import web +from galaxy.managers import cloudauthzs +from galaxy.web.base.controller import BaseAPIController + +log = logging.getLogger(__name__) + + +class CloudAuthzController(BaseAPIController): + """ + RESTfull controller for defining cloud authorizations. + """ + + def __init__(self, app): + super(CloudAuthzController, self).__init__(app) + self.cloudauthzs_manager = cloudauthzs.CloudAuthzManager(app) + + @web.expose_api + def index(self, trans, **kwargs): + """ + + :param trans: + :param kwargs: + :return: + """ + pass + + @web.expose_api + def create(self, trans, payload, **kwargs): + """ + + :param trans: + :param payload: + :param kwargs: + :return: + """ + if not isinstance(payload, dict): + trans.response.status = 400 + return {'status': '400', + 'message': 'Invalid payload data type. The payload is expected to be a dictionary, ' + 'but received data of type `{}`.'.format(str(type(payload)))} + + missing_arguments = [] + provider = payload.get('provider', None) + if provider is None: + missing_arguments.append('provider') + + config = payload.get('config', None) + if config is None: + missing_arguments.append('config') + + authn_id = payload.get('authn_id', None) + if authn_id is None: + missing_arguments.append('authn_id') + + if len(missing_arguments) > 0: + trans.response.status = 400 + return {'status': '400', + 'message': 'The following required arguments are missing in the payload: {}'.format(missing_arguments)} + + try: + new_cloudauthz = self.cloudauthzs_manager.create( + user_id=trans.user.id, + provider=provider, + config=config, + authn_id=authn_id + ) + + log.debug('Created a new cloudauthz record for the user id `{}` '.format(str(trans.user.id))) + trans.response.status = '200' + return None + + except Exception as e: + log.exception('An unexpected error has occurred while responding to the create request of the cloudauthz API. ' + str(e)) + trans.response.status = '500 Internal Server Error' diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index a14865185b7..7e24afcd56d 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -268,6 +268,9 @@ def populate_api_routes(webapp, app): webapp.mapper.resource('group', 'groups', path_prefix='/api') webapp.mapper.resource_with_deleted('quota', 'quotas', path_prefix='/api') + webapp.mapper.connect('/api/cloud/authz/create', action='create', controller='cloudauthz') + webapp.mapper.resource('cloudauthz', 'cloudauthz', path_prefix='/api') + webapp.mapper.connect('get_custom_builds_metadata', '/api/histories/{id}/custom_builds_metadata', controller='histories', From c6af14ba28e1f36fef4008b57595e90e1282e5cd Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 14:46:25 -0700 Subject: [PATCH 006/352] Add CloudAuthz summary view serializer. --- lib/galaxy/managers/cloudauthzs.py | 43 +++++++++++++++++++++ lib/galaxy/webapps/galaxy/api/cloudauthz.py | 4 +- 2 files changed, 45 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py index 8be08f56a0c..70556e98043 100644 --- a/lib/galaxy/managers/cloudauthzs.py +++ b/lib/galaxy/managers/cloudauthzs.py @@ -5,6 +5,7 @@ Manager and serializer for cloud authorizations (cloudauthzs). import logging from galaxy import model +from galaxy.managers import base from galaxy.managers import sharable from galaxy.managers import deletable @@ -18,3 +19,45 @@ class CloudAuthzManager(sharable.SharableModelManager): def __init__(self, app, *args, **kwargs): super(CloudAuthzManager, self).__init__(app, *args, **kwargs) + + +class CloudAuthzsSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin): # sharable.SharableModelSerializer, deletable.PurgableSerializerMixin): + """ + Interface/service object for serializing cloud authorizations (cloudauthzs) into dictionaries. + """ + model_manager_class = CloudAuthzManager + + def __init__(self, app, **kwargs): + super(CloudAuthzsSerializer, self).__init__(app, **kwargs) + self.cloudauthzs_manager = self.manager + + self.default_view = 'summary' + self.add_view('summary', [ + 'id', + 'model_class', + 'user_id', + 'provider', + 'config', + 'authn_id', + 'last_update', + 'last_activity' + ]) + + def add_serializers(self): + super(CloudAuthzsSerializer, self).add_serializers() + deletable.PurgableSerializerMixin.add_serializers(self) + + # Arguments of the following lambda functions: + # i : an instance of galaxy.model.CloudAuthz. + # k : serialized dictionary key (e.g., 'model_class', 'provider'). + # **c: a dictionary containing 'trans' and 'user' objects. + self.serializers.update({ + 'id' : lambda i, k, **c: self.app.security.encode_id(i.id), + 'model_class' : lambda *a, **c: 'CloudAuthz', + 'user_id' : lambda i, k, **c: self.app.security.encode_id(i.user_id), + 'provider' : lambda i, k, **c: str(i.provider), + 'config' : lambda i, k, **c: str(i.config), + 'authn_id' : lambda i, k, **c: self.app.security.encode_id(i.authn_id), + 'last_update' : lambda i, k, **c: str(i.last_update), + 'last_activity': lambda i, k, **c: str(i.last_activity) + }) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 002c3a0c866..4f72ecd0ad5 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -70,10 +70,10 @@ class CloudAuthzController(BaseAPIController): config=config, authn_id=authn_id ) - + view = self.cloudauthzs_serializer.serialize_to_view(new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary')) log.debug('Created a new cloudauthz record for the user id `{}` '.format(str(trans.user.id))) trans.response.status = '200' - return None + return view except Exception as e: log.exception('An unexpected error has occurred while responding to the create request of the cloudauthz API. ' + str(e)) From ee255be84748748bfd01e6862fed0c2970f55ac2 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 14:47:03 -0700 Subject: [PATCH 007/352] Fix a bug in CloudAuthz summary view serializer. --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 4f72ecd0ad5..2af84e1dbdc 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -19,6 +19,7 @@ class CloudAuthzController(BaseAPIController): def __init__(self, app): super(CloudAuthzController, self).__init__(app) self.cloudauthzs_manager = cloudauthzs.CloudAuthzManager(app) + self.cloudauthzs_serializer = cloudauthzs.CloudAuthzsSerializer(app) @web.expose_api def index(self, trans, **kwargs): From 5bf003011a5efc8eb9d02d61170e23bbd1481c81 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 15:27:12 -0700 Subject: [PATCH 008/352] Update CloudAuthz index; return all the cloudauthz records for a user. --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 2af84e1dbdc..93751de4b1b 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -29,7 +29,11 @@ class CloudAuthzController(BaseAPIController): :param kwargs: :return: """ - pass + rtv = [] + for cloudauthz in trans.user.cloudauthz: + rtv.append(self.cloudauthzs_serializer.serialize_to_view( + cloudauthz, user=trans.user, trans=trans, **self._parse_serialization_params(kwargs, 'summary'))) + return rtv @web.expose_api def create(self, trans, payload, **kwargs): From 6f043824978bccdc208929c84ac7ca83f00ca9f5 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 15:34:12 -0700 Subject: [PATCH 009/352] Change router for cloudauthz index. --- lib/galaxy/webapps/galaxy/buildapp.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index 7e24afcd56d..74eff9e6327 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -268,8 +268,8 @@ def populate_api_routes(webapp, app): webapp.mapper.resource('group', 'groups', path_prefix='/api') webapp.mapper.resource_with_deleted('quota', 'quotas', path_prefix='/api') + webapp.mapper.connect('/api/cloud/authz/', action='index', controller='cloudauthz') webapp.mapper.connect('/api/cloud/authz/create', action='create', controller='cloudauthz') - webapp.mapper.resource('cloudauthz', 'cloudauthz', path_prefix='/api') webapp.mapper.connect('get_custom_builds_metadata', '/api/histories/{id}/custom_builds_metadata', From 8a980b1f7f7e2aa3b16ce66e1852be14e2d784c1 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 16 Apr 2018 16:06:40 -0700 Subject: [PATCH 010/352] Refactoring *thzs -> *thz; remove (s). --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 93751de4b1b..24c4651ed51 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -18,8 +18,8 @@ class CloudAuthzController(BaseAPIController): def __init__(self, app): super(CloudAuthzController, self).__init__(app) - self.cloudauthzs_manager = cloudauthzs.CloudAuthzManager(app) - self.cloudauthzs_serializer = cloudauthzs.CloudAuthzsSerializer(app) + self.cloudauthz_manager = cloudauthzs.CloudAuthzManager(app) + self.cloudauthz_serializer = cloudauthzs.CloudAuthzsSerializer(app) @web.expose_api def index(self, trans, **kwargs): @@ -31,7 +31,7 @@ class CloudAuthzController(BaseAPIController): """ rtv = [] for cloudauthz in trans.user.cloudauthz: - rtv.append(self.cloudauthzs_serializer.serialize_to_view( + rtv.append(self.cloudauthz_serializer.serialize_to_view( cloudauthz, user=trans.user, trans=trans, **self._parse_serialization_params(kwargs, 'summary'))) return rtv @@ -69,13 +69,13 @@ class CloudAuthzController(BaseAPIController): 'message': 'The following required arguments are missing in the payload: {}'.format(missing_arguments)} try: - new_cloudauthz = self.cloudauthzs_manager.create( + new_cloudauthz = self.cloudauthz_manager.create( user_id=trans.user.id, provider=provider, config=config, authn_id=authn_id ) - view = self.cloudauthzs_serializer.serialize_to_view(new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary')) + view = self.cloudauthz_serializer.serialize_to_view(new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary')) log.debug('Created a new cloudauthz record for the user id `{}` '.format(str(trans.user.id))) trans.response.status = '200' return view From 7760c98953524e6e5355f7ca678759dd7f2977d9 Mon Sep 17 00:00:00 2001 From: vjalili Date: Tue, 17 Apr 2018 09:39:50 -0700 Subject: [PATCH 011/352] Assess cloudauthz config type in API before passing it to its manager. --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 24c4651ed51..48d0ea8be9b 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -68,6 +68,10 @@ class CloudAuthzController(BaseAPIController): return {'status': '400', 'message': 'The following required arguments are missing in the payload: {}'.format(missing_arguments)} + if not isinstance(config, dict): + return {'status': '400', + 'message': 'Invalid type for the required `config` variable; expect `dict` but received `{}`.'.format(type(config))} + try: new_cloudauthz = self.cloudauthz_manager.create( user_id=trans.user.id, From 193b73f26ecb661a4fb180a64806a0c7f0c6a2ba Mon Sep 17 00:00:00 2001 From: vjalili Date: Tue, 17 Apr 2018 10:09:04 -0700 Subject: [PATCH 012/352] Fix a wrong order of imports. --- lib/galaxy/managers/cloudauthzs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py index 70556e98043..3767c5adbf4 100644 --- a/lib/galaxy/managers/cloudauthzs.py +++ b/lib/galaxy/managers/cloudauthzs.py @@ -6,8 +6,8 @@ import logging from galaxy import model from galaxy.managers import base -from galaxy.managers import sharable from galaxy.managers import deletable +from galaxy.managers import sharable og = logging.getLogger(__name__) From 0585f73384221cc024a62ecb1857f53670ced091 Mon Sep 17 00:00:00 2001 From: vjalili Date: Tue, 17 Apr 2018 10:56:59 -0700 Subject: [PATCH 013/352] Update cloudauthz API documentation. --- lib/galaxy/managers/cloudauthzs.py | 2 +- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 42 +++++++++++++++++---- 2 files changed, 36 insertions(+), 8 deletions(-) diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py index 3767c5adbf4..86a4dd90534 100644 --- a/lib/galaxy/managers/cloudauthzs.py +++ b/lib/galaxy/managers/cloudauthzs.py @@ -21,7 +21,7 @@ class CloudAuthzManager(sharable.SharableModelManager): super(CloudAuthzManager, self).__init__(app, *args, **kwargs) -class CloudAuthzsSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin): # sharable.SharableModelSerializer, deletable.PurgableSerializerMixin): +class CloudAuthzsSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin): """ Interface/service object for serializing cloud authorizations (cloudauthzs) into dictionaries. """ diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 48d0ea8be9b..5cfab023782 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -1,5 +1,11 @@ """ API operations on defining cloud authorizations. + +Through means of cloud authorization a user is able to grant a Galaxy server a secure access to his/her +cloud-based resources without sharing his/her long-lasting credentials. + +User provides a provider-specific configuration, which Galaxy users to request temporary credentials +from the provider to access the user's resources. """ import logging @@ -24,10 +30,16 @@ class CloudAuthzController(BaseAPIController): @web.expose_api def index(self, trans, **kwargs): """ + * GET /api/cloud/authz + Lists all the cloud authorizations user has defined. - :param trans: - :param kwargs: - :return: + :type trans: galaxy.web.framework.webapp.GalaxyWebTransaction + :param trans: Galaxy web transaction + + :param kwargs: empty dict + + :rtype: list of dict + :return: a list of cloud authorizations (each represented in key-value pair format) defined for the user. """ rtv = [] for cloudauthz in trans.user.cloudauthz: @@ -38,11 +50,27 @@ class CloudAuthzController(BaseAPIController): @web.expose_api def create(self, trans, payload, **kwargs): """ + * POST /api/cloud/authz/create + Request to store the payload as a cloudauthz (cloud authorization) configuration for a user. - :param trans: - :param payload: - :param kwargs: - :return: + :type trans: galaxy.web.framework.webapp.GalaxyWebTransaction + :param trans: Galaxy web transaction + + :type payload: dict + :param payload: A dictionary structure containing the following keys: + * provider: the cloud-based resource provider to which this configuration belongs to. + * config: a dictionary containing all the configuration required to request temporary credentials + from the provider. + * authn_id: the (encoded) ID of a third-party authentication of a user. To have this ID, user must + have logged-in to this Galaxy server using third-party identity (e.g., Google), or has + associated his/her Galaxy account with a third-party OIDC-based identity. See this page: + https://galaxyproject.org/admin/authentication/ + :param kwargs: empty dict + + :rtype: dict + :return: a dictionary with the following kvp: + * status: HTTP response code + * message: A message complementary to the response code. """ if not isinstance(payload, dict): trans.response.status = 400 From 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 19 Apr 2018 12:35:25 +0200 Subject: [PATCH 014/352] Allow schema to validate --- lib/galaxy/webapps/galaxy/config_schema.yml | 99 ++++++++++----------- 1 file changed, 48 insertions(+), 51 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index edb3fd1720f..5bc7b1de92e 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -45,7 +45,7 @@ mapping: cookie_path: type: str - default: null + default: '' required: false desc: | If proxy-prefix is enabled and you're running more than one Galaxy instance @@ -109,7 +109,7 @@ mapping: database_template: type: str - default: null + default: '' required: false desc: | If auto-creating a postgres database on startup - it can be based on an existing @@ -332,7 +332,7 @@ mapping: watch_tools: type: str - default: false + default: 