From c0c587abdf23b8d5a01222cace7cc81f4b3d82f4 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 28 Aug 2018 10:40:08 -0400 Subject: [PATCH 01/20] Add page_to_raw to decode ids in the database. --- scripts/page_to_raw.py | 73 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 scripts/page_to_raw.py diff --git a/scripts/page_to_raw.py b/scripts/page_to_raw.py new file mode 100644 index 00000000000..166c1e2167b --- /dev/null +++ b/scripts/page_to_raw.py @@ -0,0 +1,73 @@ +import argparse +import logging +import os +import sys + +sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))) + +try: + from bs4 import BeautifulSoup +except ImportError: + print("Please install the BeautifulSoup 4 Python module to use this script.") + exit(4) + +import galaxy +import galaxy.app +import galaxy.config +from galaxy.objectstore import build_object_store_from_config +from galaxy.util.script import app_properties_from_args, populate_config_args +from galaxy.web.security import SecurityHelper + + +def main(argv): + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='') + parser.add_argument('-e', '--encode', action="store_true", help='Switch to encode mode') + populate_config_args(parser) + args = parser.parse_args() + properties = app_properties_from_args(args) + config = galaxy.config.Configuration(**properties) + secret = args.secret_key or config.id_secret + security_helper = SecurityHelper(id_secret=secret) + object_store = build_object_store_from_config(config) + if not config.database_connection: + logging.warning("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml") + + model = galaxy.config.init_models_from_config(config, object_store=object_store) + session = model.context.current + pagerevs = session.query(model.PageRevision).all() + for p in pagerevs: + changed = False + s = BeautifulSoup(p.content, features='lxml') + divs = s.find_all("div", class_="embedded-item") + for div in divs: + # Each of these needs to have the id split, re-encoded, and saved. + cls, hsh = div['id'].split('-') + try: + if args.encode: + # ENSURE THIS IS AN INTEGER BEFORE ENCODING + try: + int(hsh) + except ValueError: + print("SKIP: Encoding mode activated, but encountered id %s, skipping." % hsh) + new_id = security_helper.encode_id(hsh) + else: + new_id = security_helper.decode_id(hsh) + div['id'] = "%s-%s" % (cls, new_id) + changed = True + except UnicodeEncodeError: + print("Encoding error translating identifiers -- are you sure the id_secret is correct? Rolling back session so no changes are made.") + session.rollback() + exit(2) + except ValueError: + print("Decoding error -- it looks like the values are already encoded. Rolling back session so no changes are made.") + session.rollback() + exit(3) + if changed: + p.content = str(s) + session.add(p) + session.flush() + + +if __name__ == '__main__': + main(sys.argv) From a23e5d77a54710662a784d7ec1454e3af54c3097 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 28 Aug 2018 12:56:36 -0400 Subject: [PATCH 02/20] Allow pages to read both encoded and unencoded ids out of the database. Always save unencoded version, with the additional benefit of using a simpler, smaller placeholder. --- lib/galaxy/webapps/galaxy/controllers/page.py | 33 ++++++++++++++----- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 943dd0da10f..eb9ac3e1d2a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -698,6 +698,10 @@ class PageController(BaseUIController, SharableMixin, email=email, use_panels=use_panels) + def _placeholderRenderForSave(self, trans, item_class, item_id): + decoded_item_id = self.app.security.decode_id(item_id) + return '
' % (item_class, decoded_item_id) + @web.expose @web.require_login() def save(self, trans, id, content, annotations): @@ -707,6 +711,10 @@ class PageController(BaseUIController, SharableMixin, # Sanitize content content = sanitize_html(content) + processor = _PageContentProcessor(trans, self._placeholderRenderForSave) + processor.feed(content) + # Output is string, so convert to unicode for saving. + content = unicodify(processor.output(), 'utf-8') # Add a new revision to the page with the provided content. page_revision = model.PageRevision() @@ -901,12 +909,10 @@ class PageController(BaseUIController, SharableMixin, def get_item(self, trans, id): return self.get_page(trans, id) - def _get_embedded_history_html(self, trans, id): + def _get_embedded_history_html(self, trans, decoded_id): """ Returns html suitable for embedding in another page. """ - # TODO: should be moved to history controller and/or called via ajax from the template - decoded_id = self.decode_id(id) # histories embedded in pages are set to importable when embedded, check for access here history = self.history_manager.get_accessible(decoded_id, trans.user, current_history=trans.history) @@ -929,11 +935,11 @@ class PageController(BaseUIController, SharableMixin, content_dicts=contents) return filled - def _get_embedded_visualization_html(self, trans, id): + def _get_embedded_visualization_html(self, trans, encoded_id): """ Returns html suitable for embedding visualizations in another page. """ - visualization = self.get_visualization(trans, id, False, True) + visualization = self.get_visualization(trans, encoded_id, False, True) visualization.annotation = self.get_item_annotation_str(trans.sa_session, visualization.user, visualization) if not visualization: return None @@ -955,11 +961,20 @@ class PageController(BaseUIController, SharableMixin, def _get_embed_html(self, trans, item_class, item_id): """ Returns HTML for embedding an item in a page. """ item_class = self.get_class(item_class) + # Assume if item id is integer and less than 10**15, it's unencoded. + try: + decoded_id = int(item_id) + encoded_id = self.app.security.encode_id(item_id) + except ValueError: + # It's an encoded id. + encoded_id = item_id + decoded_id = self.app.security.decode_id(item_id) + decoded_id = trans.app.security.decode_id(encoded_id) + # These will all first try an unencoded id, then retry with an encoded one. if item_class == model.History: - return self._get_embedded_history_html(trans, item_id) + return self._get_embedded_history_html(trans, decoded_id) elif item_class == model.HistoryDatasetAssociation: - decoded_id = self.decode_id(item_id) dataset = self.hda_manager.get_accessible(decoded_id, trans.user) dataset = self.hda_manager.error_if_uploading(dataset) @@ -969,14 +984,14 @@ class PageController(BaseUIController, SharableMixin, return trans.fill_template("dataset/embed.mako", item=dataset, item_data=data) elif item_class == model.StoredWorkflow: - workflow = self.get_stored_workflow(trans, item_id, False, True) + workflow = self.get_stored_workflow(trans, encoded_id, False, True) workflow.annotation = self.get_item_annotation_str(trans.sa_session, workflow.user, workflow) if workflow: self.get_stored_workflow_steps(trans, workflow) return trans.fill_template("workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps) elif item_class == model.Visualization: - return self._get_embedded_visualization_html(trans, item_id) + return self._get_embedded_visualization_html(trans, encoded_id) elif item_class == model.Page: pass From b8fa78358c07fc2b0eaa53f2e02a2674cc522ef1 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 28 Aug 2018 13:21:35 -0400 Subject: [PATCH 03/20] Remove outdated comment; I refactored to handle this. --- lib/galaxy/webapps/galaxy/controllers/page.