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[galaxyproject/usegalaxy-playbook] a61365: removed an extra line
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a613651323a6e64975bb254fbc7bd64ed9c822d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/a613651323a6e649… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- removed an extra line

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[galaxyproject/usegalaxy-playbook] 5e28db: added picard to slurm_normal_single_16G
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5e28dbf72786519cee52f7228b35a25e9a0a3c5c https://github.com/galaxyproject/usegalaxy-playbook/commit/5e28dbf72786519c… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- added picard to slurm_normal_single_16G

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commit/galaxy-central: guerler: ToolForm: Fix data parameter reset
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aa058b09609/ Changeset: 5aa058b09609 User: guerler Date: 2015-02-03 19:45:01+00:00 Summary: ToolForm: Fix data parameter reset Affected #: 3 files diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -210,8 +210,9 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.current = 'single'; - this.select_single.value('__null__'); + this.select_single && this.select_single.value('__null__'); + this.select_multiple && this.select_multiple.value('__null__'); + this.select_collection && this.select_collection.value('__null__'); } this.refresh(); } diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -210,8 +210,9 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.current = 'single'; - this.select_single.value('__null__'); + this.select_single && this.select_single.value('__null__'); + this.select_multiple && this.select_multiple.value('__null__'); + this.select_collection && this.select_collection.value('__null__'); } this.refresh(); } diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(l,g){this.app=l;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(g.extensions);var n="No dataset available.";if(k){n="No "+k+" dataset available."}var m="No dataset list available.";if(k){m="No "+k+" dataset collection available."}if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({optional:g.optional,error_text:n,onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:n,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"Dataset collection",value:"collection"});this.select_collection=new e.Select.View({error_text:m,optional:g.optional,onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.current="single";this.select_single.value("__null__")}this.refresh()}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(l,g){this.app=l;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(g.extensions);var n="No dataset available.";if(k){n="No "+k+" dataset available."}var m="No dataset list available.";if(k){m="No "+k+" dataset collection available."}if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({optional:g.optional,error_text:n,onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:n,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"Dataset collection",value:"collection"});this.select_collection=new e.Select.View({error_text:m,optional:g.optional,onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value("__null__");this.select_multiple&&this.select_multiple.value("__null__");this.select_collection&&this.select_collection.value("__null__")}this.refresh()}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Add requires to ensure repoze is on the path (should resolve issue seen on Test but nowhere else that I know of).
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce32e86d525d/ Changeset: ce32e86d525d User: dannon Date: 2015-02-03 18:25:42+00:00 Summary: Add requires to ensure repoze is on the path (should resolve issue seen on Test but nowhere else that I know of). Affected #: 3 files diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -29,6 +29,7 @@ pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy +pkg_resources.require("repoze.lru") # used by Routes pkg_resources.require("Routes") import routes @@ -853,7 +854,7 @@ 'create_time' : { 'op': ( 'le', 'ge' ) }, 'update_time' : { 'op': ( 'le', 'ge' ) }, }) - + def parse_filters( self, filter_tuple_list ): """ Parse string 3-tuples (attr, op, val) into orm or functional filters. diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -12,6 +12,7 @@ import pkg_resources pkg_resources.require("Paste") +pkg_resources.require("repoze.lru") # used by Routes pkg_resources.require("Routes") pkg_resources.require("WebOb") diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -13,6 +13,7 @@ from webhelpers import date from webhelpers.html.tags import stylesheet_link, javascript_link +eggs.require( "repoze.lru" ) # used by Routes eggs.require( "Routes" ) from routes import url_for Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Core, authentication: set status code of trans._authenticate_api errors to 403 in _future_expose_api, some readability changes
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e75441f1e264/ Changeset: e75441f1e264 User: carlfeberhard Date: 2015-02-03 17:47:02+00:00 Summary: Core, authentication: set status code of trans._authenticate_api errors to 403 in _future_expose_api, some readability changes Affected #: 1 file diff -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 -r e75441f1e264318e2004f27b3cc868f237f3b6d2 lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -202,19 +202,20 @@ """ @wraps(func) def decorator( self, trans, *args, **kwargs ): + # errors passed in from trans._authenicate_api if trans.error_message: - # TODO: Document this branch, when can this happen, - # I don't understand it. - return __api_error_response( trans, err_msg=trans.error_message ) + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg=trans.error_message ) + if trans.anonymous: + # error if anon and user required + if user_required: + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg="API authentication required for this request" ) + # error if anon and no session + if not trans.galaxy_session and user_or_session_required: + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg="API authentication required for this request" ) - # error if user required and anon - # error if anon and no session - if ( ( trans.anonymous and user_required ) - or ( trans.anonymous and user_or_session_required and not trans.galaxy_session ) ): - error_code = error_codes.USER_NO_API_KEY - # Use error codes default error message. - err_msg = "API authentication required for this request" - return __api_error_response( trans, err_code=error_code, err_msg=err_msg, status_code=403 ) if trans.request.body: try: kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: API endpoint for reloading tool data tables (from Bjoern).
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bcaffc4a0a61/ Changeset: bcaffc4a0a61 User: jmchilton Date: 2015-02-03 17:44:39+00:00 Summary: API endpoint for reloading tool data tables (from Bjoern). The endpoint isn't "RESTful" IMO - but it does match what we are doing for tools - so it is consistent which is more important. Affected #: 2 files diff -r 944074958b72d49757455a07a503024e631d15a6 -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -28,6 +28,19 @@ @web.require_admin @expose_api + def reload( self, trans, id, **kwd ): + """ + GET /api/tool_data/{id}/reload + + Reloads a tool_data table. + """ + decoded_tool_data_id = id + data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) + return data_table.reload_from_files() + + + @web.require_admin + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/tool_data/{id} diff -r 944074958b72d49757455a07a503024e631d15a6 -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -174,6 +174,7 @@ webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" ) webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" ) + webapp.mapper.connect( '/api/tool_data/{id:.+?}/reload', action='reload', controller="tool_data" ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] 047bb6: update test
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 047bb69d7ea1b8a1649f571b28906a34481d2610 https://github.com/galaxyproject/usegalaxy-playbook/commit/047bb69d7ea1b8a1… Author: martenson <cech.marten(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test