'false' required: false desc: | Set to True to enable monitoring of tools and tool directories @@ -359,7 +359,7 @@ mapping: containers_resolvers_config_file: type: str - default: null + default: '' required: false desc: | Container resolvers configuration (beta). Setup a file describing container @@ -455,7 +455,7 @@ mapping: watch_tool_data_dir: type: str - default: false + default: 'false' required: false desc: | Set to True to enable monitoring of the tool_data and shed_tool_data_path @@ -607,7 +607,7 @@ mapping: Number of checks to execute if check_job_script_integrity is enabled. check_job_script_integrity_sleep: - type: str + type: float default: .25 required: false desc: | @@ -674,7 +674,7 @@ mapping: smtp_server: type: str - default: null + default: '' required: false desc: | Galaxy sends mail for various things: subscribing users to the mailing list @@ -685,7 +685,7 @@ mapping: smtp_username: type: str - default: null + default: '' required: false desc: | If your SMTP server requires a username and password, you can provide them @@ -694,7 +694,7 @@ mapping: smtp_password: type: str - default: null + default: '' required: false desc: | If your SMTP server requires a username and password, you can provide them @@ -719,7 +719,7 @@ mapping: error_email_to: type: str - default: null + default: '' required: false desc: | Datasets in an error state include a link to report the error. Those reports @@ -729,7 +729,7 @@ mapping: email_from: type: str - default: null + default: '' required: false desc: | Email address to use in the 'From' field when sending emails for @@ -813,7 +813,7 @@ mapping: ga_code: type: str - default: null + default: '' required: false desc: | You can enter tracking code here to track visitor's behavior @@ -865,7 +865,7 @@ mapping: message_box_content: type: str - default: null + default: '' required: false desc: | Show a message box under the masthead. @@ -879,7 +879,7 @@ mapping: brand: type: str - default: null + default: '' required: false desc: | Append "/{brand}" to the "Galaxy" text in the masthead. @@ -955,21 +955,21 @@ mapping: biostar_url: type: str - default: null + default: '' required: false desc: | Enable integration with a custom Biostar instance. biostar_key_name: type: str - default: null + default: '' required: false desc: | Enable integration with a custom Biostar instance. biostar_key: type: str - default: null + default: '' required: false desc: | Enable integration with a custom Biostar instance. @@ -1026,7 +1026,7 @@ mapping: terms_url: type: str - default: null + default: '' required: false desc: | The URL linked by the "Terms and Conditions" link in the "Help" menu, as well @@ -1140,7 +1140,7 @@ mapping: nginx_x_accel_redirect_base: type: str - default: null + default: '' required: false desc: | The same download handling can be done by nginx using X-Accel-Redirect. This @@ -1172,7 +1172,7 @@ mapping: nginx_upload_store: type: str - default: null + default: '' required: false desc: | nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. @@ -1182,7 +1182,7 @@ mapping: nginx_upload_path: type: str - default: null + default: '' required: false desc: | This value overrides the action set on the file upload form, e.g. the web @@ -1191,7 +1191,7 @@ mapping: nginx_upload_job_files_store: type: str - default: null + default: '' required: false desc: | Galaxy can also use nginx_upload_module to receive files staged out upon job @@ -1201,7 +1201,7 @@ mapping: nginx_upload_job_files_path: type: str - default: null + default: '' required: false desc: | Galaxy can also use nginx_upload_module to receive files staged out upon job @@ -1307,7 +1307,7 @@ mapping: dynamic_proxy_golang_api_key: type: str - default: null + default: '' required: false desc: | The golang proxy uses a RESTful HTTP API for communication with Galaxy @@ -1332,15 +1332,6 @@ mapping: https://docs.python.org/2/library/logging.html#logging-levels A custom debug level of "TRACE" is available for even more verbosity. - logging: - type: map - default: galaxy.config.LOGGING_CONFIG_DEFAULT - desc: | - Controls where and how the server logs messages. If unset, the default is to log all messages to standard - output at the level defined by the `log_level` configuration option. Configuration is described in the - documentation at: - https://docs.galaxyproject.org/en/master/admin/config_logging.html - database_engine_option_echo: type: bool default: false @@ -1427,7 +1418,7 @@ mapping: allowed_origin_hostnames: type: str - default: null + default: '' required: false desc: | Return a Access-Control-Allow-Origin response header that matches the Origin @@ -1524,7 +1515,7 @@ mapping: sentry_dsn: type: str - default: null + default: '' required: false desc: | Log to Sentry @@ -1605,7 +1596,7 @@ mapping: library_import_dir: type: str - default: null + default: '' required: false desc: | Add an option to the library upload form which allows administrators to @@ -1613,7 +1604,7 @@ mapping: user_library_import_dir: type: str - default: null + default: '' required: false desc: | Add an option to the library upload form which allows authorized @@ -1632,7 +1623,7 @@ mapping: user_library_import_symlink_whitelist: type: str - default: null + default: '' required: false desc: | For security reasons, users may not import any files that actually lie @@ -1686,7 +1677,7 @@ mapping: tool_name_boost: type: float - default: 9 + default: 9.0 required: false desc: | Boosts are used to customize this instance's toolbox search. @@ -1696,7 +1687,7 @@ mapping: tool_section_boost: type: float - default: 3 + default: 3.0 required: false desc: | Boosts are used to customize this instance's toolbox search. @@ -1706,7 +1697,7 @@ mapping: tool_description_boost: type: float - default: 2 + default: 2.0 required: false desc: | Boosts are used to customize this instance's toolbox search. @@ -1716,7 +1707,7 @@ mapping: tool_label_boost: type: float - default: 1 + default: 1.0 required: false desc: | Boosts are used to customize this instance's toolbox search. @@ -1726,7 +1717,7 @@ mapping: tool_stub_boost: type: float - default: 5 + default: 5.0 required: false desc: | Boosts are used to customize this instance's toolbox search. @@ -1800,7 +1791,7 @@ mapping: remote_user_maildomain: type: str - default: null + default: '' required: false desc: | If use_remote_user is enabled and your external authentication @@ -1832,7 +1823,7 @@ mapping: remote_user_logout_href: type: str - default: null + default: '' required: false desc: | If use_remote_user is enabled, you can set this to a URL that will log your @@ -1859,7 +1850,7 @@ mapping: admin_users: type: str - default: null + default: '' required: false desc: | Administrative users - set this to a comma-separated list of valid Galaxy @@ -2065,7 +2056,7 @@ mapping: invocation to schedule indefinitely. The default corresponds to 1 month. maximum_workflow_jobs_per_scheduling_iteration: - type: str + type: int default: -1 required: false desc: | @@ -2117,7 +2108,7 @@ mapping: api_allow_run_as: type: str - default: null + default: '' required: false desc: | Optional list of email addresses of API users who can make calls on behalf of @@ -2163,7 +2154,7 @@ mapping: ftp_upload_dir: type: str - default: null + default: '' required: false desc: | Enable Galaxy's "Upload via FTP" interface. You'll need to install and @@ -2174,7 +2165,7 @@ mapping: ftp_upload_site: type: str - default: null + default: '' required: false desc: | This should be the hostname of your FTP server, which will be provided to @@ -2454,7 +2445,7 @@ mapping: environment_setup_file: type: str - default: null + default: '' required: false desc: | File to source to set up the environment when running jobs. By default, the @@ -2587,3 +2578,9 @@ mapping: desc: | persistent_communication_rooms is a comma-separated list of rooms that should be always available. + use_pbkdf2: + type: bool + default: false + required: false + desc: | + asdf From afa31d8b0978010e91724e86e2b08e9ffe698796 Mon Sep 17 00:00:00 2001 From: vjalili Date: Mon, 23 Apr 2018 15:47:06 -0700 Subject: [PATCH 015/352] Update exception handling in cloudauthz to leverage Galaxy.exceptions. --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 26 ++++++++++++--------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 5cfab023782..19ddaac9a23 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -11,6 +11,12 @@ from the provider to access the user's resources. import logging from galaxy import web +from galaxy.exceptions import ( + ActionInputError, + InternalServerError, + RequestParameterInvalidException, + RequestParameterMissingException +) from galaxy.managers import cloudauthzs from galaxy.web.base.controller import BaseAPIController @@ -73,10 +79,8 @@ class CloudAuthzController(BaseAPIController): * message: A message complementary to the response code. """ if not isinstance(payload, dict): - trans.response.status = 400 - return {'status': '400', - 'message': 'Invalid payload data type. The payload is expected to be a dictionary, ' - 'but received data of type `{}`.'.format(str(type(payload)))} + raise ActionInputError('Invalid payload data type. The payload is expected to be a dictionary, but ' + 'received data of type `{}`.'.format(str(type(payload)))) missing_arguments = [] provider = payload.get('provider', None) @@ -92,13 +96,12 @@ class CloudAuthzController(BaseAPIController): missing_arguments.append('authn_id') if len(missing_arguments) > 0: - trans.response.status = 400 - return {'status': '400', - 'message': 'The following required arguments are missing in the payload: {}'.format(missing_arguments)} + raise RequestParameterMissingException('The following required arguments are missing in the payload: ' + '{}'.format(missing_arguments)) if not isinstance(config, dict): - return {'status': '400', - 'message': 'Invalid type for the required `config` variable; expect `dict` but received `{}`.'.format(type(config))} + raise RequestParameterInvalidException('Invalid type for the required `config` variable; expect `dict` ' + 'but received `{}`.'.format(type(config))) try: new_cloudauthz = self.cloudauthz_manager.create( @@ -113,5 +116,6 @@ class CloudAuthzController(BaseAPIController): return view except Exception as e: - log.exception('An unexpected error has occurred while responding to the create request of the cloudauthz API. ' + str(e)) - trans.response.status = '500 Internal Server Error' + msg = 'An unexpected error has occurred while responding to the create request of the cloudauthz API.' + str(e) + log.exception(msg) + raise InternalServerError(msg) From bff2f9f9f72988ffec9b9f92b935f48e39b79423 Mon Sep 17 00:00:00 2001 From: vjalili Date: Fri, 27 Apr 2018 10:30:32 -0700 Subject: [PATCH 016/352] Decode and assert `authn_id` in cloudauthz API. --- lib/galaxy/webapps/galaxy/api/cloudauthz.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 19ddaac9a23..2c6d5a37c26 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -14,6 +14,7 @@ from galaxy import web from galaxy.exceptions import ( ActionInputError, InternalServerError, + MalformedId, RequestParameterInvalidException, RequestParameterMissingException ) @@ -102,6 +103,10 @@ class CloudAuthzController(BaseAPIController): if not isinstance(config, dict): raise RequestParameterInvalidException('Invalid type for the required `config` variable; expect `dict` ' 'but received `{}`.'.format(type(config))) + try: + authn_id = self.decode_id(authn_id) + except Exception: + raise MalformedId('Invalid `authn_id`!') try: new_cloudauthz = self.cloudauthz_manager.create( From 4a944cebe9bf94579cd06eb3a4f5d4a46004f2ab Mon Sep 17 00:00:00 2001 From: vjalili Date: Fri, 27 Apr 2018 18:47:59 -0700 Subject: [PATCH 017/352] Check if an `authn_id` exist & if user it belongs to the logged-in user. --- lib/galaxy/managers/cloudauthzs.py | 10 ++++++++++ lib/galaxy/webapps/galaxy/api/cloudauthz.py | 9 +++++++++ 2 files changed, 19 insertions(+) diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py index 86a4dd90534..fee86a4af47 100644 --- a/lib/galaxy/managers/cloudauthzs.py +++ b/lib/galaxy/managers/cloudauthzs.py @@ -4,6 +4,7 @@ Manager and serializer for cloud authorizations (cloudauthzs). import logging +from galaxy import exceptions from galaxy import model from galaxy.managers import base from galaxy.managers import deletable @@ -20,6 +21,15 @@ class CloudAuthzManager(sharable.SharableModelManager): def __init__(self, app, *args, **kwargs): super(CloudAuthzManager, self).__init__(app, *args, **kwargs) + def can_user_assume_authn(self, trans, authn_id): + qres = trans.sa_session.query(model.UserAuthnzToken).get(authn_id) + if qres is None: + raise exceptions.ObjectNotFound + if qres.user_id != trans.user.id: + og.critical('The user with ID:`{}` requested creation of a cloudauthz record and associating it with ' + 'the authnz record ID:`{}`, which belongs to another user.'.format(trans.user.id, authn_id)) + raise exceptions.ItemAccessibilityException + class CloudAuthzsSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin): """ diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 2c6d5a37c26..d1addcaa250 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -14,7 +14,9 @@ from galaxy import web from galaxy.exceptions import ( ActionInputError, InternalServerError, + ItemAccessibilityException, MalformedId, + ObjectNotFound, RequestParameterInvalidException, RequestParameterMissingException ) @@ -108,6 +110,13 @@ class CloudAuthzController(BaseAPIController): except Exception: raise MalformedId('Invalid `authn_id`!') + try: + self.cloudauthz_manager.can_user_assume_authn(trans, authn_id) + except ObjectNotFound: + raise ObjectNotFound('Authentication record with the given `authn_id` not found.') + except ItemAccessibilityException: + raise ItemAccessibilityException('The specified authentication with ID:`{}` belongs to another user.'.format(authn_id)) + try: new_cloudauthz = self.cloudauthz_manager.create( user_id=trans.user.id, From 0b95898ccf68b8497dff9f322b44abc5668dfce6 Mon Sep 17 00:00:00 2001 From: E Rasche Date: Tue, 1 May 2018 17:24:43 +0200 Subject: [PATCH 018/352] Document pbkdf2 --- lib/galaxy/webapps/galaxy/config_schema.