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index eb9ac3e1d2a..b339d3b0f79 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -970,7 +970,6 @@ class PageController(BaseUIController, SharableMixin, encoded_id = item_id decoded_id = self.app.security.decode_id(item_id) decoded_id = trans.app.security.decode_id(encoded_id) - # These will all first try an unencoded id, then retry with an encoded one. if item_class == model.History: return self._get_embedded_history_html(trans, decoded_id) From f9d791c228d1dfafdaaae404ae1ec6fb94f51555 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 28 Aug 2018 16:02:07 -0400 Subject: [PATCH 04/20] Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully. --- lib/galaxy/webapps/galaxy/controllers/page.py | 14 ++++-- scripts/page_to_raw.py | 49 +++++-------------- 2 files changed, 22 insertions(+), 41 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index b339d3b0f79..7215eb335c5 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -698,10 +698,6 @@ class PageController(BaseUIController, SharableMixin, email=email, use_panels=use_panels) - def _placeholderRenderForSave(self, trans, item_class, item_id): - decoded_item_id = self.app.security.decode_id(item_id) - return '
' % (item_class, decoded_item_id) - @web.expose @web.require_login() def save(self, trans, id, content, annotations): @@ -711,7 +707,7 @@ class PageController(BaseUIController, SharableMixin, # Sanitize content content = sanitize_html(content) - processor = _PageContentProcessor(trans, self._placeholderRenderForSave) + processor = _PageContentProcessor(trans, _placeholderRenderForSave) processor.feed(content) # Output is string, so convert to unicode for saving. content = unicodify(processor.output(), 'utf-8') @@ -994,3 +990,11 @@ class PageController(BaseUIController, SharableMixin, elif item_class == model.Page: pass + + +def _placeholderRenderForSave(trans, item_class, item_id): + try: + decoded_item_id = int(item_id) + except ValueError: + decoded_item_id = trans.app.security.decode_id(item_id) + return '
' % (item_class, decoded_item_id) diff --git a/scripts/page_to_raw.py b/scripts/page_to_raw.py index 166c1e2167b..073462ab000 100644 --- a/scripts/page_to_raw.py +++ b/scripts/page_to_raw.py @@ -5,24 +5,20 @@ import sys sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))) -try: - from bs4 import BeautifulSoup -except ImportError: - print("Please install the BeautifulSoup 4 Python module to use this script.") - exit(4) - import galaxy import galaxy.app import galaxy.config from galaxy.objectstore import build_object_store_from_config +from galaxy.util import unicodify +from galaxy.util.bunch import Bunch from galaxy.util.script import app_properties_from_args, populate_config_args from galaxy.web.security import SecurityHelper +from galaxy.webapps.galaxy.controllers.page import _PageContentProcessor, _placeholderRenderForSave def main(argv): parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='') - parser.add_argument('-e', '--encode', action="store_true", help='Switch to encode mode') populate_config_args(parser) args = parser.parse_args() properties = app_properties_from_args(args) @@ -36,36 +32,17 @@ def main(argv): model = galaxy.config.init_models_from_config(config, object_store=object_store) session = model.context.current pagerevs = session.query(model.PageRevision).all() - for p in pagerevs: - changed = False - s = BeautifulSoup(p.content, features='lxml') - divs = s.find_all("div", class_="embedded-item") - for div in divs: - # Each of these needs to have the id split, re-encoded, and saved. - cls, hsh = div['id'].split('-') - try: - if args.encode: - # ENSURE THIS IS AN INTEGER BEFORE ENCODING - try: - int(hsh) - except ValueError: - print("SKIP: Encoding mode activated, but encountered id %s, skipping." % hsh) - new_id = security_helper.encode_id(hsh) - else: - new_id = security_helper.decode_id(hsh) - div['id'] = "%s-%s" % (cls, new_id) - changed = True - except UnicodeEncodeError: - print("Encoding error translating identifiers -- are you sure the id_secret is correct? Rolling back session so no changes are made.") - session.rollback() - exit(2) - except ValueError: - print("Decoding error -- it looks like the values are already encoded. Rolling back session so no changes are made.") - session.rollback() - exit(3) - if changed: - p.content = str(s) + mock_trans = Bunch(app=Bunch(security=security_helper), sa_session=session) + try: + for p in pagerevs: + processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave) + processor.feed(p.content) + p.content = unicodify(processor.output(), 'utf-8') session.add(p) + except Exception: + logging.exception("Error parsing page, rolling everything back. Please report this error.") + session.rollback() + exit(2) session.flush() From f01726dc6f27492a20007ca51d4dda82f1eb43c8 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 11:01:33 -0400 Subject: [PATCH 05/20] Almost there, one more (preexisting) bug to fix. This adds validation on save and correct processing to the page writer. --- lib/galaxy/webapps/galaxy/controllers/page.py | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 7215eb335c5..70e5f1577f0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -992,9 +992,31 @@ class PageController(BaseUIController, SharableMixin, pass +PLACEHOLDER_TEMPLATE = ''' +
+

Embedded Galaxy {class_shorthand} - '{item_name}'

+

[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]

+
''' + +# This is a mapping of the id portion of page contents to the cssclass/shortname. +PAGE_CLASS_MAPPING = { + 'History': 'History', + 'HistoryDatasetAssociation': 'Dataset', + 'StoredWorkflow': 'Workflow', + 'Visualization': 'Visualization' +} + + def _placeholderRenderForSave(trans, item_class, item_id): try: decoded_item_id = int(item_id) except ValueError: decoded_item_id = trans.app.security.decode_id(item_id) - return '