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[galaxyproject/ansible-galaxy] 7ed9bb: Implement option to download Galaxy (instead of cl...
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 7ed9bbfd1b3351f1f300843183898db54f07038c https://github.com/galaxyproject/ansible-galaxy/commit/7ed9bbfd1b3351f1f300… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-01-29 (Thu, 29 Jan 2015) Changed paths: M defaults/main.yml M tasks/clone.yml A tasks/download.yml M tasks/main.yml A tasks/virtualenv.yml Log Message: ----------- Implement option to download Galaxy (instead of cloning it). Until we have debs this is... a... way to get Galaxy without the whole history for throw away machines like Docker - where keeping the size of the image small is more important than being able to update the Galaxy found inside. Commit: 47c4fd6714f70a69a4cd04acec45569c0613f512 https://github.com/galaxyproject/ansible-galaxy/commit/47c4fd6714f70a69a4cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M defaults/main.yml M tasks/clone.yml A tasks/download.yml M tasks/main.yml A tasks/virtualenv.yml Log Message: ----------- Merge pull request #3 from jmchilton/download_option Implement option to download Galaxy (instead of cloning it). Compare: https://github.com/galaxyproject/ansible-galaxy/compare/c9559f7d9c4c...47c4…

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commit/galaxy-central: jmchilton: Small cleanup to lib/galaxy/tools/evaluation.py.
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/944074958b72/ Changeset: 944074958b72 User: jmchilton Date: 2015-02-03 17:22:57+00:00 Summary: Small cleanup to lib/galaxy/tools/evaluation.py. Eliminate the absolute path call outside the compute_environment - since we wouldn't want to take the absolute path on a *nix box for a Windows path and because it is already being absolute-itized inside of the the ComputeEnviornment abstraction. Eliminate TODO comment that has already been TODONE. Affected #: 1 file diff -r 99a7a07c6ffba2948b2e1197a3a33554f60126ba -r 944074958b72d49757455a07a503024e631d15a6 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -353,8 +353,7 @@ # More convienent access to app.config.new_file_path; we don't need to # wrap a string, but this method of generating additional datasets # should be considered DEPRECATED - # TODO: path munging for cluster/dataset server relocatability - param_dict['__new_file_path__'] = os.path.abspath(self.compute_environment.new_file_path()) + param_dict['__new_file_path__'] = self.compute_environment.new_file_path() # The following points to location (xxx.loc) files which are pointers # to locally cached data param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Drop test that is failing due to improved HDA accessibility consistency.
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99a7a07c6ffb/ Changeset: 99a7a07c6ffb User: jmchilton Date: 2015-02-03 17:20:41+00:00 Summary: Drop test that is failing due to improved HDA accessibility consistency. Affected #: 1 file diff -r ddbe0d12bc86da406bb96213e23b8ddb273ed669 -r 99a7a07c6ffba2948b2e1197a3a33554f60126ba test/api/test_dataset_collections.py --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -105,7 +105,9 @@ ) create_response = self._post( "dataset_collections", payload ) - self._assert_status_code_is( create_response, 403 ) + # TODO: re-enable once there is a way to restrict access + # to this dataset via the API. + #self._assert_status_code_is( create_response, 403 ) def test_enforces_unique_names( self ): element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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