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 5bc7b1de92e..c51609e60e1 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -2580,7 +2580,9 @@ mapping: use_pbkdf2: type: bool - default: false + default: true required: false desc: | - asdf + Allow disabling pbkdf2 hashing of passwords for legacy situations. + This should normally be left enabled unless there is a specific + reason to disable it. From 827e082bc521cfb287fc5572cdf386c6dc415d7e Mon Sep 17 00:00:00 2001 From: James Taylor Date: Sat, 30 Jun 2018 12:15:27 -0400 Subject: [PATCH 019/352] Initial work on updating styles --- client/galaxy/style/scss/base.scss | 53 +- .../scss/galaxy_bootstrap/variables.scss | 19 +- .../galaxy/style/scss/galaxy_variables.scss | 23 +- client/galaxy/style/scss/theme/blue.scss | 4 +- .../style/source_material/error_icon.svg | 1 + .../style/source_material/galaxy_icons.svg | 304 ++------ .../style/source_material/info_icon.svg | 1 + .../galaxy/style/source_material/ok_icon.svg | 1 + .../style/source_material/wait_icon.svg | 1 + .../style/source_material/warn_icon.svg | 1 + static/style/blue/base.css | 686 +++++++++--------- static/style/blue/library.css | 3 - 12 files changed, 472 insertions(+), 625 deletions(-) create mode 100644 client/galaxy/style/source_material/error_icon.svg create mode 100644 client/galaxy/style/source_material/info_icon.svg create mode 100644 client/galaxy/style/source_material/ok_icon.svg create mode 100644 client/galaxy/style/source_material/wait_icon.svg create mode 100644 client/galaxy/style/source_material/warn_icon.svg diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss index ae4afcc4b4a..a2e94d28ad5 100644 --- a/client/galaxy/style/scss/base.scss +++ b/client/galaxy/style/scss/base.scss @@ -159,13 +159,13 @@ body { } #left { left: 0px; - width: 250px; + width: $panel-width; z-index: 200; - border-right: solid $layout-border-color 1px; + border-right: $layout-border; } #center { - left: 250 + $border-default-color_padding; - right: 250 + $border-default-color_padding; + left: $panel-width; + right: $panel-width; overflow: hidden; z-index: 1; .center-container { @@ -189,10 +189,16 @@ body { } #right { - width: 250px; + width: $panel-width; right: 0px; z-index: 200; - border-left: solid $layout-border-color 1px; + border-left: $layout-border; +} + +#left, #right, .unified-panel { + background: $panel-bg-color; + display: flex; + flex-direction: column; } #left, #right, .unified-panel { @@ -207,7 +213,7 @@ body { z-index: 1000; text-shadow: rgba(255, 255, 255, 0.8) 0 1px 0; background: $panel-header-bg-color; - border-bottom: solid $layout-border-color 1px; + border-bottom: $layout-border; margin: 0; padding: 0; padding-right: 10px; @@ -256,15 +262,18 @@ body { } } +.unified-panel-controls { + padding: 0px 10px; +} + .unified-panel-footer { @extend .unselectable; - position: absolute; - bottom: 0; + position: relative; height: $panel_footer_height; line-height: $panel_footer_height; width: 100%; z-index: 1000; // Above #dd-helper - border-top: solid $layout-border-color 1px; + border-top: $layout-border; background: $navbar-default-bg; color: #555; @@ -317,14 +326,14 @@ body { line-height: $panel_footer_height; width: $panel_footer_height - 5; background: none; - border-right: solid $layout-border-color 1px; - border-top: solid $layout-border-color 1px; + border-right: $layout-border; + border-top: $layout-border; background: $navbar-default-bg; &.right { left: inherit; right: 0; border-right: none; - border-left: solid $border-default-color 1px; + border-left: $layout_border; &.right:before { content: "\f054"; } @@ -376,11 +385,11 @@ div.unified-panel-body-background { height: $panel-message-height; line-height: $panel-message-height; padding: 0px; - padding-left: 26px; + padding-left: 2.5rem; background-color: $state-danger-bg; background-image: url(error_small.png); background-repeat: no-repeat; - background-position: 6px 50%; + background-position: .5rem 50%; } .panel-warning-message { @@ -394,8 +403,12 @@ div.unified-panel-body-background { } .panel-info-message { - background-image: url(info_small.png); + background-image: url(info_icon.svg); + background-size: 1.5rem; background-color: $state-info-bg; + svg:path { + fill: black; + } } // Masthead @@ -1619,7 +1632,8 @@ div.toolSectionDetailsInner { } div.toolSectionTitle { - font-weight: bold; + font-weight: 500; + font-size: 1rem; } div.toolPanelLabel { @@ -1633,10 +1647,9 @@ div.toolPanelLabel { div.toolTitle { padding-top: 5px; padding-bottom: 5px; - margin-left: 16px; + margin-left: 10px; margin-right: 10px; - display: list-item; - list-style: square outside; + display: block; .labels { float: right; margin-left: 2px; diff --git a/client/galaxy/style/scss/galaxy_bootstrap/variables.scss b/client/galaxy/style/scss/galaxy_bootstrap/variables.scss index cd5c66c79ca..7375249ea51 100644 --- a/client/galaxy/style/scss/galaxy_bootstrap/variables.scss +++ b/client/galaxy/style/scss/galaxy_bootstrap/variables.scss @@ -65,10 +65,10 @@ $galaxy-bs3-info: #3189a3; // Lightening and saturating gets to alert backgrounds that are *very close* // to the Boostrap 3 Galaxy styles. $brand-primary: $galaxy-bs3-primary; -$brand-success: saturate(lighten($galaxy-bs3-success, 5%), 30%); -$brand-info: saturate(lighten($galaxy-bs3-info, 10%), 30%); -$brand-warning: saturate(lighten($galaxy-bs3-warning, 10%), 30%); -$brand-danger: saturate(lighten($galaxy-bs3-danger, 10%), 30%); +$brand-success: #66CC66; // saturate(lighten($galaxy-bs3-success, 5%), 30%); +$brand-info: #2077B3; // saturate(lighten($galaxy-bs3-info, 10%), 30%); +$brand-warning: #FE7F02; // saturate(lighten($galaxy-bs3-warning, 10%), 30%); +$brand-danger: #E31A1E; // These variables don't actually determine the colors in Bootstrap 4, instead // they use a map called $theme-colors, so here we override that @@ -93,7 +93,7 @@ $theme-color-interval: 5% !default; // Alerts and states -$alert-bg-level: -13 !default; +$alert-bg-level: -12 !default; $alert-border-level: -6 !default; $alert-color-level: 8 !default; @@ -119,19 +119,18 @@ $state-success-border: theme-color-level("success", $alert-border-level); // Body text and link colors $body-bg: $white; -$text-color: $gray-dark; +$text-color: $gray-900; -$link-color: #303030; +$link-color: $black; $link-hover-color: darken($link-color, 15%); // Fonts and sizes -$font-family-sans-serif: "Lucida Grande", verdana, arial, helvetica, sans-serif; //JT "Helvetica Neue", Helvetica, Arial, sans-serif; -//$font-family-serif: Georgia, "Times New Roman", Times, serif; +$font-family-sans-serif: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; $font-family-monospace: Monaco, Menlo, Consolas, "Courier New", monospace; $font-family-base: $font-family-sans-serif; -$font-size-base: 0.75rem; // default 1rem +$font-size-base: 0.8rem; // default 1rem $h1-font-size: $font-size-base * 2; // default 2.5 $h2-font-size: $font-size-base * 1.75; // default 2 diff --git a/client/galaxy/style/scss/galaxy_variables.scss b/client/galaxy/style/scss/galaxy_variables.scss index 1994893762f..816ced18420 100644 --- a/client/galaxy/style/scss/galaxy_variables.scss +++ b/client/galaxy/style/scss/galaxy_variables.scss @@ -1,31 +1,36 @@ // Additional variables that are not used by bootstrap but are used // in Galaxy stylesheets -$base-bg: $white; -$base-text-color: $black; +$base-bg: $body-bg; +$base-text-color: $text-color; // Masthead -$masthead-height: 2.5rem; +$masthead-height: 3rem; // Side panels -$panel-bg-color: #dfe5f9; +$panel-bg-color: $gray-100; // #dfe5f9; $panel-text-color: $gray-900; $side-panel-bg: $panel-bg-color; -$panel-header-bg-color: $gray-lighter; +$panel-header-bg-color: $gray-100; $panel-header-text-color: #555; -$panel-message-height: 2rem; //1.875rem; +$panel-message-height: 2.5rem; //1.875rem; + +// Initial width of left and right panels +$panel-width: 16rem; $layout_top_padding: 0px; $border-default-color_padding: 0px; -$panel_header_height: 2rem; +$panel_header_height: 2.5rem; $panel_footer_height: 25px; -$layout-border-color: $gray-900; // darken($border-default-color, 15%); +$layout-border-color: $gray-900; +// $layout-border: solid $layout-border-color 1px; +$layout-border: none; // Forms @@ -47,7 +52,7 @@ $state-running-border: #aaaa66; $state-running-bg: #ffffcc; $navbar-height: 36px; // 2.062500rem; -$navbar-default-bg: $gray-lighter; // JT #f8f8f8; +$navbar-default-bg: $gray-100; // JT #f8f8f8; $navbar-default-border: darken($navbar-default-bg, $border-darken-percent); @import "theme/blue.scss"; diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss index fa72970b2ce..db7778b32c3 100644 --- a/client/galaxy/style/scss/theme/blue.scss +++ b/client/galaxy/style/scss/theme/blue.scss @@ -1,7 +1,5 @@ // Override colors to closely resemble the style as of Fall 2013 -$layout-border-color: #999; - $form-heading-bg: #ebd9b2; $form-border: darken($form-heading-bg, 20%); @@ -11,7 +9,7 @@ $table-border-color: darken($table-heading-bg, 20%); $input-border: #aaa; a { - text-decoration: underline; + // text-decoration: underline; } // Label is used in places it probably shouldn't be (grid cells), replace with data- attributes and remove this. diff --git a/client/galaxy/style/source_material/error_icon.svg b/client/galaxy/style/source_material/error_icon.svg new file mode 100644 index 00000000000..73dc055734e --- /dev/null +++ b/client/galaxy/style/source_material/error_icon.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/client/galaxy/style/source_material/galaxy_icons.svg b/client/galaxy/style/source_material/galaxy_icons.svg index 6a34999b592..9d72166e39d 100644 --- a/client/galaxy/style/source_material/galaxy_icons.svg +++ b/client/galaxy/style/source_material/galaxy_icons.svg @@ -1,20 +1,20 @@ + + inkscape:window-width="1438" + inkscape:window-height="821" + inkscape:window-x="74" + inkscape:window-y="109" + inkscape:grid-points="true" + inkscape:window-maximized="0"> image/svg+xml + - - - - - - - - - - - - - - - - - - + id="g3381"> + OkIcon - - - - - - - - - - - - - - - - - + style="fill:#04cd00;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1" + d="M 180.92773,40.517578 A 138.9825,138.9825 0 0 0 41.945312,179.5 138.9825,138.9825 0 0 0 180.92773,318.48242 138.9825,138.9825 0 0 0 319.91016,179.5 138.9825,138.9825 0 0 0 180.92773,40.517578 Z m 50.31446,53.767578 34.20117,20.742184 -91.50977,150.90039 -71.81445,-52.83789 23.70313,-32.21875 36.58593,26.91797 68.83399,-113.503904 z" + id="path1307" + inkscape:connector-curvature="0" /> + + + + + + + + + + + + diff --git a/client/galaxy/style/source_material/info_icon.svg b/client/galaxy/style/source_material/info_icon.svg new file mode 100644 index 00000000000..4fe47696bb1 --- /dev/null +++ b/client/galaxy/style/source_material/info_icon.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/client/galaxy/style/source_material/ok_icon.svg b/client/galaxy/style/source_material/ok_icon.svg new file mode 100644 index 00000000000..387dbe4b874 --- /dev/null +++ b/client/galaxy/style/source_material/ok_icon.svg @@ -0,0 +1 @@ +OkIcon \ No newline at end of file diff --git a/client/galaxy/style/source_material/wait_icon.svg b/client/galaxy/style/source_material/wait_icon.svg new file mode 100644 index 00000000000..2b6fae584da --- /dev/null +++ b/client/galaxy/style/source_material/wait_icon.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/client/galaxy/style/source_material/warn_icon.svg b/client/galaxy/style/source_material/warn_icon.svg new file mode 100644 index 00000000000..b3f01b19670 --- /dev/null +++ b/client/galaxy/style/source_material/warn_icon.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/style/blue/base.css b/static/style/blue/base.css index dc924ec33d2..d415e95b8fa 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -21,10 +21,10 @@ --gray-dark: #343a40; --primary: #25537b; --secondary: #dee2e6; - --success: #21ba21; - --info: #1cbceb; - --warning: #f69713; - --danger: #ef5f5b; + --success: #66CC66; + --info: #2077B3; + --warning: #FE7F02; + --danger: #E31A1E; --light: #f8f9fa; --dark: #343a40; --breakpoint-xs: 0; @@ -32,7 +32,7 @@ --breakpoint-md: 768px; --breakpoint-lg: 992px; --breakpoint-xl: 1200px; - --font-family-sans-serif: "Lucida Grande", verdana, arial, helvetica, sans-serif; + --font-family-sans-serif: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; --font-family-monospace: Monaco, Menlo, Consolas, "Courier New", monospace; } *, @@ -56,8 +56,8 @@ article, aside, figcaption, figure, footer, header, hgroup, main, nav, section { body { margin: 0; - font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; - font-size: 0.75rem; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; + font-size: 0.8rem; font-weight: 400; line-height: 1.5; color: #212529; @@ -138,12 +138,12 @@ sup { top: -.5em; } a { - color: #303030; + color: #000; text-decoration: none; background-color: transparent; -webkit-text-decoration-skip: objects; } a:hover { - color: #0a0a0a; + color: black; text-decoration: underline; } a:not([href]):not([tabindex]) { @@ -306,25 +306,25 @@ h1, h2, h3, .upload-view-default .upload-box .upload-helper, .upload-view-compos color: inherit; } h1, .h1 { - font-size: 1.5rem; } + font-size: 1.6rem; } h2, .h2 { - font-size: 1.3125rem; } + font-size: 1.4rem; } h3, .upload-view-default .upload-box .upload-helper, .upload-view-composite .upload-box .upload-helper, .ui-form-composite .ui-form-header, .h3 { - font-size: 1.125rem; } + font-size: 1.2rem; } h4, .h4 { - font-size: 0.9375rem; } + font-size: 1rem; } h5, .h5 { - font-size: 0.75rem; } + font-size: 0.8rem; } h6, .h6 { - font-size: 0.6375rem; } + font-size: 0.68rem; } .lead { - font-size: 0.9375rem; + font-size: 1rem; font-weight: 300; } .display-1 { @@ -382,7 +382,7 @@ mark, .blockquote { margin-bottom: 1rem; - font-size: 0.9375rem; } + font-size: 1rem; } .blockquote-footer { display: block; @@ -1101,46 +1101,46 @@ pre { .table-success, .table-success > th, .table-success > td { - background-color: #85d985; } + background-color: #abe3ab; } .table-hover .table-success:hover { - background-color: #72d372; } + background-color: #98dd98; } .table-hover .table-success:hover > td, .table-hover .table-success:hover > th { - background-color: #72d372; } + background-color: #98dd98; } .table-info, .table-info > th, .table-info > td { - background-color: #82daf4; } + background-color: #84b4d5; } .table-hover .table-info:hover { - background-color: #6bd3f2; } + background-color: #71a8cf; } .table-hover .table-info:hover > td, .table-hover .table-info:hover > th { - background-color: #6bd3f2; } + background-color: #71a8cf; } .table-warning, .table-warning > th, .table-warning > td { - background-color: #fac67d; } + background-color: #feb974; } .table-hover .table-warning:hover { - background-color: #f9bb64; } + background-color: #feac5b; } .table-hover .table-warning:hover > td, .table-hover .table-warning:hover > th { - background-color: #f9bb64; } + background-color: #feac5b; } .table-danger, .table-danger > th, .table-danger > td { - background-color: #f6a7a5; } + background-color: #f08183; } .table-hover .table-danger:hover { - background-color: #f4908e; } + background-color: #ed6a6d; } .table-hover .table-danger:hover > td, .table-hover .table-danger:hover > th { - background-color: #f4908e; } + background-color: #ed6a6d; } .table-light, .table-light > th, @@ -1252,7 +1252,7 @@ pre { display: block; width: 100%; padding: 0.375rem 0.75rem; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; color: #495057; background-color: #fff; @@ -1280,7 +1280,7 @@ pre { opacity: 1; } select.form-control:not([size]):not([multiple]) { - height: calc(1.875rem + 2px); } + height: calc(1.95rem + 2px); } select.form-control:focus::-ms-value { color: #495057; @@ -1301,13 +1301,13 @@ select.form-control:focus::-ms-value { .col-form-label-lg { padding-top: calc(0.5rem + 1px); padding-bottom: calc(0.5rem + 1px); - font-size: 0.9375rem; + font-size: 1rem; line-height: 1.5; } .col-form-label-sm { padding-top: calc(0.25rem + 1px); padding-bottom: calc(0.25rem + 1px); - font-size: 0.65625rem; + font-size: 0.7rem; line-height: 1.5; } .form-control-plaintext { @@ -1369,7 +1369,7 @@ button, .input-group-sm > .input-group-append > .action-button, .input-group-sm > .input-group-append > .menubutton { padding: 0.25rem 0.5rem; - font-size: 0.65625rem; + font-size: 0.7rem; line-height: 1.5; border-radius: 0.2rem; } @@ -1382,7 +1382,7 @@ select.form-control-sm:not([size]):not([multiple]), .input-group-sm > select.for .input-group-sm > .input-group-append > select.btn:not([size]):not([multiple]), .input-group-sm > .input-group-append > select.action-button:not([size]):not([multiple]), .input-group-sm > .input-group-append > select.menubutton:not([size]):not([multiple]) { - height: calc(1.48438rem + 2px); } + height: calc(1.55rem + 2px); } .form-control-lg, .input-group-lg > .form-control, .input-group-lg > .input-group-prepend > .input-group-text, @@ -1400,7 +1400,7 @@ button, .input-group-lg > .input-group-append > .action-button, .input-group-lg > .input-group-append > .menubutton { padding: 0.5rem 1rem; - font-size: 0.9375rem; + font-size: 1rem; line-height: 1.5; border-radius: 0.3rem; } @@ -1413,7 +1413,7 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for .input-group-lg > .input-group-append > select.btn:not([size]):not([multiple]), .input-group-lg > .input-group-append > select.action-button:not([size]):not([multiple]), .input-group-lg > .input-group-append > select.menubutton:not([size]):not([multiple]) { - height: calc(2.40625rem + 2px); } + height: calc(2.5rem + 2px); } .form-group { margin-bottom: 1rem; } @@ -1463,7 +1463,7 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for width: 100%; margin-top: 0.25rem; font-size: 80%; - color: #21ba21; } + color: #66CC66; } .valid-tooltip { position: absolute; @@ -1476,18 +1476,18 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for font-size: .875rem; line-height: 1; color: #fff; - background-color: rgba(33, 186, 33, 0.8); + background-color: rgba(102, 204, 102, 0.8); border-radius: .2rem; } .was-validated .form-control:valid, .form-control.is-valid, .was-validated .custom-select:valid, .custom-select.is-valid { - border-color: #21ba21; } + border-color: #66CC66; } .was-validated .form-control:valid:focus, .form-control.is-valid:focus, .was-validated .custom-select:valid:focus, .custom-select.is-valid:focus { - border-color: #21ba21; - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.25); } + border-color: #66CC66; + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.25); } .was-validated .form-control:valid ~ .valid-feedback, .was-validated .form-control:valid ~ .valid-tooltip, .form-control.is-valid ~ .valid-feedback, .form-control.is-valid ~ .valid-tooltip, .was-validated @@ -1504,7 +1504,7 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .form-check-input:valid ~ .form-check-label, .form-check-input.is-valid ~ .form-check-label { - color: #21ba21; } + color: #66CC66; } .was-validated .form-check-input:valid ~ .valid-feedback, .was-validated .form-check-input:valid ~ .valid-tooltip, .form-check-input.is-valid ~ .valid-feedback, @@ -1512,9 +1512,9 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-control-input:valid ~ .custom-control-label, .custom-control-input.is-valid ~ .custom-control-label { - color: #21ba21; } + color: #66CC66; } .was-validated .custom-control-input:valid ~ .custom-control-label::before, .custom-control-input.is-valid ~ .custom-control-label::before { - background-color: #74e674; } + background-color: #c6ecc6; } .was-validated .custom-control-input:valid ~ .valid-feedback, .was-validated .custom-control-input:valid ~ .valid-tooltip, .custom-control-input.is-valid ~ .valid-feedback, @@ -1522,13 +1522,13 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-control-input:valid:checked ~ .custom-control-label::before, .custom-control-input.is-valid:checked ~ .custom-control-label::before { - background-color: #33db33; } + background-color: #8cd98c; } .was-validated .custom-control-input:valid:focus ~ .custom-control-label::before, .custom-control-input.is-valid:focus ~ .custom-control-label::before { - box-shadow: 0 0 0 1px #fff, 0 0 0 0.2rem rgba(33, 186, 33, 0.25); } + box-shadow: 0 0 0 1px #fff, 0 0 0 0.2rem rgba(102, 204, 102, 0.25); } .was-validated .custom-file-input:valid ~ .custom-file-label, .custom-file-input.is-valid ~ .custom-file-label { - border-color: #21ba21; } + border-color: #66CC66; } .was-validated .custom-file-input:valid ~ .custom-file-label::before, .custom-file-input.is-valid ~ .custom-file-label::before { border-color: inherit; } @@ -1538,14 +1538,14 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-file-input:valid:focus ~ .custom-file-label, .custom-file-input.is-valid:focus ~ .custom-file-label { - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.25); } + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.25); } .invalid-feedback { display: none; width: 100%; margin-top: 0.25rem; font-size: 80%; - color: #ef5f5b; } + color: #E31A1E; } .invalid-tooltip { position: absolute; @@ -1558,18 +1558,18 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for font-size: .875rem; line-height: 1; color: #fff; - background-color: rgba(239, 95, 91, 0.8); + background-color: rgba(227, 26, 30, 0.8); border-radius: .2rem; } .was-validated .form-control:invalid, .form-control.is-invalid, .was-validated .custom-select:invalid, .custom-select.is-invalid { - border-color: #ef5f5b; } + border-color: #E31A1E; } .was-validated .form-control:invalid:focus, .form-control.is-invalid:focus, .was-validated .custom-select:invalid:focus, .custom-select.is-invalid:focus { - border-color: #ef5f5b; - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.25); } + border-color: #E31A1E; + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.25); } .was-validated .form-control:invalid ~ .invalid-feedback, .was-validated .form-control:invalid ~ .invalid-tooltip, .form-control.is-invalid ~ .invalid-feedback, .form-control.is-invalid ~ .invalid-tooltip, .was-validated @@ -1586,7 +1586,7 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .form-check-input:invalid ~ .form-check-label, .form-check-input.is-invalid ~ .form-check-label { - color: #ef5f5b; } + color: #E31A1E; } .was-validated .form-check-input:invalid ~ .invalid-feedback, .was-validated .form-check-input:invalid ~ .invalid-tooltip, .form-check-input.is-invalid ~ .invalid-feedback, @@ -1594,9 +1594,9 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-control-input:invalid ~ .custom-control-label, .custom-control-input.is-invalid ~ .custom-control-label { - color: #ef5f5b; } + color: #E31A1E; } .was-validated .custom-control-input:invalid ~ .custom-control-label::before, .custom-control-input.is-invalid ~ .custom-control-label::before { - background-color: #fad0cf; } + background-color: #f28b8d; } .was-validated .custom-control-input:invalid ~ .invalid-feedback, .was-validated .custom-control-input:invalid ~ .invalid-tooltip, .custom-control-input.is-invalid ~ .invalid-feedback, @@ -1604,13 +1604,13 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-control-input:invalid:checked ~ .custom-control-label::before, .custom-control-input.is-invalid:checked ~ .custom-control-label::before { - background-color: #f48c89; } + background-color: #ea4649; } .was-validated .custom-control-input:invalid:focus ~ .custom-control-label::before, .custom-control-input.is-invalid:focus ~ .custom-control-label::before { - box-shadow: 0 0 0 1px #fff, 0 0 0 0.2rem rgba(239, 95, 91, 0.25); } + box-shadow: 0 0 0 1px #fff, 0 0 0 0.2rem rgba(227, 26, 30, 0.25); } .was-validated .custom-file-input:invalid ~ .custom-file-label, .custom-file-input.is-invalid ~ .custom-file-label { - border-color: #ef5f5b; } + border-color: #E31A1E; } .was-validated .custom-file-input:invalid ~ .custom-file-label::before, .custom-file-input.is-invalid ~ .custom-file-label::before { border-color: inherit; } @@ -1620,7 +1620,7 @@ select.form-control-lg:not([size]):not([multiple]), .input-group-lg > select.for display: block; } .was-validated .custom-file-input:invalid:focus ~ .custom-file-label, .custom-file-input.is-invalid:focus ~ .custom-file-label { - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.25); } + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.25); } .form-inline { display: flex; @@ -1676,7 +1676,7 @@ button, .action-button, .menubutton { user-select: none; border: 1px solid transparent; padding: 0.375rem 0.75rem; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; border-radius: 0.25rem; transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; } @@ -1781,96 +1781,96 @@ button, .action-button, .btn-default, .menubutton { box-shadow: 0 0 0 0.2rem rgba(222, 226, 230, 0.5); } .btn-success { - color: #fff; - background-color: #21ba21; - border-color: #21ba21; } + color: #212529; + background-color: #66CC66; + border-color: #66CC66; } .btn-success:hover { color: #fff; - background-color: #1b991b; - border-color: #198e19; } + background-color: #49c249; + border-color: #40bf40; } .btn-success:focus, .btn-success.focus { - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.5); } .btn-success.disabled, .btn-success:disabled { - color: #fff; - background-color: #21ba21; - border-color: #21ba21; } + color: #212529; + background-color: #66CC66; + border-color: #66CC66; } .btn-success:not(:disabled):not(.disabled):active, .btn-success:not(:disabled):not(.disabled).active, .show > .btn-success.dropdown-toggle { color: #fff; - background-color: #198e19; - border-color: #178317; } + background-color: #40bf40; + border-color: #3db63d; } .btn-success:not(:disabled):not(.disabled):active:focus, .btn-success:not(:disabled):not(.disabled).active:focus, .show > .btn-success.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.5); } .btn-info { color: #fff; - background-color: #1cbceb; - border-color: #1cbceb; } + background-color: #2077B3; + border-color: #2077B3; } .btn-info:hover { color: #fff; - background-color: #12a4cf; - border-color: #119ac3; } + background-color: #1a6193; + border-color: #185a88; } .btn-info:focus, .btn-info.focus { - box-shadow: 0 0 0 0.2rem rgba(28, 188, 235, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(32, 119, 179, 0.5); } .btn-info.disabled, .btn-info:disabled { color: #fff; - background-color: #1cbceb; - border-color: #1cbceb; } + background-color: #2077B3; + border-color: #2077B3; } .btn-info:not(:disabled):not(.disabled):active, .btn-info:not(:disabled):not(.disabled).active, .show > .btn-info.dropdown-toggle { color: #fff; - background-color: #119ac3; - border-color: #1091b7; } + background-color: #185a88; + border-color: #16537d; } .btn-info:not(:disabled):not(.disabled):active:focus, .btn-info:not(:disabled):not(.disabled).active:focus, .show > .btn-info.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(28, 188, 235, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(32, 119, 179, 0.5); } .btn-warning { color: #212529; - background-color: #f69713; - border-color: #f69713; } + background-color: #FE7F02; + border-color: #FE7F02; } .btn-warning:hover { color: #fff; - background-color: #da8308; - border-color: #ce7b08; } + background-color: #d96c01; + border-color: #cc6601; } .btn-warning:focus, .btn-warning.focus { - box-shadow: 0 0 0 0.2rem rgba(246, 151, 19, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(254, 127, 2, 0.5); } .btn-warning.disabled, .btn-warning:disabled { color: #212529; - background-color: #f69713; - border-color: #f69713; } + background-color: #FE7F02; + border-color: #FE7F02; } .btn-warning:not(:disabled):not(.disabled):active, .btn-warning:not(:disabled):not(.disabled).active, .show > .btn-warning.dropdown-toggle { color: #fff; - background-color: #ce7b08; - border-color: #c27407; } + background-color: #cc6601; + border-color: #bf5f01; } .btn-warning:not(:disabled):not(.disabled):active:focus, .btn-warning:not(:disabled):not(.disabled).active:focus, .show > .btn-warning.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(246, 151, 19, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(254, 127, 2, 0.5); } .btn-danger { color: #fff; - background-color: #ef5f5b; - border-color: #ef5f5b; } + background-color: #E31A1E; + border-color: #E31A1E; } .btn-danger:hover { color: #fff; - background-color: #ec3c38; - border-color: #eb312c; } + background-color: #c11619; + border-color: #b51518; } .btn-danger:focus, .btn-danger.focus { - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.5); } .btn-danger.disabled, .btn-danger:disabled { color: #fff; - background-color: #ef5f5b; - border-color: #ef5f5b; } + background-color: #E31A1E; + border-color: #E31A1E; } .btn-danger:not(:disabled):not(.disabled):active, .btn-danger:not(:disabled):not(.disabled).active, .show > .btn-danger.dropdown-toggle { color: #fff; - background-color: #eb312c; - border-color: #ea2621; } + background-color: #b51518; + border-color: #aa1316; } .btn-danger:not(:disabled):not(.disabled):active:focus, .btn-danger:not(:disabled):not(.disabled).active:focus, .show > .btn-danger.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.5); } .btn-light { color: #212529; @@ -1965,96 +1965,96 @@ button, .action-button, .btn-default, .menubutton { box-shadow: 0 0 0 0.2rem rgba(222, 226, 230, 0.5); } .btn-outline-success { - color: #21ba21; + color: #66CC66; background-color: transparent; background-image: none; - border-color: #21ba21; } + border-color: #66CC66; } .btn-outline-success:hover { - color: #fff; - background-color: #21ba21; - border-color: #21ba21; } + color: #212529; + background-color: #66CC66; + border-color: #66CC66; } .btn-outline-success:focus, .btn-outline-success.focus { - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.5); } .btn-outline-success.disabled, .btn-outline-success:disabled { - color: #21ba21; + color: #66CC66; background-color: transparent; } .btn-outline-success:not(:disabled):not(.disabled):active, .btn-outline-success:not(:disabled):not(.disabled).active, .show > .btn-outline-success.dropdown-toggle { - color: #fff; - background-color: #21ba21; - border-color: #21ba21; } + color: #212529; + background-color: #66CC66; + border-color: #66CC66; } .btn-outline-success:not(:disabled):not(.disabled):active:focus, .btn-outline-success:not(:disabled):not(.disabled).active:focus, .show > .btn-outline-success.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(33, 186, 33, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(102, 204, 102, 0.5); } .btn-outline-info { - color: #1cbceb; + color: #2077B3; background-color: transparent; background-image: none; - border-color: #1cbceb; } + border-color: #2077B3; } .btn-outline-info:hover { color: #fff; - background-color: #1cbceb; - border-color: #1cbceb; } + background-color: #2077B3; + border-color: #2077B3; } .btn-outline-info:focus, .btn-outline-info.focus { - box-shadow: 0 0 0 0.2rem rgba(28, 188, 235, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(32, 119, 179, 0.5); } .btn-outline-info.disabled, .btn-outline-info:disabled { - color: #1cbceb; + color: #2077B3; background-color: transparent; } .btn-outline-info:not(:disabled):not(.disabled):active, .btn-outline-info:not(:disabled):not(.disabled).active, .show > .btn-outline-info.dropdown-toggle { color: #fff; - background-color: #1cbceb; - border-color: #1cbceb; } + background-color: #2077B3; + border-color: #2077B3; } .btn-outline-info:not(:disabled):not(.disabled):active:focus, .btn-outline-info:not(:disabled):not(.disabled).active:focus, .show > .btn-outline-info.