' % (item_class, decoded_item_id) + class_shorthand = PAGE_CLASS_MAPPING[item_class] + return PLACEHOLDER_TEMPLATE.format( + item_class=item_class, + class_shorthand=class_shorthand, + class_shorthand_lower=class_shorthand.lower(), + item_id=decoded_item_id, + item_name='' + ) From eb8d80b6d248eaeb7218ce0ad324be93634ca805 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 12:18:27 -0400 Subject: [PATCH 06/20] Handle item name fetching, enforce accessible --- lib/galaxy/webapps/galaxy/controllers/page.py | 19 ++++++++++++++++++- scripts/page_to_raw.py | 2 +- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 70e5f1577f0..0e07d0a43a8 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1012,11 +1012,28 @@ def _placeholderRenderForSave(trans, item_class, item_id): decoded_item_id = int(item_id) except ValueError: decoded_item_id = trans.app.security.decode_id(item_id) + item_name = '' + if item_class == 'History': + history = trans.sa_session.query(trans.model.History).get(decoded_item_id) + history = managers.base.security_check(trans, history, False, True) + item_name = history.name + elif item_class == 'HistoryDatasetAssociation': + hda = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(decoded_item_id) + history = managers.base.security_check(trans, hda , False, True) + item_name = hda.name + elif item_class == 'StoredWorkflow': + wf = trans.sa_session.query(trans.model.StoredWorkflow).get(decoded_item_id) + wf = managers.base.security_check(trans, wf, False, True) + item_name = wf.name + elif item_class == 'Visualization': + visualization = trans.sa_session.query(trans.model.Visualization).get(decoded_item_id) + visualization = managers.base.security_check(trans, visualization, False, True) + item_name = visualization.title class_shorthand = PAGE_CLASS_MAPPING[item_class] return PLACEHOLDER_TEMPLATE.format( item_class=item_class, class_shorthand=class_shorthand, class_shorthand_lower=class_shorthand.lower(), item_id=decoded_item_id, - item_name='' + item_name=item_name ) diff --git a/scripts/page_to_raw.py b/scripts/page_to_raw.py index 073462ab000..93d1af7fa2f 100644 --- a/scripts/page_to_raw.py +++ b/scripts/page_to_raw.py @@ -32,7 +32,7 @@ def main(argv): model = galaxy.config.init_models_from_config(config, object_store=object_store) session = model.context.current pagerevs = session.query(model.PageRevision).all() - mock_trans = Bunch(app=Bunch(security=security_helper), sa_session=session) + mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session) try: for p in pagerevs: processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave) From 2fa6dedf4e22351b88bb0706992928c306137cea Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 13:06:21 -0400 Subject: [PATCH 07/20] Only display encoded ids in editor as well. --- lib/galaxy/webapps/galaxy/controllers/page.py | 20 ++++++++++++++++--- templates/webapps/galaxy/page/editor.mako | 2 +- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 0e07d0a43a8..db52c8fffd5 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -620,7 +620,11 @@ class PageController(BaseUIController, SharableMixin, id = self.decode_id(id) page = trans.sa_session.query(model.Page).get(id) assert page.user == trans.user - return trans.fill_template("page/editor.mako", page=page) + content = page.latest_revision.content + processor = _PageContentProcessor(trans, _placeholderRenderForEdit) + processor.feed(content) + content = unicodify(processor.output(), 'utf-8') + return trans.fill_template("page/editor.mako", page=page, content=content) @web.expose @web.require_login("use Galaxy pages") @@ -1007,11 +1011,17 @@ PAGE_CLASS_MAPPING = { } -def _placeholderRenderForSave(trans, item_class, item_id): +def _placeholderRenderForEdit(trans, item_class, item_id): + return _placeholderRenderForSave(trans, item_class, item_id, encode=True) + + +def _placeholderRenderForSave(trans, item_class, item_id, encode=False): try: decoded_item_id = int(item_id) + encoded_item_id = trans.app.security.encode_id(item_id) except ValueError: decoded_item_id = trans.app.security.decode_id(item_id) + encoded_item_id = item_id item_name = '' if item_class == 'History': history = trans.sa_session.query(trans.model.History).get(decoded_item_id) @@ -1030,10 +1040,14 @@ def _placeholderRenderForSave(trans, item_class, item_id): visualization = managers.base.security_check(trans, visualization, False, True) item_name = visualization.title class_shorthand = PAGE_CLASS_MAPPING[item_class] + if encode: + item_id = encoded_item_id + else: + item_id = decoded_item_id return PLACEHOLDER_TEMPLATE.format( item_class=item_class, class_shorthand=class_shorthand, class_shorthand_lower=class_shorthand.lower(), - item_id=decoded_item_id, + item_id=item_id, item_name=item_name ) diff --git a/templates/webapps/galaxy/page/editor.mako b/templates/webapps/galaxy/page/editor.mako index cd4e17cc17a..3885a55f71c 100644 --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -55,7 +55,7 @@
- +
From 4fa1cc38eacbc20622f81bbe7505df0d21480b72 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 13:08:26 -0400 Subject: [PATCH 08/20] Rename page 'fixer' script --- scripts/{page_to_raw.py => pages_identifier_conversion.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename scripts/{page_to_raw.py => pages_identifier_conversion.py} (100%) diff --git a/scripts/page_to_raw.py b/scripts/pages_identifier_conversion.py similarity index 100% rename from scripts/page_to_raw.py rename to scripts/pages_identifier_conversion.py From f8273572f7aaf08cc94c06d8569b26089c231fa4 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 16:00:44 -0400 Subject: [PATCH 09/20] Fix (unrelated to the changes in this PR -- bonus bug) name injection for embedded objects. --- client/galaxy/scripts/galaxy.pages.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js index d5cca10e0cb..1188ded5dd2 100644 --- a/client/galaxy/scripts/galaxy.pages.js +++ b/client/galaxy/scripts/galaxy.pages.js @@ -444,10 +444,11 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm if ($("#make-importable:checked").val() != null) make_importable = true; grid.$("input[name=id]:checked").each(function() { + var elt = $(this); // Get item ID and name. - var item_id = $(this).val(); + var item_id = elt.val(); // Use ':first' because there are many labels in table; the first one is the item name. - var item_name = $(`label[for='${item_id}']:first`).text(); + var item_name = elt.closest('td').next('td').find('label').text(); if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular); From 5ffff7f1b455a6a0f95377f715421ee8229b56f5 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 29 Aug 2018 16:05:33 -0400 Subject: [PATCH 10/20] Client build. Looks like we accidentally committed the map references? Leaving that in place, but we had agreed to drop them. --- static/scripts/bundled/extended.bundled.js | 2 +- static/scripts/galaxy.pages.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js index 88a63efb325..f0dbdad9562 100644 --- a/static/scripts/bundled/extended.bundled.js +++ b/static/scripts/bundled/extended.bundled.js @@ -46,5 +46,5 @@ s=n,l=t("
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    ",{Continue:hide_modal}):hide_modal(),l.showWorkflowParameters()},beforeSubmit:function(t){show_message("Loading workflow","progress")}}),window.make_popupmenu&&make_popupmenu(t("#workflow-options-button"),{Save:d,"Save As":n,Run:function(){window.location=Galaxy.root+"workflows/run?id="+l.options.id},"Edit Attributes":function(){l.workflow.clear_active_node()},"Auto Re-layout":i,Close:c});var h=t.jStorage.get("overview-size");void 0!==h&&t("#overview-border").css({width:h,height:h}),t.jStorage.get("overview-off")?s():a(),t("#overview-border").bind("dragend",function(e,n){var i=t(this).offsetParent(),r=i.offset(),a=Math.max(i.width()-(n.offsetX-r.left),i.height()-(n.offsetY-r.top));t.jStorage.set("overview-size",a+"px")}),t("#close-viewport").click(function(){"0px"===t("#overview-border").css("right")?s():a()}),window.onbeforeunload=function(){if(workflow&&l.workflow.has_changes)return"There are unsaved changes to your workflow which will be lost."},this.options.workflows.length>0&&t("#left").find(".toolMenu").append(this._buildToolPanelWorkflows()),t("div.toolSectionBody").hide(),t("div.toolSectionTitle > span").wrap("");var f=null;t("div.toolSectionTitle").each(function(){var e=t(this).next("div.toolSectionBody");t(this).click(function(){e.is(":hidden")?(f&&f.slideUp("fast"),f=e,e.slideDown("fast")):(e.slideUp("fast"),f=null)})}),(0,C.default)("workflow-name","workflow-name",l.urls.rename_async,"new_name"),t("#workflow-tag").click(function(){return t(".tag-area").click(),!1}),(0,C.default)("workflow-annotation","workflow-annotation",l.urls.annotate_async,"new_annotation",25,!0,4)},_buildToolPanelWorkflows:function(){var e=this,n=t('
    Workflows
    ');return r.each(this.options.workflows,function(i){if(i.id!==e.options.id){var r=new k.default.ButtonIcon({icon:"fa fa-copy",cls:"ui-button-icon-plain",tooltip:(0,c.default)("Copy and insert individual steps"),onclick:function(){i.step_count<2?e.copy_into_workflow(i.id,i.name):Galaxy.modal.show({title:(0,c.default)("Warning"),body:"This will copy "+i.step_count+" new steps into your workflow.",buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){Galaxy.modal.hide(),e.copy_into_workflow(i.id,i.name)}}})}}),a=t("").attr("href","#").html(i.name).on("click",function(){e.add_node_for_subworkflow(i.latest_id,i.name)});n.find(".toolSectionBg").append(t("
    ").addClass("toolTitle").append(a).append(r.$el))}}),n},copy_into_workflow:function(e){var n=this;this._workflowLoadAjax(e,{success:function(e){n.workflow.from_simple(e,!1);var i="";t.each(e.upgrade_messages,function(e,r){i+="
  • Step "+(parseInt(e,10)+1)+": "+n.workflow.nodes[e].name+"
      ",t.each(r,function(t,e){i+="
    • "+e+"
      • "}),i+="
    • "}),i?window.show_modal("Subworkflow embedded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.
      "+i+"
    ",{Continue:hide_modal}):hide_modal()},beforeSubmit:function(t){show_message("Importing workflow","progress")}})},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=window.workflow_globals.workflow=new f.default(this,t("#canvas-container"))},scroll_to_nodes:function(){var e,n,i=t("#canvas-viewport"),r=t("#canvas-container");n=r.width()"+n+"";return e+=""},showWorkflowParameters:function(){var e=/\$\{.+?\}/g,n=[],i=t("#workflow-parameters-container"),r=t("#workflow-parameters-box"),a="",o=[];t.each(this.workflow.nodes,function(i,r){r.config_form&&r.config_form.inputs&&u.default.deepeach(r.config_form.inputs,function(t){if("string"==typeof t.value){var n=t.value.match(e);n&&(o=o.concat(n))}}),r.post_job_actions&&t.each(r.post_job_actions,function(n,i){i.action_arguments&&t.each(i.action_arguments,function(t,n){var i=n.match(e);i&&(o=o.concat(i))})}),o&&t.each(o,function(e,i){-1===t.inArray(i,n)&&n.push(i)})}),n&&0!==n.length?(t.each(n,function(t,e){a+="
    "+e.substring(2,e.length-1)+"
    "}),i.html(a),r.show()):(i.html(a),r.hide())},showAttributes:function(){t(".right-content").hide(),t("#edit-attributes").show()},showForm:function(e,n){var i="right-content",r=i+"-"+n.id,a=t("#"+i);if(e&&0==a.find("#"+r).length){var o=t('
    ');if(e.node=n,e.workflow=this.workflow,e.datatypes=this.datatypes,e.icon=y.default[n.type],e.cls="ui-portlet-narrow",n){var s="tool"==n.type?"Tool":"Default";o.append(new w.default[s](e).form.$el),a.append(o)}else Galaxy.emit.debug("workflow-view::initialize()","Node not found in workflow.")}t("."+i).hide(),a.find("#"+r).show(),a.show(),a.scrollTop()},isSubType:function(t,e){return t=this.ext_to_type[t],e=this.ext_to_type[e],this.type_to_type[t]&&e in this.type_to_type[t]},prebuildNode:function(e,n,i){var r=this,a=t("
    "),o=t("
    "+n+"
    ");s(o.find(".nodeTitle"),e),a.append(o),a.css("left",t(window).scrollLeft()+20),a.css("top",t(window).scrollTop()+20),a.append(t("
    "));var l=new m.default(this,{element:a});l.type=e,l.content_id=i;var c="
    loading tool info...
    ";a.find(".toolFormBody").append(c);var d=t("
    ");"subworkflow"!==e&&d.append(t("
    ").addClass("fa-icon-button fa fa-files-o node-clone").click(function(t){l.clone()})),d.append(t("
    ").addClass("fa-icon-button fa fa-times node-destroy").click(function(t){l.destroy()})),a.appendTo("#canvas-container");var u=t("#canvas-container").position(),h=t("#canvas-container").parent(),f=a.width(),p=a.height();return a.css({left:-u.left+h.width()/2-f/2,top:-u.top+h.height()/2-p/2}),d.prependTo(a.find(".toolFormTitle")),f+=d.width()+10,a.css("width",f),a.bind("dragstart",function(){r.workflow.activate_node(l)}).bind("dragend",function(){r.workflow.node_changed(this),r.workflow.fit_canvas_to_nodes(),r.canvas_manager.draw_overview()}).bind("dragclickonly",function(){r.workflow.activate_node(l)}).bind("drag",function(e,n){var i=t(this).offsetParent().offset(),r=n.offsetX-i.left,a=n.offsetY-i.top;t(this).css({left:r,top:a}),t(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(e,n(0),n(2),n(1))},function(t,e,n){"use strict";(function(t){function i(t,e){this.app=t,this.canvas_container=e,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(e,"__esModule",{value:!0});var r=n(410),a=function(t){return t&&t.__esModule?t:{default:t}}(r),o=n(20),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(o);t.extend(i.prototype,{canLabelOutputWith:function(t){return!t||!(t in this.workflowOutputLabels)},registerOutputLabel:function(t){t&&(this.workflowOutputLabels[t]=!0)},unregisterOutputLabel:function(t){t&&delete this.workflowOutputLabels[t]},updateOutputLabel:function(t,e){t&&this.unregisterOutputLabel(t),this.canLabelOutputWith(e)||s.warning("Workflow contains duplicate workflow output labels "+e+". This must be fixed before it can be saved."),e&&this.registerOutputLabel(e)},attemptUpdateOutputLabel:function(t,e,n){return!!this.canLabelOutputWith(n)&&(t.labelWorkflowOutput(e,n),t.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(t,e,n){var i=this.app.prebuildNode(t,e,n);return this.add_node(i),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(i),i},add_node:function(t){t.id=this.id_counter,t.element.attr("id","wf-node-step-"+t.id),t.element.attr("node-label",t.label),this.id_counter++,this.nodes[t.id]=t,this.has_changes=!0,t.workflow=this},remove_node:function(t){this.active_node==t&&this.clear_active_node(),delete this.nodes[t.id],this.has_changes=!0},remove_all:function(){var e=this;t.each(this.nodes,function(t,n){n.destroy(),e.remove_node(n)})},rectify_workflow_outputs:function(){var e=!1,n=!1;if(t.each(this.nodes,function(i,r){r.workflow_outputs&&r.workflow_outputs.length>0&&(e=!0),t.each(r.post_job_actions,function(t,e){"HideDatasetAction"===e.action_type&&(n=!0)})}),!1!==e||!1!