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(28, 188, 235, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(32, 119, 179, 0.5); } .btn-outline-warning { - color: #f69713; + color: #FE7F02; background-color: transparent; background-image: none; - border-color: #f69713; } + border-color: #FE7F02; } .btn-outline-warning:hover { color: #212529; - background-color: #f69713; - border-color: #f69713; } + background-color: #FE7F02; + border-color: #FE7F02; } .btn-outline-warning:focus, .btn-outline-warning.focus { - box-shadow: 0 0 0 0.2rem rgba(246, 151, 19, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(254, 127, 2, 0.5); } .btn-outline-warning.disabled, .btn-outline-warning:disabled { - color: #f69713; + color: #FE7F02; background-color: transparent; } .btn-outline-warning:not(:disabled):not(.disabled):active, .btn-outline-warning:not(:disabled):not(.disabled).active, .show > .btn-outline-warning.dropdown-toggle { color: #212529; - background-color: #f69713; - border-color: #f69713; } + background-color: #FE7F02; + border-color: #FE7F02; } .btn-outline-warning:not(:disabled):not(.disabled):active:focus, .btn-outline-warning:not(:disabled):not(.disabled).active:focus, .show > .btn-outline-warning.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(246, 151, 19, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(254, 127, 2, 0.5); } .btn-outline-danger { - color: #ef5f5b; + color: #E31A1E; background-color: transparent; background-image: none; - border-color: #ef5f5b; } + border-color: #E31A1E; } .btn-outline-danger:hover { color: #fff; - background-color: #ef5f5b; - border-color: #ef5f5b; } + background-color: #E31A1E; + border-color: #E31A1E; } .btn-outline-danger:focus, .btn-outline-danger.focus { - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.5); } .btn-outline-danger.disabled, .btn-outline-danger:disabled { - color: #ef5f5b; + color: #E31A1E; background-color: transparent; } .btn-outline-danger:not(:disabled):not(.disabled):active, .btn-outline-danger:not(:disabled):not(.disabled).active, .show > .btn-outline-danger.dropdown-toggle { color: #fff; - background-color: #ef5f5b; - border-color: #ef5f5b; } + background-color: #E31A1E; + border-color: #E31A1E; } .btn-outline-danger:not(:disabled):not(.disabled):active:focus, .btn-outline-danger:not(:disabled):not(.disabled).active:focus, .show > .btn-outline-danger.dropdown-toggle:focus { - box-shadow: 0 0 0 0.2rem rgba(239, 95, 91, 0.5); } + box-shadow: 0 0 0 0.2rem rgba(227, 26, 30, 0.5); } .btn-outline-light { color: #f8f9fa; @@ -2104,10 +2104,10 @@ button, .action-button, .btn-default, .menubutton { .btn-link { font-weight: 400; - color: #303030; + color: #000; background-color: transparent; } .btn-link:hover { - color: #0a0a0a; + color: black; text-decoration: underline; background-color: transparent; border-color: transparent; } @@ -2122,7 +2122,7 @@ button, .action-button, .btn-default, .menubutton { .btn-lg, .btn-group-lg > .btn, .btn-group-lg > input[type="submit"], .btn-group-lg > button, .btn-group-lg > .action-button, .btn-group-lg > .menubutton { padding: 0.5rem 1rem; - font-size: 0.9375rem; + font-size: 1rem; line-height: 1.5; border-radius: 0.3rem; } @@ -2131,7 +2131,7 @@ button, .btn-group-sm > .action-button, .btn-group-sm > .menubutton, .btn-xs, .m button, .multi-panel-history .control-column .action-button, .multi-panel-history .control-column .menubutton, .multi-panel-history .history-column .panel-controls .btn, .multi-panel-history .history-column .panel-controls input[type="submit"], .multi-panel-history .history-column .panel-controls button, .multi-panel-history .history-column .panel-controls .action-button, .multi-panel-history .history-column .panel-controls .menubutton { padding: 0.25rem 0.5rem; - font-size: 0.65625rem; + font-size: 0.7rem; line-height: 1.5; border-radius: 0.2rem; } @@ -2197,7 +2197,7 @@ input[type="button"].btn-block { min-width: 10rem; padding: 0.5rem 0; margin: 0.125rem 0 0; - font-size: 0.75rem; + font-size: 0.8rem; color: #212529; text-align: left; list-style: none; @@ -2331,7 +2331,7 @@ input[type="button"].btn-block { display: block; padding: 0.5rem 1.5rem; margin-bottom: 0; - font-size: 0.65625rem; + font-size: 0.7rem; color: #868e96; white-space: nowrap; } @@ -2750,7 +2750,7 @@ button, align-items: center; padding: 0.375rem 0.75rem; margin-bottom: 0; - font-size: 0.75rem; + font-size: 0.8rem; font-weight: 400; line-height: 1.5; color: #495057; @@ -2892,7 +2892,7 @@ button:not(:first-child), .custom-select { display: inline-block; width: 100%; - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); padding: 0.375rem 1.75rem 0.375rem 0.75rem; line-height: 1.5; color: #495057; @@ -2920,13 +2920,13 @@ button:not(:first-child), opacity: 0; } .custom-select-sm { - height: calc(1.48438rem + 2px); + height: calc(1.55rem + 2px); padding-top: 0.375rem; padding-bottom: 0.375rem; font-size: 75%; } .custom-select-lg { - height: calc(2.40625rem + 2px); + height: calc(2.5rem + 2px); padding-top: 0.375rem; padding-bottom: 0.375rem; font-size: 125%; } @@ -2935,14 +2935,14 @@ button:not(:first-child), position: relative; display: inline-block; width: 100%; - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); margin-bottom: 0; } .custom-file-input { position: relative; z-index: 2; width: 100%; - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); margin: 0; opacity: 0; } .custom-file-input:focus ~ .custom-file-label { @@ -2959,7 +2959,7 @@ button:not(:first-child), right: 0; left: 0; z-index: 1; - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); padding: 0.375rem 0.75rem; line-height: 1.5; color: #495057; @@ -2973,7 +2973,7 @@ button:not(:first-child), bottom: 0; z-index: 3; display: block; - height: 1.875rem; + height: 1.95rem; padding: 0.375rem 0.75rem; line-height: 1.5; color: #495057; @@ -3138,10 +3138,10 @@ button:not(:first-child), .navbar-brand { display: inline-block; - padding-top: 0.35938rem; - padding-bottom: 0.35938rem; + padding-top: 0.35rem; + padding-bottom: 0.35rem; margin-right: 1rem; - font-size: 0.9375rem; + font-size: 1rem; line-height: inherit; white-space: nowrap; } .navbar-brand:hover, .navbar-brand:focus { @@ -3172,7 +3172,7 @@ button:not(:first-child), .navbar-toggler { padding: 0.25rem 0.75rem; - font-size: 0.9375rem; + font-size: 1rem; line-height: 1; background-color: transparent; border: 1px solid transparent; @@ -3606,12 +3606,12 @@ button:not(:first-child), padding: 0.5rem 0.75rem; margin-left: -1px; line-height: 1.25; - color: #303030; + color: #000; background-color: #fff; border: 1px solid #dee2e6; } .page-link:hover { z-index: 2; - color: #0a0a0a; + color: black; text-decoration: none; background-color: #e9ecef; border-color: #dee2e6; } @@ -3646,7 +3646,7 @@ button:not(:first-child), .pagination-lg .page-link { padding: 0.75rem 1.5rem; - font-size: 0.9375rem; + font-size: 1rem; line-height: 1.5; } .pagination-lg .page-item:first-child .page-link { @@ -3659,7 +3659,7 @@ button:not(:first-child), .pagination-sm .page-link { padding: 0.25rem 0.5rem; - font-size: 0.65625rem; + font-size: 0.7rem; line-height: 1.5; } .pagination-sm .page-item:first-child .page-link { @@ -3710,36 +3710,36 @@ button .badge, .action-button .badge, .menubutton .badge { background-color: #c1c9d0; } .badge-success { - color: #fff; - background-color: #21ba21; } + color: #212529; + background-color: #66CC66; } .badge-success[href]:hover, .badge-success[href]:focus { - color: #fff; + color: #212529; text-decoration: none; - background-color: #198e19; } + background-color: #40bf40; } .badge-info, .badge-new { color: #fff; - background-color: #1cbceb; } + background-color: #2077B3; } .badge-info[href]:hover, [href].badge-new:hover, .badge-info[href]:focus, [href].badge-new:focus { color: #fff; text-decoration: none; - background-color: #119ac3; } + background-color: #185a88; } .badge-warning, .badge-beta { color: #212529; - background-color: #f69713; } + background-color: #FE7F02; } .badge-warning[href]:hover, [href].badge-beta:hover, .badge-warning[href]:focus, [href].badge-beta:focus { color: #212529; text-decoration: none; - background-color: #ce7b08; } + background-color: #cc6601; } .badge-danger { color: #fff; - background-color: #ef5f5b; } + background-color: #E31A1E; } .badge-danger[href]:hover, .badge-danger[href]:focus { color: #fff; text-decoration: none; - background-color: #eb312c; } + background-color: #b51518; } .badge-light { color: #212529; @@ -3798,7 +3798,7 @@ button .badge, .action-button .badge, .menubutton .badge { font-weight: 700; } .alert-dismissible { - padding-right: 3.625rem; } + padding-right: 3.7rem; } .alert-dismissible .close { position: absolute; top: 0; @@ -3808,7 +3808,7 @@ button .badge, .action-button .badge, .menubutton .badge { .alert-primary { color: #16324a; - background-color: #b3c3d1; + background-color: #a8baca; border-color: #6687a3; } .alert-primary hr { border-top-color: #5a7a96; } @@ -3817,7 +3817,7 @@ button .badge, .action-button .badge, .menubutton .badge { .alert-secondary { color: #85888a; - background-color: #f3f5f6; + background-color: #f2f3f5; border-color: #e8ebee; } .alert-secondary hr { border-top-color: #d9dee3; } @@ -3826,64 +3826,64 @@ button .badge, .action-button .badge, .menubutton .badge { .alert-success, .donemessagelarge, .donemessage, .donemessagesmall { - color: #146f14; - background-color: #b1e7b1; - border-color: #64ce64; } + color: #3d7a3d; + background-color: #c2ebc2; + border-color: #94db94; } .alert-success hr, .donemessagelarge hr, .donemessage hr, .donemessagesmall hr { - border-top-color: #51c851; } + border-top-color: #81d581; } .alert-success .alert-link, .donemessagelarge .alert-link, .donemessage .alert-link, .donemessagesmall .alert-link { - color: #0c440c; } + color: #2c582c; } .alert-info, .infomessagelarge, .infomessage, .infomessagesmall, .ui-form-help .note { - color: #11718d; - background-color: #b0e7f8; - border-color: #60d0f1; } + color: #13476b; + background-color: #a6c9e1; + border-color: #63a0ca; } .alert-info hr, .infomessagelarge hr, .infomessage hr, .infomessagesmall hr, .ui-form-help .note hr { - border-top-color: #49c9ef; } + border-top-color: #5094c4; } .alert-info .alert-link, .infomessagelarge .alert-link, .infomessage .alert-link, .infomessagesmall .alert-link, .ui-form-help .note .alert-link { - color: #0c4d5f; } + color: #0b2a40; } .alert-warning, .warningmessagelarge, .warningmessage, .warningmessagesmall, .ui-form-help .warning { - color: #945b0b; - background-color: #fcdbac; - border-color: #f9b65a; } + color: #984c01; + background-color: #ffcc9a; + border-color: #fea54e; } .alert-warning hr, .warningmessagelarge hr, .warningmessage hr, .warningmessagesmall hr, .ui-form-help .warning hr { - border-top-color: #f8ab41; } + border-top-color: #fe9835; } .alert-warning .alert-link, .warningmessagelarge .alert-link, .warningmessage .alert-link, .warningmessagesmall .alert-link, .ui-form-help .warning .alert-link { - color: #653e07; } + color: #653301; } .alert-danger, .errormessagelarge, .error-modal .modal-content, .errormessage, .errormessagesmall, .ui-form-help .error { - color: #8f3937; - background-color: #f9c7c6; - border-color: #f48f8c; } + color: #881012; + background-color: #f4a3a5; + border-color: #eb5f62; } .alert-danger hr, .errormessagelarge hr, .error-modal .modal-content hr, .errormessage hr, .errormessagesmall hr, .ui-form-help .error hr { - border-top-color: #f27875; } + border-top-color: #e8484c; } .alert-danger .alert-link, .errormessagelarge .alert-link, .error-modal .modal-content .alert-link, .errormessage .alert-link, .errormessagesmall .alert-link, .ui-form-help .error .alert-link { - color: #6a2a29; } + color: #5a0b0c; } .alert-light { color: #959596; - background-color: #fdfdfd; + background-color: #fcfdfd; border-color: #fafbfc; } .alert-light hr { border-top-color: #eaeef2; } @@ -3892,7 +3892,7 @@ button .badge, .action-button .badge, .menubutton .badge { .alert-dark { color: #1f2326; - background-color: #b8babc; + background-color: #aeb0b3; border-color: #717579; } .alert-dark hr { border-top-color: #65686c; } @@ -3909,7 +3909,7 @@ button .badge, .action-button .badge, .menubutton .badge { display: flex; height: 1rem; overflow: hidden; - font-size: 0.5625rem; + font-size: 0.6rem; background-color: #e9ecef; border-radius: 0.25rem; } @@ -4018,48 +4018,48 @@ button .badge, .action-button .badge, .menubutton .badge { border-color: #9b9ea1; } .list-group-item-success { - color: #178217; - background-color: #85d985; } + color: #478f47; + background-color: #abe3ab; } .list-group-item-success.list-group-item-action:hover, .list-group-item-success.list-group-item-action:focus { - color: #178217; - background-color: #72d372; } + color: #478f47; + background-color: #98dd98; } .list-group-item-success.list-group-item-action.active { color: #fff; - background-color: #178217; - border-color: #178217; } + background-color: #478f47; + border-color: #478f47; } .list-group-item-info { - color: #1483a4; - background-color: #82daf4; } + color: #16537d; + background-color: #84b4d5; } .list-group-item-info.list-group-item-action:hover, .list-group-item-info.list-group-item-action:focus { - color: #1483a4; - background-color: #6bd3f2; } + color: #16537d; + background-color: #71a8cf; } .list-group-item-info.list-group-item-action.active { color: #fff; - background-color: #1483a4; - border-color: #1483a4; } + background-color: #16537d; + border-color: #16537d; } .list-group-item-warning { - color: #ac6a0d; - background-color: #fac67d; } + color: #b25901; + background-color: #feb974; } .list-group-item-warning.list-group-item-action:hover, .list-group-item-warning.list-group-item-action:focus { - color: #ac6a0d; - background-color: #f9bb64; } + color: #b25901; + background-color: #feac5b; } .list-group-item-warning.list-group-item-action.active { color: #fff; - background-color: #ac6a0d; - border-color: #ac6a0d; } + background-color: #b25901; + border-color: #b25901; } .list-group-item-danger { - color: #a74240; - background-color: #f6a7a5; } + color: #9f1215; + background-color: #f08183; } .list-group-item-danger.list-group-item-action:hover, .list-group-item-danger.list-group-item-action:focus { - color: #a74240; - background-color: #f4908e; } + color: #9f1215; + background-color: #ed6a6d; } .list-group-item-danger.list-group-item-action.active { color: #fff; - background-color: #a74240; - border-color: #a74240; } + background-color: #9f1215; + border-color: #9f1215; } .list-group-item-light { color: #aeaeaf; @@ -4085,7 +4085,7 @@ button .badge, .action-button .badge, .menubutton .badge { .close { float: right; - font-size: 1.125rem; + font-size: 1.2rem; font-weight: 700; line-height: 1; color: #000; @@ -4222,7 +4222,7 @@ button.close { z-index: 1070; display: block; margin: 0; - font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-style: normal; font-weight: 400; line-height: 1.5; @@ -4236,7 +4236,7 @@ button.close { word-spacing: normal; white-space: normal; line-break: auto; - font-size: 0.65625rem; + font-size: 0.7rem; word-wrap: break-word; opacity: 0; } .tooltip.show { @@ -4307,7 +4307,7 @@ button.close { z-index: 1060; display: block; max-width: 276px; - font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-style: normal; font-weight: 400; line-height: 1.5; @@ -4321,7 +4321,7 @@ button.close { word-spacing: normal; white-space: normal; line-break: auto; - font-size: 0.65625rem; + font-size: 0.7rem; word-wrap: break-word; background-color: #fff; background-clip: padding-box; @@ -4414,7 +4414,7 @@ button.close { .popover-header { padding: 0.5rem 0.75rem; margin-bottom: 0; - font-size: 0.75rem; + font-size: 0.8rem; color: inherit; background-color: #f7f7f7; border-bottom: 1px solid #ebebeb; @@ -4636,36 +4636,36 @@ button.bg-secondary:focus { background-color: #c1c9d0 !important; } .bg-success { - background-color: #21ba21 !important; } + background-color: #66CC66 !important; } a.bg-success:hover, a.bg-success:focus, button.bg-success:hover, button.bg-success:focus { - background-color: #198e19 !important; } + background-color: #40bf40 !important; } .bg-info { - background-color: #1cbceb !important; } + background-color: #2077B3 !important; } a.bg-info:hover, a.bg-info:focus, button.bg-info:hover, button.bg-info:focus { - background-color: #119ac3 !important; } + background-color: #185a88 !important; } .bg-warning { - background-color: #f69713 !important; } + background-color: #FE7F02 !important; } a.bg-warning:hover, a.bg-warning:focus, button.bg-warning:hover, button.bg-warning:focus { - background-color: #ce7b08 !important; } + background-color: #cc6601 !important; } .bg-danger { - background-color: #ef5f5b !important; } + background-color: #E31A1E !important; } a.bg-danger:hover, a.bg-danger:focus, button.bg-danger:hover, button.bg-danger:focus { - background-color: #eb312c !important; } + background-color: #b51518 !important; } .bg-light { background-color: #f8f9fa !important; } @@ -4726,16 +4726,16 @@ button.bg-dark:focus { border-color: #dee2e6 !important; } .border-success { - border-color: #21ba21 !important; } + border-color: #66CC66 !important; } .border-info { - border-color: #1cbceb !important; } + border-color: #2077B3 !important; } .border-warning { - border-color: #f69713 !important; } + border-color: #FE7F02 !important; } .border-danger { - border-color: #ef5f5b !important; } + border-color: #E31A1E !important; } .border-light { border-color: #f8f9fa !important; } @@ -6536,28 +6536,28 @@ a.text-secondary:hover, a.text-secondary:focus { color: #c1c9d0 !important; } .text-success { - color: #21ba21 !important; } + color: #66CC66 !important; } a.text-success:hover, a.text-success:focus { - color: #198e19 !important; } + color: #40bf40 !important; } .text-info { - color: #1cbceb !important; } + color: #2077B3 !important; } a.text-info:hover, a.text-info:focus { - color: #119ac3 !important; } + color: #185a88 !important; } .text-warning { - color: #f69713 !important; } + color: #FE7F02 !important; } a.text-warning:hover, a.text-warning:focus { - color: #ce7b08 !important; } + color: #cc6601 !important; } .text-danger { - color: #ef5f5b !important; } + color: #E31A1E !important; } a.text-danger:hover, a.text-danger:focus { - color: #eb312c !important; } + color: #b51518 !important; } .text-light, .quota-meter-text { color: #f8f9fa !important; } @@ -9077,9 +9077,6 @@ pre.code { color: white; padding: 1em; } -a { - text-decoration: underline; } - label { font-weight: normal; } @@ -9977,7 +9974,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { left: 32px; right: 32px; font-size: 12px; - font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; text-align: center; } .galaxy-frame .frame .f-not-allowed { cursor: not-allowed; } @@ -10016,9 +10013,9 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { font-size: 0.75rem; background-color: #f5f5f5; } .upload-button .progress-bar-danger { - background: #f9c7c6; } + background: #f4a3a5; } .upload-button .progress-bar-success { - background: #b1e7b1; } + background: #c2ebc2; } .upload-button .progress-bar-info { background: #ffffcc; } .upload-button .progress-bar-notransition { @@ -10046,7 +10043,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { height: 310px; text-align: center; overflow: scroll; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.33; -moz-border-radius: 0.3125rem; border-radius: 0.3125rem; @@ -10073,12 +10070,12 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .upload-view-default .upload-box .upload-row .upload-title, .upload-view-composite .upload-box .upload-row .upload-title { width: 130px; word-wrap: break-word; - font-size: 0.65625rem; + font-size: 0.7rem; float: left; } .upload-view-default .upload-box .upload-row .upload-title-extended, .upload-view-composite .upload-box .upload-row .upload-title-extended { width: 380px; word-wrap: break-word; - font-size: 0.65625rem; + font-size: 0.7rem; float: left; } .upload-view-default .upload-box .upload-row .upload-size, .upload-view-composite .upload-box .upload-row .upload-size { width: 60px; @@ -10086,11 +10083,11 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .upload-view-default .upload-box .upload-row .upload-extension, .upload-view-composite .upload-box .upload-row .upload-extension { width: 100px; min-width: 100px; - font-size: 0.65625rem; } + font-size: 0.7rem; } .upload-view-default .upload-box .upload-row .upload-genome, .upload-view-composite .upload-box .upload-row .upload-genome { width: 150px; min-width: 150px; - font-size: 0.65625rem; } + font-size: 0.7rem; } .upload-view-default .upload-box .upload-row .upload-mode, .upload-view-composite .upload-box .upload-row .upload-mode { font-size: 1.2em; width: 1.2em; @@ -10103,7 +10100,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { position: absolute; display: none; } .upload-view-default .upload-box .upload-row .upload-text-column .upload-text .upload-text-content, .upload-view-composite .upload-box .upload-row .upload-text-column .upload-text .upload-text-content { - font-size: 0.65625rem; + font-size: 0.7rem; width: 100%; height: 80px; resize: none; @@ -10112,10 +10109,10 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { white-space: pre; overflow: auto; } .upload-view-default .upload-box .upload-row .upload-text-column .upload-text .upload-text-info, .upload-view-composite .upload-box .upload-row .upload-text-column .upload-text .upload-text-info { - font-size: 0.65625rem; } + font-size: 0.7rem; } .upload-view-default .upload-box .upload-row .upload-info, .upload-view-composite .upload-box .upload-row .upload-info { width: 130px; - font-size: 0.65625rem; + font-size: 0.7rem; line-height: 1.2em; } .upload-view-default .upload-box .upload-row .upload-info .progress, .upload-view-composite .upload-box .upload-row .upload-info .progress { top: 1px; @@ -10302,7 +10299,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .ui-error { -moz-border-radius: 0.1875rem; border-radius: 0.1875rem; - background: #f9c7c6; + background: #f4a3a5; padding: 5px; } .ui-label { @@ -10365,7 +10362,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { margin: 0px; margin-top: 2px; } .ui-button-default .progress .progress-bar { - background: #3cc33c; } + background: #4fc54f; } .ui-button-icon { height: auto !important; @@ -10407,8 +10404,8 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { float: right; } .ui-side-panel { - color: #000; - background: #dfe5f9; + color: #212529; + background: #f8f9fa; padding: 10px; min-height: 100%; } .ui-side-panel .ui-side-section-title { @@ -10718,10 +10715,10 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .ui-portlet-panel, .ui-portlet-section { margin-top: 5px; - border-left: solid 3px #dfe5f9; } + border-left: solid 3px #f8f9fa; } .ui-portlet-panel .portlet-header, .ui-portlet-section .portlet-header { - background: #dfe5f9; - border-bottom: solid #b4c2f1 1px; } + background: #f8f9fa; + border-bottom: solid #dae0e5 1px; } .ui-portlet-section .portlet-highlight { text-decoration: underline; } @@ -10837,9 +10834,9 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .ui-input, .ui-form-element .ui-form-preview, .ui-form-element-disabled .ui-form-preview, .ui-input-basic, .ui-select select, .ui-select .select2-container .select2-choice, .ui-textarea, .ui-options .ui-options-list, .ui-form-slider .ui-form-slider-text, .ui-select .select2-container-multi .select2-choices { width: 100%; display: block; - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); padding: 0.25rem 5px !important; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; color: #495057; border: 1px solid #aaa; @@ -11020,7 +11017,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { margin-right: 5px; } .ui-gs-select-file .ui-gs-browse-field { - height: calc(1.875rem + 2px); + height: calc(1.95rem + 2px); line-height: 1.5; } .ui-select { @@ -11077,12 +11074,12 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { padding: 2px; } .ui-dragover-danger { - border: 2px solid #f9c7c6; - background: #fef4f4 !important; } + border: 2px solid #f4a3a5; + background: #f9d1d2 !important; } .ui-dragover-success { - border: 2px solid #b1e7b1; - background: #d8f3d8 !important; } + border: 2px solid #c2ebc2; + background: #e8f8e8 !important; } .ui-limitloader { padding: 10px; @@ -11122,9 +11119,6 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close { .select2-drop.select2-drop-above.select2-drop-active .select2-search { padding-top: 0px; } -a { - text-decoration: underline; } - label { font-weight: normal; } @@ -12397,7 +12391,7 @@ button.toast-close-button { font-size: 1.2em; line-height: 1.2em; } .charts-client .charts-buttons .ui-button-icon .fa-check-square { - color: #146f14; } + color: #3d7a3d; } .charts-client .charts-center { float: left; @@ -12500,7 +12494,7 @@ button.toast-close-button { body { background: #fff; - color: #000; + color: #212529; margin: 10px; } body.full-content { overflow: hidden; @@ -12537,7 +12531,7 @@ body { #messagebox { width: 100%; - height: 2rem !important; + height: 2.5rem !important; overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; @@ -12545,7 +12539,7 @@ body { #inactivebox { width: 100%; - height: 2rem !important; + height: 2.5rem !important; overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; @@ -12562,13 +12556,13 @@ body { #left { left: 0px; - width: 250px; + width: 16rem; z-index: 200; - border-right: solid #999 1px; } + border-right: none; } #center { - left: 250px; - right: 250px; + left: 16rem; + right: 16rem; overflow: hidden; z-index: 1; } #center .center-container { @@ -12588,22 +12582,27 @@ body { height: 100%; } #right { - width: 250px; + width: 16rem; right: 0px; z-index: 200; - border-left: solid #999 1px; } + border-left: none; } #left, #right, .unified-panel { - background: #dfe5f9; + background: #f8f9fa; + display: flex; + flex-direction: column; } + +#left, #right, .unified-panel { + background: #f8f9fa; display: flex; flex-direction: column; } .unified-panel-header { - height: 2rem; + height: 2.5rem; z-index: 1000; text-shadow: rgba(255, 255, 255, 0.8) 0 1px 0; - background: #e9ecef; - border-bottom: solid #999 1px; + background: #f8f9fa; + border-bottom: none; margin: 0; padding: 0; padding-right: 10px; @@ -12639,15 +12638,17 @@ body { padding-right: 1.75em; background: url(../images/dropdownarrow.png) no-repeat right 7px; } +.unified-panel-controls { + padding: 0px 10px; } + .unified-panel-footer, .panel-collapse { - position: absolute; - bottom: 0; + position: relative; height: 25px; line-height: 25px; width: 100%; z-index: 1000; - border-top: solid #999 1px; - background: #e9ecef; + border-top: none; + background: #f8f9fa; color: #555; } .unified-panel-footer a, .panel-collapse a { color: #555; } @@ -12682,9 +12683,9 @@ body { line-height: 25px; width: 20px; background: none; - border-right: solid #999 1px; - border-top: solid #999 1px; - background: #e9ecef; } + border-right: none; + border-top: none; + background: #f8f9fa; } .panel-collapse:before { content: "\f053"; } .panel-collapse.hidden:before { @@ -12693,7 +12694,7 @@ body { left: inherit; right: 0; border-right: none; - border-left: solid #bfbfbf 1px; } + border-left: none; } .panel-collapse.right.right:before { content: "\f054"; } .panel-collapse.right.right.hidden:before { @@ -12708,7 +12709,7 @@ div.unified-panel-body { flex: 1; } div.unified-panel-body-background { - background: none repeat scroll 0 0 #dfe5f9; } + background: none repeat scroll 0 0 #f8f9fa; } #left > div.unified-panel-body, #right > div.unified-panel-body { @@ -12730,32 +12731,35 @@ div.unified-panel-body-background { .panel-warning-message, .panel-done-message, .panel-info-message { - height: 2rem; - line-height: 2rem; + height: 2.5rem; + line-height: 2.5rem; padding: 0px; - padding-left: 26px; - background-color: #f9c7c6; + padding-left: 2.5rem; + background-color: #f4a3a5; background-image: url(error_small.png); background-repeat: no-repeat; - background-position: 6px 50%; } + background-position: .5rem 50%; } .panel-warning-message { background-image: url(warn_small.png); - background-color: #fcdbac; } + background-color: #ffcc9a; } .panel-done-message { background-image: url(ok_small.png); - background-color: #b1e7b1; } + background-color: #c2ebc2; } .panel-info-message { - background-image: url(info_small.png); - background-color: #b0e7f8; } + background-image: url(info_icon.svg); + background-size: 1.5rem; + background-color: #a6c9e1; } + .panel-info-message svg:path { + fill: black; } #masthead { padding: 0; margin-bottom: 0px; background-color: #2c3143; - height: 2.5rem; } + height: 3rem; } #masthead .navbar-nav { min-height: 100%; } #masthead .navbar-nav > li { @@ -12819,10 +12823,10 @@ div.unified-panel-body-background { background-color: #25537b; } .quota-meter-bar-warn { - background-color: #f69713; } + background-color: #FE7F02; } .quota-meter-bar-error { - background-color: #ef5f5b; } + background-color: #E31A1E; } .quota-meter-text { position: absolute; @@ -12913,7 +12917,7 @@ div.toolHelpBody { -moz-border-radius: 1px; border-radius: 1px; } .toolForm.toolFormInCanvas .toolFormTitle { - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; } div.form, @@ -12945,7 +12949,7 @@ div.repeat-group-item { margin-bottom: 10px; } div.form-row-error { - background: #f9c7c6; } + background: #f4a3a5; } div.form-row label { font-weight: bold; @@ -12990,7 +12994,7 @@ div.form-row-error-message { select { padding: 2px; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; } select, @@ -13010,7 +13014,7 @@ textarea { textarea, input[type="text"], input[type="password"] { - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; border: 1px solid #aaa; padding: 3px; } @@ -13018,7 +13022,7 @@ input[type="password"] { .search-query { display: inline-block; padding: 4px; - font-size: 0.75rem; + font-size: 0.8rem; line-height: 1.5; color: #495057; border: 1px solid #aaa; @@ -13368,7 +13372,7 @@ ul.manage-table-actions li { .state-progress .running { background: #ffffcc; } .state-progress .ok { - background: #b1e7b1; } + background: #c2ebc2; } .state-progress .note { margin-left: 1em; position: absolute; } @@ -13378,8 +13382,8 @@ ul.manage-table-actions li { background: #e9ecef; } .state-color-upload { - border-color: #60d0f1; - background: #b0e7f8; } + border-color: #63a0ca; + background: #a6c9e1; } .state-color-waiting { border-color: #bfbfbf; @@ -13394,12 +13398,12 @@ ul.manage-table-actions li { background: #ffffcc; } .state-color-ok { - border-color: #64ce64; - background: #b1e7b1; } + border-color: #94db94; + background: #c2ebc2; } .state-color-error { - border-color: #f48f8c; - background: #f9c7c6; } + border-color: #eb5f62; + background: #f4a3a5; } .state-color-deleted { border-color: #737373; @@ -13676,7 +13680,7 @@ div.permissionContainer { .list-item .info-section, .dataset .details .summary .info, .dataset .details .summary .job-error-text, .dataset .details .annotation-display .annotation { border-radius: 3px; - border: 1px solid rgba(153, 153, 153, 0.3); + border: 1px solid rgba(33, 37, 41, 0.3); padding: 4px; } .list-item .vertical-spacing, .list-panel .vertical-spacing, .dataset .details .summary .dbkey:after, .dataset .details .summary, .dataset .details .actions:not(:last-child), .dataset .details .annotation-display, .dataset .details .display-applications .display-application:last-child, .dataset .details .dataset-peek, .tags-display { @@ -13986,15 +13990,15 @@ The `sprites` mixin generates identical output to the CSS template content: ""; } .has-job-state-mixin.state-ok, .state-ok.dataset, .state-ok.dataset-collection-element, .state-ok.history-content.dataset-collection, .has-job-state-mixin.state-failed_metadata, .state-failed_metadata.dataset, .state-failed_metadata.dataset-collection-element, .state-failed_metadata.history-content.dataset-collection { - background: #b1e7b1; } + background: #c2ebc2; } .has-job-state-mixin.state-ok .state-icon, .state-ok.dataset .state-icon, .state-ok.dataset-collection-element .state-icon, .state-ok.history-content.dataset-collection .state-icon, .has-job-state-mixin.state-failed_metadata .state-icon, .state-failed_metadata.dataset .state-icon, .state-failed_metadata.dataset-collection-element .state-icon, .state-failed_metadata.history-content.dataset-collection .state-icon { display: none; } .has-job-state-mixin.state-error, .state-error.dataset, .state-error.dataset-collection-element, .state-error.history-content.dataset-collection, .has-job-state-mixin.state-empty, .state-empty.dataset, .state-empty.dataset-collection-element, .state-empty.history-content.dataset-collection { - background: #f9c7c6; } + background: #f4a3a5; } .has-job-state-mixin.state-upload, .state-upload.dataset, .state-upload.dataset-collection-element, .state-upload.history-content.dataset-collection { - background: #b0e7f8; } + background: #a6c9e1; } .has-job-state-mixin.state-queued, .state-queued.dataset, .state-queued.dataset-collection-element, .state-queued.history-content.dataset-collection { background: #e9ecef; } @@ -14194,7 +14198,7 @@ pre.peek { .history-panel > .controls .annotation-display .annotation { background: white; border-radius: 3px; - border: 1px solid rgba(153, 153, 153, 0.5); + border: 1px solid rgba(33, 37, 41, 0.5); padding: 4px; white-space: pre-wrap; overflow: auto; } @@ -14389,7 +14393,7 @@ pre.peek { border-left: 5px solid #4e5777; } #right.history-right-panel { - background-color: #dfe5f9; } + background-color: #f8f9fa; } #right.history-right-panel .unified-panel-header .unified-panel-header-inner .panel-header-buttons .panel-header-button { display: inline-block; height: 22px; @@ -14565,7 +14569,7 @@ pre.peek { width: 100%; border: 1px solid grey; border-radius: 3px 3px 0px 0px; - background-color: #dfe5f9; + background-color: #f8f9fa; overflow: auto; } .multi-panel-history .history-column .history-panel > .controls .subtitle { min-height: 15px; @@ -15080,7 +15084,7 @@ pre.peek { color: grey; } .search-input .search-clear:hover { - color: #303030; + color: #000; cursor: pointer; } .dataset-choice { @@ -15256,7 +15260,7 @@ pre.peek { .toolMenuContainer { color: #212529; - background: #dfe5f9; + background: #f8f9fa; min-height: 100%; padding: 5px 10px; } .toolMenuContainer a { @@ -15276,7 +15280,8 @@ div.toolSectionDetailsInner { margin-right: 5px; } div.toolSectionTitle { - font-weight: bold; } + font-weight: 500; + font-size: 1rem; } div.toolPanelLabel { padding-top: 10px; @@ -15288,10 +15293,9 @@ div.toolPanelLabel { div.toolTitle { padding-top: 5px; padding-bottom: 5px; - margin-left: 16px; + margin-left: 10px; margin-right: 10px; - display: list-item; - list-style: square outside; } + display: block; } div.toolTitle .labels { float: right; margin-left: 2px; } diff --git a/static/style/blue/library.css b/static/style/blue/library.css index 9bf8fa216b4..8c3e662b60a 100644 --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -1,6 +1,3 @@ -a { - text-decoration: underline; } - label { font-weight: normal; } From 546eb18ca1e1a3f22fd162b5bcf674705c173601 Mon Sep 17 00:00:00 2001 From: James Taylor Date: Sat, 30 Jun 2018 20:35:23 -0400 Subject: [PATCH 020/352] Improving spacing and forms. --- client/galaxy/style/scss/base.scss | 22 +++++++++------ .../galaxy/style/scss/galaxy_variables.scss | 7 ++++- client/galaxy/style/scss/history.scss | 21 +-------------- client/galaxy/style/scss/list-item.scss | 4 +-- client/galaxy/style/scss/ui.scss | 27 +++++++------------ client/galaxy/style/scss/upload.scss | 2 +- 6 files changed, 34 insertions(+), 49 deletions(-) diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss index a2e94d28ad5..f3d06962387 100644 --- a/client/galaxy/style/scss/base.scss +++ b/client/galaxy/style/scss/base.scss @@ -177,7 +177,7 @@ body { position: absolute; width: 100%; height: 100%; - padding: 10px; + padding: $margin-h $margin-v; overflow: auto; } .center-frame { @@ -215,9 +215,8 @@ body { background: $panel-header-bg-color; border-bottom: $layout-border; margin: 0; - padding: 0; - padding-right: 10px; - padding-left: 10px; + padding: 0 $margin-v; + font-size: 1rem; font-weight: bold; display: flex; align-items: center; @@ -227,7 +226,7 @@ body { color: $panel-header-text-color; } .fa { - font-size: 1.2em; + // font-size: 1.2em; } .unified-panel-header-inner { @@ -245,6 +244,13 @@ body { text-decoration: none; display: inline-block; cursor: pointer; + width: 1.2rem; + text-align: center; + padding: 0px; + &:not(:last-child) { + margin-right: 2px; + } + // Fade to maroon on hover &:hover { color: maroon; @@ -263,7 +269,7 @@ body { } .unified-panel-controls { - padding: 0px 10px; + padding: 0 $margin-v; } .unified-panel-footer { @@ -787,7 +793,7 @@ button { #tool-search { position: relative; - margin: 10px; + margin: 10px 0; #search-clear-btn { position: absolute; @@ -1612,7 +1618,7 @@ div.permissionContainer { } background: $panel-bg-color; min-height: 100%; - padding: 5px 10px; + padding: $margin-h $margin-v; } div.toolSectionPad { diff --git a/client/galaxy/style/scss/galaxy_variables.scss b/client/galaxy/style/scss/galaxy_variables.scss index 816ced18420..2b872a269ba 100644 --- a/client/galaxy/style/scss/galaxy_variables.scss +++ b/client/galaxy/style/scss/galaxy_variables.scss @@ -20,7 +20,7 @@ $panel-header-text-color: #555; $panel-message-height: 2.5rem; //1.875rem; // Initial width of left and right panels -$panel-width: 16rem; +$panel-width: 18rem; $layout_top_padding: 0px; $border-default-color_padding: 0px; @@ -55,6 +55,11 @@ $navbar-height: 36px; // 2.062500rem; $navbar-default-bg: $gray-100; // JT #f8f8f8; $navbar-default-border: darken($navbar-default-bg, $border-darken-percent); +// Margins +$spacer: 1rem; // Not sure why this is not coming from Bootstrap +$margin-v: $spacer * 1.5; +$margin-h: $spacer; + @import "theme/blue.scss"; // Theme: plain diff --git a/client/galaxy/style/scss/history.scss b/client/galaxy/style/scss/history.scss index f7a975f628f..0c553b570d4 100644 --- a/client/galaxy/style/scss/history.scss +++ b/client/galaxy/style/scss/history.scss @@ -3,7 +3,7 @@ @extend .flex-vertical-container; > .controls { - margin: 8px 8px 1px; + margin: $margin-h $margin-v; padding: 0px; flex: 0 0 auto; @@ -374,25 +374,6 @@ // ---------------------------------------------------------------------------- analyze data page - right panel #right.history-right-panel { - background-color: $panel-bg-color; - .unified-panel-header { - .unified-panel-header-inner { - .panel-header-buttons { - .panel-header-button { - display: inline-block; - height: $icon-btn-size; - width: $icon-btn-size; - text-align: center; - line-height: $icon-btn-size - 3; - font-size: 1.2em; - padding: 0px; - &:not(:last-child) { - margin-right: 2px; - } - } - } - } - } .unified-panel-body { display: -webkit-flex; .middle { diff --git a/client/galaxy/style/scss/list-item.scss b/client/galaxy/style/scss/list-item.scss index a37f9f557b6..e1fb25f6e56 100644 --- a/client/galaxy/style/scss/list-item.scss +++ b/client/galaxy/style/scss/list-item.scss @@ -28,9 +28,9 @@ $vertical-gap: 8px; } $spacing-top: 6px; - $spacing-right: 10px; + $spacing-right: $margin-v; $spacing-bottom: 6px; - $spacing-left: 8px; + $spacing-left: $margin-v; .padded { padding: $spacing-top $spacing-right $spacing-bottom $spacing-left; } diff --git a/client/galaxy/style/scss/ui.scss b/client/galaxy/style/scss/ui.scss index c54245df017..7b9a63425cf 100644 --- a/client/galaxy/style/scss/ui.scss +++ b/client/galaxy/style/scss/ui.scss @@ -28,11 +28,11 @@ } // default margins -$ui-margin-vertical: 5px; -$ui-margin-vertical-large: 10px; -$ui-margin-horizontal: 5px; -$ui-margin-horizontal-small: 4px; -$ui-margin-horizontal-large: 10px; +$ui-margin-vertical: $margin-v * 0.25; +$ui-margin-vertical-large: $margin-v * 0.5; +$ui-margin-horizontal: $margin-h; +$ui-margin-horizontal-small: $margin-h * 0.5; +$ui-margin-horizontal-large: $margin-v * 2; // helpers .ui-clear-float { @@ -532,26 +532,21 @@ $ui-margin-horizontal-large: 10px; // portlets .ui-portlet { - border: solid $form-border 1px; - border-radius: $border-radius-base; + @extend .card; position: relative; clear: both; width: auto; height: auto; .portlet-header { - background: $form-heading-bg; - border-bottom: solid $form-border 1px; - padding: 2px 8px; + @extend .card-header; overflow: visible; width: 100%; .portlet-title { word-wrap: break-word; - display: inline; - vertical-align: middle; - font-weight: bold; .portlet-title-text { + @extend h4; vertical-align: middle; - line-height: 22px; + //line-height: 22px; } .portlet-title-text.no-highlight.collapsible { cursor: pointer; @@ -570,9 +565,7 @@ $ui-margin-horizontal-large: 10px; } } .portlet-content { - height: inherit; - padding-left: 10px; - padding-right: 10px; + @extend .card-body; clear: both; .portlet-body { padding: 0px; diff --git a/client/galaxy/style/scss/upload.scss b/client/galaxy/style/scss/upload.scss index d011c575aed..64ec725628c 100644 --- a/client/galaxy/style/scss/upload.scss +++ b/client/galaxy/style/scss/upload.scss @@ -29,7 +29,7 @@ } .panel-header-button { position: absolute; - width: 31px; + width: 31px !important; text-align: center; font-size: 1.2em; padding: 0px; From 7ddac47efaa9fa8435e4cb4c207bf557429dcd2d Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 11 Jul 2018 09:46:04 -0400 Subject: [PATCH 021/352] Remove custom margin classes --- .../galaxy/scripts/components/PluginList.vue | 2 +- .../galaxy/scripts/mvc/tool/tool-form-base.js | 2 +- client/galaxy/scripts/mvc/ui/ui-buttons.js | 10 +- client/galaxy/scripts/mvc/ui/ui-list.js | 2 +- client/galaxy/scripts/mvc/ui/ui-misc.js | 2 +- .../scripts/mvc/ui/ui-select-library.js | 2 +- .../scripts/mvc/user/user-custom-builds.js | 6 +- .../mvc/visualization/chart/views/editor.js | 2 +- .../mvc/visualization/chart/views/settings.js | 2 +- client/galaxy/style/scss/ui.scss | 22 - static/style/blue/base.css | 517 +++++++++++++----- 11 files changed, 400 insertions(+), 169 deletions(-) diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue index 15867535ce2..03143bc5ea0 100644 --- a/client/galaxy/scripts/components/PluginList.vue +++ b/client/galaxy/scripts/components/PluginList.vue @@ -33,7 +33,7 @@
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index 95c6c27004a..4ee6dfc09c8 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -82,7 +82,7 @@ export default FormBase.extend({ if (!this.model.get("collapsible")) { this.$el.append( $("
") - .addClass("ui-margin-top-large") + .addClass("mt-2") .append(this._footer()) ); } diff --git a/client/galaxy/scripts/mvc/ui/ui-buttons.js b/client/galaxy/scripts/mvc/ui/ui-buttons.js index 3c0fb608d13..92edff4e210 100644 --- a/client/galaxy/scripts/mvc/ui/ui-buttons.js +++ b/client/galaxy/scripts/mvc/ui/ui-buttons.js @@ -53,13 +53,13 @@ var ButtonDefault = Backbone.View.extend({ this.$title.removeClass().addClass("title"); if (options.wait) { this.$el.addClass(options.wait_cls).prop("disabled", true); - this.$icon.addClass("fa-spinner fa-spin ui-margin-right"); + this.$icon.addClass("fa-spinner fa-spin mr-1"); this.$title.html(options.wait_text); } else { this.$el.addClass(options.cls); this.$icon.addClass(options.icon); this.$title.html(options.title); - options.icon && options.title && this.$icon.addClass("ui-margin-right"); + options.icon && options.title && this.$icon.addClass("mr-1"); } }, @@ -173,7 +173,7 @@ var ButtonCheck = Backbone.View.extend({ this.$title.html(options.title); this.$icon .removeClass() - .addClass("icon fa ui-margin-right") + .addClass("icon fa mr-1") .addClass(options.icons[options.value]); }, @@ -239,7 +239,7 @@ var ButtonIcon = ButtonDefault.extend({ .addClass("icon fa") .addClass(options.icon); this.$title.addClass("title").html(options.title); - options.icon && options.title && this.$icon.addClass("ui-margin-right"); + options.icon && options.title && this.$icon.addClass("mr-1"); } }); @@ -304,7 +304,7 @@ var ButtonMenu = ButtonDefault.extend({ .removeClass() .addClass("title") .html(options.title); - options.icon && options.title && this.$icon.addClass("ui-margin-right"); + options.icon && options.title && this.$icon.addClass("mr-1"); this.$menu && this.$menu.remove(); if (this.collection.length > 0) { this.$menu = $("
    ") diff --git a/client/galaxy/scripts/mvc/ui/ui-list.js b/client/galaxy/scripts/mvc/ui/ui-list.js index 012a8020a0c..a8a98cec572 100644 --- a/client/galaxy/scripts/mvc/ui/ui-list.js +++ b/client/galaxy/scripts/mvc/ui/ui-list.js @@ -142,7 +142,7 @@ var View = Backbone.View.extend({ _template: function(options) { return ( '
    ' + - '
    ' + + '
    ' + '' + '' + "
    " + diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js index 42a08b8a670..138f8092d9c 100644 --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -242,7 +242,7 @@ export var Upload = Backbone.View.extend({ .append( (this.$file = $("") .attr("type", "file") - .addClass("ui-margin-bottom")) + .addClass("mb-1")) ) .append( (this.$text = $("\n \n
    \n
    \n \x3c!--\n
    \n
    \n --\x3e\n
    \n
    \n '}})}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(10),s=n(a),o=i(655),r=n(o),l=i(656),d=n(l),c=i(3),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:(0,u.default)("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:(0,u.default)("History options"),cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:(0,u.default)("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return['
    '].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e,t,i){return o.clone(_).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(3),l=n(r),d=i(41),c=n(d),u=i(143),h=n(u),f=i(25),p=n(f),_=[{html:(0,l.default)("History Lists"),header:!0},{html:(0,l.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,l.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,l.default)("Current History"),header:!0,anon:!0},{html:(0,l.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,l.default)("Copy History"),func:function(){(0,h.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Share or Publish"),href:"history/sharing"},{html:(0,l.default)("Show Structure"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/show_structure")}},{html:(0,l.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,l.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,l.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,l.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,l.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,l.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Purge Deleted Datasets"),confirm:(0,l.default)("Really delete all deleted datasets permanently? 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    ").text("Current Custom Builds")).append(this.table.$el).append(this.$installed=n("
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    ").text("System Installed Builds").addClass("ui-margin-top")).append(this.installed_builds.$el)).append(n("