==n){var i=this;t.each(this.nodes,function(n,r){if("tool"===r.type){var a=!1;null===r.post_job_actions&&(r.post_job_actions={},a=!0);var o=[];t.each(r.post_job_actions,function(t,e){"HideDatasetAction"==e.action_type&&o.push(t)}),o.length>0&&t.each(o,function(t,e){a=!0,delete r.post_job_actions[e]}),e&&t.each(r.output_terminals,function(t,e){if(!0==!r.isWorkflowOutput(e.name)){a=!0;var n={action_type:"HideDatasetAction",output_name:e.name,action_arguments:{}};r.post_job_actions["HideDatasetAction"+e.name]=null,r.post_job_actions["HideDatasetAction"+e.name]=n}}),i.active_node==r&&!0===a&&i.reload_active_node()}})}},to_simple:function(){var e={};return t.each(this.nodes,function(n,i){var r={};t.each(i.input_terminals,function(e,n){r[n.name]=null;var i=[];t.each(n.connectors,function(t,e){if(e.handle1){var a={id:e.handle1.node.id,output_name:e.handle1.name},o=n.attributes.input.input_subworkflow_step_id;void 0!==o&&(a.input_subworkflow_step_id=o),i[t]=a,r[n.name]=i}})});var a={};i.post_job_actions&&t.each(i.post_job_actions,function(t,e){var n={action_type:e.action_type,output_name:e.output_name,action_arguments:e.action_arguments};a[e.action_type+e.output_name]=null,a[e.action_type+e.output_name]=n}),i.workflow_outputs||(i.workflow_outputs=[]);var o={id:i.id,type:i.type,content_id:i.content_id,tool_version:i.config_form.version,tool_state:i.tool_state,errors:i.errors,input_connections:r,position:t(i.element).position(),annotation:i.annotation,post_job_actions:i.post_job_actions,uuid:i.uuid,label:i.label,workflow_outputs:i.workflow_outputs};e[i.id]=o}),{steps:e}},from_simple:function(e,n){var i=void 0===n||n,r=this,o=0;i?r.name=e.name:o=Object.keys(r.nodes).length;var s=o,l=!1;t.each(e.steps,function(e,n){var a=r.app.prebuildNode(n.type,n.name,n.content_id);i||(n.uuid=null,t.each(n.workflow_outputs,function(t,e){e.uuid=null})),a.init_field_data(n),n.position&&a.element.css({top:n.position.top,left:n.position.left}),a.id=parseInt(n.id)+o,a.element.attr("id","wf-node-step-"+a.id),a.element.attr("node-label",n.label),r.nodes[a.id]=a,s=Math.max(s,parseInt(e)+o),l||(a.workflow_outputs.length>0?l=!0:t.each(a.post_job_actions||[],function(t,e){"HideDatasetAction"===e.action_type&&(l=!0)}))}),r.id_counter=s+1,t.each(e.steps,function(e,n){var i=r.nodes[parseInt(e)+o];t.each(n.input_connections,function(e,n){n&&(t.isArray(n)||(n=[n]),t.each(n,function(t,n){var s=r.nodes[parseInt(n.id)+o],l=new a.default;l.connect(s.output_terminals[n.output_name],i.input_terminals[e]),l.redraw()}))}),l&&t.each(i.output_terminals,function(e,n){if(void 0===i.post_job_actions["HideDatasetAction"+n.name]){i.addWorkflowOutput(n.name);t(i.element).find(".callout."+n.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),r.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,t("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var t=this.active_node;this.clear_active_node(),this.activate_node(t)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),document.activeElement.blur(),this.app.showAttributes()},activate_node:function(t){this.active_node!=t&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(t.config_form,t),t.make_active(),this.active_node=t)},node_changed:function(t,e){this.has_changes=!0,this.active_node==t&&e&&(this.check_changes_in_active_form(),this.app.showForm(t.config_form,t)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var e={},n={};t.each(this.nodes,function(t,i){void 0===e[t]&&(e[t]=0),void 0===n[t]&&(n[t]=[])}),t.each(this.nodes,function(i,r){t.each(r.input_terminals,function(i,a){t.each(a.connectors,function(t,i){var a=i.handle1.node;e[r.id]+=1,n[a.id].push(r.id)})})});for(var i=[];;){var r=[];for(var a in e)0===e[a]&&r.push(a);if(0===r.length)break;i.push(r);for(var o in r){var s=r[o];delete e[s];for(var l in n[s])e[n[s][l]]-=1}}if(!e.length){var c=this.nodes,d=80;t.each(i,function(e,n){n.sort(function(e,n){return t(c[e].element).position().top-t(c[n].element).position().top});var i=0,r=30;t.each(n,function(e,n){var a=c[n],o=t(a.element);t(o).css({top:r,left:d}),i=Math.max(i,t(o).width()),r+=t(o).height()+30}),d+=i+80}),t.each(c,function(t,e){e.redraw()})}},bounds_for_all_nodes:function(){var e,n=1/0,i=-1/0,r=1/0,a=-1/0;return t.each(this.nodes,function(o,s){var l=t(s.element);e=l.position(),n=Math.min(n,e.left),i=Math.max(i,e.left+l.width()),r=Math.min(r,e.top),a=Math.max(a,e.top+l.width())}),{xmin:n,xmax:i,ymin:r,ymax:a}},fit_canvas_to_nodes:function(){function e(t,e){return Math.ceil(t/e)*e}function n(t,e){if(t3*e){return-(t-(Math.ceil(t%e/e)+1)*e)}return 0}var i=this.bounds_for_all_nodes(),r=this.canvas_container.position(),a=this.canvas_container.parent(),o=n(i.xmin,100),s=n(i.ymin,100);o=Math.max(o,r.left),s=Math.max(s,r.top);var l=r.left-o,c=r.top-s,d=e(i.xmax+100,100)+o,u=e(i.ymax+100,100)+s;d=Math.max(d,-l+a.width()),u=Math.max(u,-c+a.height()),this.canvas_container.css({left:l,top:c,width:d,height:u}),this.canvas_container.children().each(function(){var e=t(this).position();t(this).css("left",e.left+o),t(this).css("top",e.top+s)})}}),e.default=i}).call(e,n(0))},function(t,e,n){"use strict";(function(t){function n(t,e,n){this.app=t,this.cv=e,this.cc=this.cv.find("#canvas-container"),this.overview=n,this.oc=n.find("#overview-canvas"),this.ov=n.find("#overview-viewport"),this.init_drag(),this.init_copy_paste()}function i(t){this.panel=t}Object.defineProperty(e,"__esModule",{value:!0}),t.extend(n.prototype,{init_drag:function(){var e=this,n=function(t,n){t=Math.min(t,e.cv.width()/2),t=Math.max(t,-e.cc.width()+e.cv.width()/2),n=Math.min(n,e.cv.height()/2),n=Math.max(n,-e.cc.height()+e.cv.height()/2),e.cc.css({left:t,top:n}),e.cv.css({"background-position-x":t,"background-position-y":n}),e.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new i(this)});var r,a;this.cv.bind("click",function(){document.activeElement.blur()}).bind("dragstart",function(){var n=t(this).offset(),i=e.cc.position();a=i.top-n.top,r=i.left-n.left}).bind("drag",function(t,e){n(e.offsetX+r,e.offsetY+a)}).bind("dragend",function(){e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),this.overview.click(function(t){if(e.overview.hasClass("blockaclick"))e.overview.removeClass("blockaclick");else{var i=e.cc.width(),r=e.cc.height(),a=e.oc.width(),o=e.oc.height(),s=t.pageX-e.oc.offset().left-e.ov.width()/2,l=t.pageY-e.oc.offset().top-e.ov.height()/2;n(-s/a*i,-l/o*r),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}}),this.ov.bind("drag",function(t,i){var r=e.cc.width(),a=e.cc.height(),o=e.oc.width(),s=e.oc.height(),l=i.offsetX-e.overview.offset().left,c=i.offsetY-e.overview.offset().top;n(-l/o*r,-c/s*a)}).bind("dragend",function(){e.overview.addClass("blockaclick"),e.app.workflow.fit_canvas_to_nodes(),e.draw_overview()}),t("#overview-border").bind("drag",function(n,i){var r=t(this).offsetParent(),a=r.offset(),o=Math.max(r.width()-(i.offsetX-a.left),r.height()-(i.offsetY-a.top));t(this).css({width:o,height:o}),e.draw_overview()}),t("#overview-border div").bind("drag",function(){})},init_copy_paste:function(){var t=this;document.addEventListener("copy",function(e){""===window.getSelection().toString()&&(t.app.workflow.active_node&&"subworkflow"!==t.app.workflow.active_node.type&&e.clipboardData.setData("application/json",JSON.stringify({nodeId:t.app.workflow.active_node.id})),e.preventDefault())}),document.addEventListener("paste",function(e){if(document.activeElement&&"textarea"!==document.activeElement.type&&"text"!==document.activeElement.type){var n;try{n=JSON.parse(e.clipboardData.getData("application/json")).nodeId}catch(t){}n&&t.app.workflow.nodes.hasOwnProperty(n)&&t.app.workflow.nodes[n].clone(),e.preventDefault()}})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,n=this.oc,i=this.ov,r=t.width(),a=t.height(),o=n.width(),s=n.height(),l=t.position();i.css({left:-l.left/r*o,top:-l.top/a*s,width:e.width()/r*o-2,height:e.height()/a*s-2})},draw_overview:function(){var e,n,i,r,a=t("#overview-canvas"),o=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=t("#canvas-container").width(),c=t("#canvas-container").height(),d=this.cv.width(),u=this.cv.height();l0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(d,u,h,f),s.strokeRect(d,u,h,f)}),this.update_viewport_overlay()}}),t.extend(i.prototype,{test:function(e,n){var i=this;clearTimeout(this.timeout);var r=e.pageX,a=e.pageY,o=t(this.panel),s=o.position(),l=o.width(),c=o.height(),d=o.parent(),u=d.width(),h=d.height(),f=d.offset(),p=f.left,_=f.top,g=p+d.width(),m=_+d.height(),v=-(l-u/2),y=-(c-h/2),b=u/2,w=h/2,x=!1,k=0;r-5g?s.left>v&&(k=Math.min(23,s.left-v),o.css("left",s.left-k),x=!0):a-5<_?s.topm&&s.top>y&&(k=Math.min(23,s.top-v),o.css("top",s.top-k+"px"),x=!0),x&&(n(),this.timeout=setTimeout(function(){i.test(e,n)},50))},stop:function(){clearTimeout(this.timeout)}}),e.default=n}).call(e,n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(5),s=a(o),l=n(720),c=a(l),d=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return i.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);){var e=this.getWorkflowOutput(t);this.workflow_outputs.splice(i.indexOf(this.workflow_outputs,e),1)}},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var n={output_name:t};return e&&(n.label=e),this.workflow_outputs.push(n),!0}return!1},labelWorkflowOutput:function(t,e){var n=!1,i=null;if(this.isWorkflowOutput(t)){var r=this.getWorkflowOutput(t);i=r.label,r.label=e,n=i!=e}else n=this.addWorkflowOutput(t,e);return n&&(this.app.workflow.updateOutputLabel(i,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),n},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return r.each(t,function(t,n){n.connectors.length>0&&e.push(n)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var n=t[e];if(n.connectors.length>0&&n.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return r.each(t,function(t,n){n.mapOver().isCollection&&n.connectors.length>0&&e.push(n)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return r.each(t,function(t,n){n.mapOver().isCollection&&e.push(n)}),e},hasMappedOverInputTerminals:function(){var t=!1;return i.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){r.each(this.input_terminals,function(t,e){e.redraw()}),r.each(this.output_terminals,function(t,e){e.redraw()})},clone:function(){var t=this,e={name:this.name,label:this.label,annotation:this.annotation,post_job_actions:this.post_job_actions},n=this.app.workflow.create_node(this.type,this.name,this.content_id);s.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{type:this.type,tool_id:this.content_id,tool_state:this.tool_state},success:function(i){var 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t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),r(t).removeClass("toolForm-active")},set_tool_version:function(){"tool"===this.type&&this.config_form&&(this.tool_version=this.config_form.version,this.content_id=this.config_form.id)},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.set_tool_version(),this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,n=new c.default({el:this.element[0],node:e});e.nodeView=n,r.each(t.data_inputs,function(t,e){n.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&n.addRule(),r.each(t.data_outputs,function(t,e){n.addDataOutput(e)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,n=e.nodeView,a=[];if(r.each(n.outputViews,function(e,n){var r=n.output.name,o=t.data_outputs,s=!1;i.each(o,function(t){t.name==r&&(s=!0)}),!1===s&&a.push(r)}),i.each(a,function(t){i.each(n.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),n.outputViews[t].remove(),delete n.outputViews[t],delete e.output_terminals[t]}),r.each(e.workflow_outputs,function(t,n){n&&!e.output_terminals[n.output_name]&&e.workflow_outputs.splice(t,1)}),r.each(t.data_outputs,function(t,i){n.outputViews[i.name]?(e.output_terminals[i.name].datatypes=i.extensions,e.output_terminals[i.name].destroyInvalidConnections()):n.addDataOutput(i)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.set_tool_version(),this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var o=t.post_job_actions;this.post_job_actions=o||{}}e.nodeView.renderToolErrors();var s=n.$("div.inputs"),l=n.newInputsDiv(),c={};i.each(t.data_inputs,function(t){var n=e.nodeView.addDataInput(t,l);c[t.name]=n}),i.each(i.difference(i.values(n.terminalViews),i.values(c)),function(t){t.el.terminal.destroy()}),n.terminalViews=c,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&n.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=r(this.element).find(".toolFormBody");e.find("div").remove();var n="
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s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:n,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:m,InputCollectionTerminalView:_,OutputCollectionTerminalView:v}}).call(e,n(2),n(1),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0});var o=n(20),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(o);window.workflow_globals=window.workflow_globals||{};var l={isCollection:!1,canMatch:function(){return!1},canMapOver:function(){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},c={isCollection:!0,canMatch:function(t){return l!==t},canMapOver:function(){return!1},toString:function(){return"AnyCollectionType[]"},append:function(){return c},equal:function(t){return t===this}};t.extend(a.prototype,{append:function(t){return t===l?this:t===c?t:new a(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==l&&(t===c||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===l)return!1;if(t===c)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new a(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var d=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||l,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(l)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),u=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){r.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),r.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:l},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),h=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||r.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),r.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),f=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||r.