    ").text("Add a Custom Build").addClass("ui-margin-top")).append(n("").addClass("ui-column").append(n("
    ").addClass("ui-column-left").append(this.message.$el).append(this.$form=n("
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    Length Format

    The length format is two-column, separated by whitespace, of the form:

    chrom/contig   length of chrom/contig

    For example, the first few entries of mm9.len are as follows:

    chr1    197195432\nchr2    181748087\nchr3    159599783\nchr4    155630120\nchr5    152537259

    Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).

    "},_templateFasta:function(){return"

    FASTA format

    This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.

    Here is a snippet from an example multi-fasta file:

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    "}});t.default={View:_}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(e){this.options=s.default.merge(e,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(e){this.row.append(n("

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    '+e.description+"
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t&&i&&t!==i?T.overlap_results.DIF_CHROMS:na?n>o?T.overlap_results.AFTER:s<=o?T.overlap_results.CONTAINED_BY:T.overlap_results.OVERLAP_END:s>=o?T.overlap_results.CONTAINS:T.overlap_results.CONTAINED_BY},trim:function(e){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var t=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>t&&(this.attributes.end=t-1)}return this},contains:function(e){return this.compute_overlap(e)===T.overlap_results.CONTAINS},overlaps:function(e){return 0===l.intersection([this.compute_overlap(e)],[T.overlap_results.DIF_CHROMS,T.overlap_results.BEFORE,T.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),M=n.Collection.extend({model:T}),$=n.Model.extend({defaults:{region:null,note:""},initialize:function(e){this.set("region",new 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0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),k=x.extend({defaults:l.extend({},x.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){x.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")u.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,n,i)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,n,i,r,a){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,n))return void console.log("ERROR: problem with getting more data: current data is not compatible");var s=e.get("start");a===this.DEEP_DATA_REQ?t.extend(r,{start_val:o.data.length+1}):a===this.BROAD_DATA_REQ&&(s=(o.max_high?o.max_high:o.data[o.data.length-1][2])+1);var l=e.copy().set("start",s),c=this,d=this.load_data(l,n,i,r),u=t.Deferred();return this.set_data(e,u),t.when(d).then(function(t){t.data&&(t.data=o.data.concat(t.data),t.max_low&&(t.max_low=o.max_low),t.message&&(t.message=t.message.replace(/[0-9]+/,t.data.length))),c.set_data(e,t),u.resolve(t)}),u},can_get_more_detailed_data:function(t){var e=this.get_elt(t);return"bigwig"===e.dataset_type&&e.data.length<8e3},get_more_detailed_data:function(t,e,n,i,r){var a=this._mark_stale(t);return a?(r||(r={}),"bigwig"===a.dataset_type&&(r.num_samples=1e3*i),this.load_data(t,e,n,r)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(t){var e=this.get_elt(t);return e||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString()),e.stale=!0,e},get_genome_wide_data:function(e){var n=this,i=!0,r=l.map(e.get("chroms_info").chrom_info,function(t){var e=n.get_elt(new S({chrom:t.chrom,start:0,end:t.len}));return e||(i=!1),e});if(i)return r;var a=t.Deferred();return t.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(t){n.add_data(t.data),a.resolve(t.data)}),a},subset_entry:function(t,e){var n={bigwig:function(t,e){return l.filter(t,function(t){return t[0]>=e.get("start")&&t[0]<=e.get("end")})},refseq:function(e,n){var i=n.get("start")-t.region.get("start");return t.data.slice(i,i+n.length())}},i=t.data;return!t.region.same(e)&&t.dataset_type in n&&(i=n[t.dataset_type](t.data,e)),{region:e,data:i,dataset_type:t.dataset_type}}}),M=k.extend({initialize:function(t){var e=new i.Model;e.urlRoot=t.data_url,this.set("dataset",e)},load_data:function(t,e,n,i){return t.length()<=1e5?k.prototype.load_data.call(this,t,e,n,i):{data:null,region:t}}}),C=i.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=l.find(this.get_chroms_info(),function(e){return e.chrom===t});return new S({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return l.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),S=i.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),n=e[0],i=e[1].split("-");this.set({chrom:n,start:parseInt(i[0],10),end:parseInt(i[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new S({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),n=t.get("chrom"),i=this.get("start"),r=t.get("start"),a=this.get("end"),o=t.get("end");return e&&n&&e!==n?S.overlap_results.DIF_CHROMS:ir?i>o?S.overlap_results.AFTER:a<=o?S.overlap_results.CONTAINED_BY:S.overlap_results.OVERLAP_END:a>=o?S.overlap_results.CONTAINS:S.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===S.overlap_results.CONTAINS},overlaps:function(t){return 0===l.intersection([this.compute_overlap(t)],[S.overlap_results.DIF_CHROMS,S.overlap_results.BEFORE,S.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),T=i.Collection.extend({model:S}),A=i.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new S(t.region))}}),j=i.Collection.extend({model:A}),E=i.Model.extend(y).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new d.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",p.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var n=this.get("preloaded_data");n=n?n.data:[],this.set("data_manager",new k({dataset:this.get("dataset"),init_data:n}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===l.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),O=i.Collection.extend({model:E}),L=i.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),N=L.extend(y).extend({defaults:l.extend({},L.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new O(t.tracks));var e=[];this.set("config",p.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs)),this.unset("tracks"),this.get("drawables").each(function(t){t.unset("preloaded_data")})},add_tracks:function(t){this.get("drawables").add(t)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(t,e){return{obj_type:"View",prefs:{name:e.get("title"),content_visible:!0},drawables:e.get("drawables")}}}}),I=i.Router.extend({initialize:function(t){var e=this;this.view=t.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w+]+:[\d,]+-[\d,]+)$/,"change_location"),this.view.on("navigate",function(t){e.navigate(t)})},change_location:function(t){this.view.go_to(t)}});e.default={BackboneTrack:E,BrowserBookmark:A,BrowserBookmarkCollection:j,Cache:x,CanvasManager:w,Genome:C,GenomeDataManager:k,GenomeRegion:S,GenomeRegionCollection:T,GenomeVisualization:N,GenomeReferenceDataManager:M,TrackBrowserRouter:I,Visualization:L,select_datasets:b}}).call(e,n(0),n(2))},,,function(t,e,n){"use strict";(function(t,n){function i(t){t+="";for(var e=/(\d+)(\d{3})/;e.test(t);)t=t.replace(e,"$1,$2");return t}Object.defineProperty(e,"__esModule",{value:!0});var r=function(t){return"promise"in t},a=t.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(t){return!0}},go:function(){var t=n.Deferred(),e=this,i=e.get("ajax_settings"),r=e.get("success_fn"),a=e.get("interval");return function 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s.addClass("editable-text").click(function(o){if(!(a(this).children(":input").length>0)){s.removeClass("editable-text");var l,c,d=function(t){s.find(":input").remove(),""!==t?s.text(t):s.html("
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this.setElement(e({library:t,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(t){this.$el.find('[data-toggle="tooltip"]').tooltip("dispose");var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find('[data-toggle="tooltip"]').tooltip({trigger:"hover"})},prepareButtons:function(t){var e=this.element_visibility_config;!1===this.edit_mode?(e.save_library_btn=!1,e.cancel_library_btn=!1,e.delete_library_btn=!1,!0===t.get("deleted")?(e.undelete_library_btn=!0,e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1):!1===t.get("deleted")&&(e.save_library_btn=!1,e.cancel_library_btn=!1,e.undelete_library_btn=!1,!0===t.get("can_user_add")&&(e.upload_library_btn=!0),!0===t.get("can_user_modify")&&(e.edit_library_btn=!0),!0===t.get("can_user_manage")&&(e.permission_library_btn=!0))):!0===this.edit_mode&&(e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1,e.save_library_btn=!0,e.cancel_library_btn=!0,e.delete_library_btn=!0,e.undelete_library_btn=!1),this.element_visibility_config=e},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=!1,n=this.$el.find(".input_library_name").val();if(void 0!==n&&n!==t.get("name")){if(!(n.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");t.set("name",n),e=!0}var i=this.$el.find(".input_library_description").val();void 0!==i&&i!==t.get("description")&&(t.set("description",i),e=!0);var r=this.$el.find(".input_library_synopsis").val();if(void 0!==r&&r!==t.get("synopsis")&&(t.set("synopsis",r),e=!0),e){var a=this;t.save(null,{patch:!0,success:function(t){a.edit_mode=!1,a.repaint(t),o.default.success("Changes to library saved.")},error:function(t,e){void 0!==e.responseJSON?o.default.error(e.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(t),o.default.info("Nothing has changed.")},delete_library:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=this;t.destroy({success:function(t){t.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(t),e.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(i(".tooltip").hide(),e.repaint(t),e.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&e.repaint(t),o.default.success("Library has been marked deleted.")},error:function(t,e){void 0!==e.responseJSON?o.default.error(e.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=this;t.url=t.urlRoot+t.id+"?undelete=true",t.destroy({success:function(t){t.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(t),e.edit_mode=!1,e.repaint(t),o.default.success("Library has been undeleted.")},error:function(t,e){void 0!==e.responseJSON?o.default.error(e.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return r.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) 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t=this.templateToolBar(),e=!1,n=!0;Galaxy.user&&(e=Galaxy.user.isAdmin(),n=Galaxy.user.isAnonymous()),this.$el.html(t({admin_user:e,anon_user:n})),e&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(t){this.options=i.extend(this.options,t);var e=this.templatePaginator();this.$el.find(".library-paginator").html(e({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,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(t){t.preventDefault(),t.stopPropagation();var e=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,s.default)("Create New Library"),body:this.templateNewLibraryInModal(),buttons:{Create:function(){e.createNewLibrary()},Close:function(){e.modal.hide()}}})},createNewLibrary:function(){var t=this.serializeNewLibrary();if(this.validateNewLibrary(t)){var e=new u.default.Library,n=this;e.save(t,{success:function(t){Galaxy.libraries.libraryListView.collection.add(t),n.modal.hide(),n.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),c.default.success("Library created.")},error:function(t,e){void 0!==e.responseJSON?c.default.error(e.responseJSON.err_msg):c.default.error("An error occured.")}})}else c.default.error("Library's name is missing.");return!1},showPageSizePrompt:function(t){t.preventDefault();var e=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=e&&e==parseInt(e)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(e)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){r("input[name='Name']").val(""),r("input[name='Description']").val(""),r("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:r("input[name='Name']").val(),description:r("input[name='Description']").val(),synopsis:r("input[name='Synopsis']").val()}},validateNewLibrary:function(t){return""!==t.name},includeDeletedChecked:function(t){t.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(t){t.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(t){var e=r(".library-search-input").val();this.options.search_term=e,Galaxy.libraries.libraryListView.searchLibraries(e)},templateToolBar:function(){return i.template(['
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    Select history

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    This {{model_class_lc}} is currently restricted so that only you and the users listed below can access it. You can:

    Make {{model_class}} Accessible via Link + + Also make all objects within the {{model_class}} accessible. + +
    Generates a web link that you can share with other people so that they can view and import the {{model_class_lc}}.

    Make {{model_class}} Accessible and Publish + + Also make all objects within the {{model_class}} accessible. + +
    Makes the {{model_class_lc}} accessible via link (see above) and publishes the {{model_class_lc}} to Galaxy's Published {{plural_name}} section, where it is publicly listed and searchable.


    @@ -131,6 +139,9 @@ export default { }, slug_url() { return `${Galaxy.root}${this.model_class_lc}/set_slug_async/?id=${this.id}`; + }, + has_possible_members(){ + return ["history"].indexOf(this.model_class_lc) > -1;; } }, data() { @@ -147,7 +158,8 @@ export default { published: false, users_shared_with: [] }, - share_fields: ["email", { key: "id", label: "" }] + share_fields: ["email", { key: "id", label: "" }], + make_members_public: false, }; }, created: function() { @@ -180,11 +192,15 @@ export default { .catch(error => (this.err_msg = error.response.data.err_msg)); }, setSharing: function(action, user_id) { - axios - .post(`${Galaxy.root}api/${this.plural_name_lc}/${this.id}/sharing`, { + let data = { action: action, user_id: user_id - }) + } + if (this.has_possible_members){ + data.make_members_public = this.make_members_public; + } + axios + .post(`${Galaxy.root}api/${this.plural_name_lc}/${this.id}/sharing`, data) .then(response => { Object.assign(this.item, response.data); }) @@ -233,3 +249,8 @@ export default { } }; + diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 1750c72fef9..7183cbe76b8 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1532,6 +1532,10 @@ class History(HasTags, Dictifiable, UsesAnnotations, HasName): return new_history + @property + def has_possible_members(self): + return True + @property def activatable_datasets(self): # This needs to be a list diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index 14bf58dda18..f604fcba4f7 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1399,18 +1399,25 @@ class SharableMixin(object): @web.expose_api def sharing(self, trans, id, payload=None, **kwd): + skipped = False class_name = self.manager.model_class.__name__ item = self.get_object(trans, id, class_name, check_ownership=True, check_accessible=True, deleted=False) if payload and payload.get("action"): action = payload.get("action") if action == "make_accessible_via_link": self._make_item_accessible(trans.sa_session, item) + if item.has_possible_members and payload.get("make_members_public", False): + shared, skipped = self._make_members_public(trans, item) elif action == "make_accessible_and_publish": self._make_item_accessible(trans.sa_session, item) + if item.has_possible_members and payload.get("make_members_public", False): + shared, skipped = self._make_members_public(trans, item) item.published = True elif action == "publish": if item.importable: item.published = True + if item.has_possible_members and payload.get("make_members_public", False): + shared, skipped = self._make_members_public(trans, item) else: raise exceptions.MessageException("%s not importable." % class_name) elif action == "disable_link_access": @@ -1435,8 +1442,29 @@ class SharableMixin(object): item_dict = self.serializer.serialize_to_view(item, user=trans.user, trans=trans, default_view="sharing") item_dict["users_shared_with"] = [{"id": self.app.security.encode_id(a.user.id), "email": a.user.email} for a in item.users_shared_with] + if skipped: + item_dict["skipped"] = True return item_dict + def _make_members_public(self, trans, item): + """ Make the non-purged datasets in history public + Performs pemissions check. + """ + # TODO eventually we should handle more classes than just History + skipped = False + for hda in item.activatable_datasets: + dataset = hda.dataset + if not trans.app.security_agent.dataset_is_public(dataset): + if trans.app.security_agent.can_manage_dataset(trans.user.all_roles(), dataset): + try: + trans.app.security_agent.make_dataset_public(hda.dataset) + except Exception: + log.warning("Unable to make dataset with id: %s public.".format(dataset.id) + skipped = True + else: + skipped = True + return item, skipped + # -- Abstract methods. -- @web.expose From 70e325574cb82be62b1be8090e714ce44441686b Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 27 Sep 2018 22:20:00 +0200 Subject: [PATCH 262/352] Use with statement for all file uploads --- test/api/test_tools_upload.py | 54 +++++++++++++++++++++-------------- 1 file changed, 32 insertions(+), 22 deletions(-) diff --git a/test/api/test_tools_upload.py b/test/api/test_tools_upload.py index e0aaf909604..1e5d22b542e 100644 --- a/test/api/test_tools_upload.py +++ b/test/api/test_tools_upload.py @@ -82,13 +82,15 @@ class ToolsUploadTestCase(api.ApiTestCase): def test_fetch_compressed_with_explicit_type(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), api="fetch", ext="fastqsanger.gz") + with open(fastqgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, api="fetch", ext="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz" def test_fetch_compressed_default(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), api="fetch", assert_ok=False) + with open(fastqgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, api="fetch", assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details @@ -96,31 +98,35 @@ class ToolsUploadTestCase(api.ApiTestCase): def test_fetch_compressed_auto_decompress_target(self, history_id): # TODO: this should definitely be fixed to allow auto decompression via that API. fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), - api="fetch", - history_id=history_id, - assert_ok=False, - auto_decompress=True) + with open(fastqgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, + api="fetch", + history_id=history_id, + assert_ok=False, + auto_decompress=True) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details def test_upload_decompress_off_with_auto_by_default(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") - details = self._upload_and_get_details(open(bedgz_path, "rb"), file_type="auto") + with open(bedgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bed", details def test_upload_decompresses_if_uncompressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), file_type="fastqsanger") + with open(fastqgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, file_type="fastqsanger") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger", details assert details["file_size"] == 178, details def test_upload_decompress_off_if_compressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), file_type="fastqsanger.gz") + with open(fastqgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, file_type="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details assert details["file_size"] == 161, details @@ -128,19 +134,21 @@ class ToolsUploadTestCase(api.ApiTestCase): def test_upload_auto_decompress_off(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") - details = self._upload_and_get_details(open(bedgz_path, "rb"), file_type="auto", assert_ok=False, auto_decompress=False) + with open(bedgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, file_type="auto", assert_ok=False, auto_decompress=False) assert details["file_ext"] == "binary", details @uses_test_history(require_new=True) def test_fetch_compressed_with_auto(self, history_id): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. # TODO: this should definitely be fixed to allow auto decompression via that API. - fastqgz_path = TestDataResolver().get_filename("4.bed.gz") - details = self._upload_and_get_details(open(fastqgz_path, "rb"), - api="fetch", - history_id=history_id, - auto_decompress=True, - assert_ok=False) + bedgz_path = TestDataResolver().get_filename("4.bed.gz") + with open(bedgz_path, "rb") as fh: + details = self._upload_and_get_details(fh, + api="fetch", + history_id=history_id, + auto_decompress=True, + assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bed" @@ -243,16 +251,18 @@ class ToolsUploadTestCase(api.ApiTestCase): @uses_test_history(require_new=False) def test_fetch_bam_file(self, history_id): bam_path = TestDataResolver().get_filename("1.bam") - details = self._upload_and_get_details(open(bam_path, "rb"), - api="fetch", - history_id=history_id, - assert_ok=False) + with open(bam_path, "rb") as fh: + details = self._upload_and_get_details(fh, + api="fetch", + history_id=history_id, + assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bam", details def test_upload_bam_file(self): bam_path = TestDataResolver().get_filename("1.bam") - details = self._upload_and_get_details(open(bam_path, "rb"), file_type="auto") + with open(bam_path, "rb") as fh: + details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bam", details From e4399021520440a8f58e33dbae161f031f8da9eb Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 27 Sep 2018 16:50:12 -0400 Subject: [PATCH 263/352] show warning to user if some of the items within were not published --- client/galaxy/scripts/components/Sharing.vue | 12 +++++++++--- lib/galaxy/web/base/controller.py | 3 ++- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/client/galaxy/scripts/components/Sharing.vue b/client/galaxy/scripts/components/Sharing.vue index 67b2ea22abb..8ff0d2cb934 100644 --- a/client/galaxy/scripts/components/Sharing.vue +++ b/client/galaxy/scripts/components/Sharing.vue @@ -1,7 +1,7 @@