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){return!!this.connected()&&(!this.multiple||!!this._collectionAttached())},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(r.first(r.values(this.node.output_terminals)).mapOver()):r.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var n=this.datatypes[e];if("input"==n)return!0;var i=[];if(i=i.concat(t.datatypes),t.node.post_job_actions)for(var r in t.node.post_job_actions){var a=t.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!==a.output_name&&a.output_name!=t.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(t){var e=l;t.isCollection&&(e=t.collectionType);var n=t.mapOver();return n.isCollection&&(e=n.append(e)),e}}),p=f.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._otherCollectionType(e);n.isCollection&&this.setMapOver(n)}},attachable:function(t){var e=this._otherCollectionType(t),n=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(n.isCollection&&n.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(r.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!n.isCollection&&this._producesAcceptableDatatype(t)}}),_=f.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?r.each(t.collection_types,function(t){e.push(new a(t))}):e.push(c),this.collectionTypes=e},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._effectiveMapOver(e);this.setMapOver(n)}},_effectiveMapOver:function(t){var e=this.collectionTypes,n=this._otherCollectionType(t);if(!r.some(e,function(t){return t.canMatch(n)}))for(var i in e){var a=e[i];if(n.canMapOver(a)){var o=n.effectiveMapOver(a);if(o!=l)return o}}return l},_effectiveCollectionTypes:function(){var t=this.mapOver();return r.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var n=this._effectiveCollectionTypes(),i=this.mapOver();if(r.some(n,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(i.isCollection)return!1;if(r.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),g=u.extend({initialize:function(t){if(u.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=c}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=c}e.collectionType!=this.collectionType.collectionType&&r.each(this.connectors,function(t){s.warning("Destroying a connection because collection type has changed."),t.destroy()}),this.collectionType=e}});e.default={InputTerminal:p,OutputTerminal:h,InputCollectionTerminal:_,OutputCollectionTerminal:g,TerminalMapping:d,CollectionTypeDescription:a,NULL_COLLECTION_TYPE_DESCRIPTION:l,ANY_COLLECTION_TYPE_DESCRIPTION:c}}).call(e,n(0),n(2),n(1))},function(t,e,n){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var i=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),r=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,i=e.name,r=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(i=i+" ("+e.extensions.join(", ")+")"),this.$el.html(i),this.calloutView=null,["tool","subworkflow"].indexOf(r.type)>=0){var o=new a({label:i,output:e,node:r});this.calloutView=o,this.$el.append(o.el),this.$el.hover(function(){o.hoverImage()},function(){o.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,i=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(n("
    ").append(n("").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;i.isWorkflowOutput(t)?(i.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(i.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});e.default={DataInputView:i,DataOutputView:r}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t){var e=t.model.attributes,n=e.workflow,i=e.node;e.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:i.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),e.inputs.unshift({type:"text",name:"__label",label:"Label",value:i.label,help:(0,d.default)("Add a step label."),fixed:!0,onchange:function(e){var r=!1;for(var a in n.nodes){var o=n.nodes[a];if(o.label&&o.label==e&&o.id!=i.id){r=!0;break}}var s=t.data.match("__label");t.element_list[s].model.set("error_text",r&&"Duplicate label. Please fix this before saving the workflow."),t.trigger("change")}})}function o(t,e,n,i){var r=i.node.post_job_actions;e=e||[],e.push(t);for(var a in t.inputs){var s=t.inputs[a];if(s.action){if(s.name="pja__"+n+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var c=r[s.action+n];if(c){for(var d in e)e[d].expanded=!0;s.pja_arg?s.value=c.action_arguments&&c.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&o(s,e.slice(0),n,i)}}function s(t,e){var n=[],i=[],r=e.datatypes,a=e.node,s=e.workflow;for(var l in r)n.push({0:r[l],1:r[l]});for(l in a.input_terminals)i.push(a.input_terminals[l].name);n.sort(function(t,e){return t.label>e.label?1:t.labelhere     for more information. Valid inputs are: '+i.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:n,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:(0,d.default)("Assign columns"),type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return o(u,[],t,e),u}function l(t){var e=t.model.attributes,n=e.inputs,i=e.node,r=i.post_job_actions,a=i.output_terminals&&Object.keys(i.output_terminals)[0];if(a){n.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+a])),ignore:"false",help:(0,d.default)("An email notification will be sent when the job has completed."),payload:{host:window.location.host}}),n.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var o in i.output_terminals)n.push(s(o,e))}}Object.defineProperty(e,"__esModule",{value:!0});var c=n(3),d=r(c),u=n(5),h=r(u),f=n(26),p=r(f),_=n(55),g=r(_),m=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new p.default(h.default.merge(t,{onchange:function(){h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:n.id,type:n.type,content_id:n.content_id,inputs:e.form.data.create()},success:function(t){n.update_field_data(t)}})}})),a(this.form),this.form.render()}}),v=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new g.default(h.default.merge(t,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(t,n){e._customize(n),t.resolve()},buildmodel:function(t,e){e.model.get("postchange")(t,e)},postchange:function(t,r){var a=r.model.attributes,o={tool_id:a.id,tool_version:a.version,type:"tool",inputs:i.extend(!0,{},r.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",o),h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:o,success:function(i){r.model.set(i.config_form),e._customize(r),r.update(i.config_form),r.errors(i.config_form),n.update_field_data(i),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",e),t.reject()}})}}))},_customize:function(t){var e=t.model.attributes;h.default.deepeach(e.inputs,function(t){t.type&&(-1!=["data","data_collection"].indexOf(t.type)?(t.type="hidden",t.info="Data input '"+t.name+"' ("+h.default.textify(t.extensions)+")",t.value={__class__:"RuntimeValue"}):t.fixed||(t.collapsible_value={__class__:"RuntimeValue"},t.is_workflow=t.options&&0===t.options.length||-1!=["integer","float"].indexOf(t.type)))}),h.default.deepeach(e.inputs,function(t){"conditional"===t.type&&(t.test_param.collapsible_value=void 0)}),l(t),a(t)}});e.default={Default:m,Tool:v}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(1),c=r(l),d=n(224),u=r(d),h=n(15),f=a(h),p=n(5),_=a(p),g=n(33),m=a(g),v=n(31),y=a(v);n(150);var b=t.Model.extend({is_visible:function(t,e){var n=t.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),w={drawTicks:function(t,e,n,i,r){var a=t.append("g").selectAll("g").data(e).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"}),o=[],s=[],l=function(t){return t.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(t){return t.label})},formatNum:function(t,e){if(void 0===e&&(e=2),null===t)return null;var n=null;if(Math.abs(t)<1)n=t.toPrecision(e);else{var i=Math.round(t.toPrecision(e));t=Math.abs(t),t<1e3?n=i:t<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":t<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},x=t.Model.extend({}),k=t.View.extend({className:"circster",initialize:function(t){this.genome=t.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var e=this.model.get("config");e.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),e.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"!==t.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"===t.get("track_type")})},get_tracks_bounds:function(){var t=this.get_circular_tracks(),e=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-t.length*(e+n)+n-this.label_arc_height,a=u.range(r,i/2,e+n);return c.map(a,function(t){return[t,t+e]})},render:function(){var t=this,e=t.$el.width(),n=t.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=t.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(t.$el[0]).append("svg").attr("width",e).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var e=d.event.scale;s.attr("transform","translate("+d.event.translate+") scale("+e+")"),t.scale!==e&&(t.zoom_drag_timeout&&clearTimeout(t.zoom_drag_timeout),t.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+e/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(e,n){var i=new T({el:s.append("g")[0],track:e,radius_bounds:o[n],genome:t.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(e){var n=new A({el:s.append("g")[0],track:e,radius_bounds:o[0],genome:t.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new C({el:s.append("g")[0],track:new x,radius_bounds:c,genome:t.genome,total_gap:a}),this.label_track_view.render()},add_track:function(t){var e=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===t.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new A({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:n,genome:this.genome,total_gap:e});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])}),c.each(this.chords_views,function(t){t.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new T({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();c.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),c.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),M=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new b;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),s=o.attr("chrom"),l=n.genome.get_chrom_region(s),d=n.track.get("data_manager");d.can_get_more_detailed_data(l)&&(a=n.track.get("data_manager").get_more_detailed_data(l,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=c.find(n.chroms_layout,function(t){return t.data.chrom===s}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=c.reject(c.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=c.zip(n,i);c.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var s=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return c.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),C=M.extend({initialize:function(t){M.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});c.extend(C.prototype,w);var S=M.extend({initialize:function(t){M.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return i?t.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",e.data.chrom).attr("d",i):null},_get_path_function:function(t,e){if("string"==typeof e||!e.data||0===e.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,e.data.length]).range([t.startAngle,t.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(t){return n(t[1])}).angle(function(t,e){return i(e)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var t=this,e=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),e,!0).classed("min_max",!0);c.each(n,function(e){i(e).click(function(){new m.default.ConfigSettingCollectionView({collection:t.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var t=this,e=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>.08}),n=c.filter(e,function(t,e){return e%3==0}),i=c.flatten(c.map(n,function(e){return t._data_bounds_ticks_fn()(e)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"})}},_data_bounds_ticks_fn:function(){var t=this;return function(e){return[{radius:t.radius_bounds[0],angle:e.startAngle,label:t.formatNum(t.data_bounds[0])},{radius:t.radius_bounds[1],angle:e.startAngle,label:t.formatNum(t.data_bounds[1])}]}},get_data_bounds:function(t){}});c.extend(S.prototype,w);var T=S.extend({get_data_bounds:function(t){var e=c.flatten(c.map(t,function(t){return t?c.map(t.data,function(t){return parseInt(t[1],10)||0}):0}));return[c.min(e),this._quantile(e,.98)||c.max(e)]}}),A=M.extend({render:function(){var t=this;i.when(t.track.get("data_manager").data_is_ready()).then(function(){i.when(t.track.get("data_manager").get_genome_wide_data(t.genome)).then(function(e){var n=[],i=t.genome.get_chroms_info();c.each(e,function(e,r){var a=i[r].chrom,o=c.map(e.data,function(e){var 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e=this.templatePaginator();r("body").find(".folder-paginator").html(e({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(t){this.options=i.extend(this.options,t),!0===this.options.can_add_library_item?r(".add-library-items").show():r(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(r(".dataset-manipulation").show(),r(".logged-dataset-manipulation").hide()):(r(".logged-dataset-manipulation").show(),r(".dataset-manipulation").show()):(r(".logged-dataset-manipulation").hide(),r(".dataset-manipulation").hide()),this.$el.find('[data-toggle="tooltip"]').tooltip({trigger:"hover"})},createFolderFromModal:function(t){var e=this;t.preventDefault(),t.stopPropagation();var n=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,l.default)("Create New Folder"),body:n(),buttons:{Create:function(){e.createNewFolderEvent()},Close:function(){Galaxy.modal.hide()}}})},createNewFolderEvent:function(){var e=this.serializeNewFolder();if(this.validateNewFolder(e)){var n,i=new p.default.FolderAsModel,r=t.history.fragment.split("/");n=r.indexOf("page")>-1?r[r.length-3]:r[r.length-1],i.url=i.urlRoot+n,i.save(e,{success:function(t){Galaxy.modal.hide(),h.default.success("Folder created."),t.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(t)},error:function(t,e){Galaxy.modal.hide(),void 0!==e.responseJSON?h.default.error(e.responseJSON.err_msg):h.default.error("An error occurred.")}})}else h.default.error("Folder's name is 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    ","
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      ","
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