Merge pull request #6683 from mvdbeek/expose_workflow_versions

Expose workflow versions

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -14,6 +14,7 @@ class Workflow {
         this.has_changes = false;
         this.active_form_has_changes = false;
         this.workflowOutputLabels = {};
+        this.workflow_version = 0;
     }
     canLabelOutputWith(label) {
         if (label) {
@@ -215,6 +216,7 @@ class Workflow {
         var max_id = offset;
         // First pass, nodes
         var using_workflow_outputs = false;
+        wf.workflow_version = data.version;
         $.each(data.steps, (id, step) => {
             var node = wf.app.prebuildNode(step.type, step.name, step.content_id);
             // If workflow being copied into another, wipe UUID and let

client/galaxy/scripts/mvc/workflow/workflow-view.js

@@ -94,6 +94,7 @@ export default Backbone.View.extend({
                 window.document.location = self.urls.workflow_index;
             }
         };
+        var workflow_index = self.urls.workflow_index;
         var save_current_workflow = (eventObj, success_callback) => {
             show_message("Saving workflow", "progress");
             self.workflow.check_changes_in_active_form();
@@ -126,7 +127,9 @@ export default Backbone.View.extend({
                     self.workflow.name = data.name;
                     self.workflow.has_changes = false;
                     self.workflow.stored = true;
+                    self.workflow.workflow_version = data.version;
                     self.showWorkflowParameters();
+                    self.build_version_select();
                     if (data.errors) {
                         window.show_modal("Saving workflow", body, {
                             Ok: hide_modal
@@ -270,47 +273,106 @@ export default Backbone.View.extend({
         this.ext_to_type = this.datatypes_mapping.ext_to_class_name;
         this.type_to_type = this.datatypes_mapping.class_to_classes;
 
-        // Load workflow definition
-        this._workflowLoadAjax(self.options.id, {
-            success: function(data) {
-                self.reset();
-                self.workflow.from_simple(data, true);
-                self.workflow.has_changes = false;
-                self.workflow.fit_canvas_to_nodes();
-                self.scroll_to_nodes();
-                self.canvas_manager.draw_overview();
-                // Determine if any parameters were 'upgraded' and provide message
-                var upgrade_message = "";
-                _.each(data.steps, (step, step_id) => {
-                    var details = "";
-                    if (step.errors) {
-                        details += `<li>${step.errors}</li>`;
-                    }
-                    _.each(data.upgrade_messages[step_id], m => {
-                        details += `<li>${m}</li>`;
-                    });
-                    if (details) {
-                        upgrade_message += `<li>Step ${parseInt(step_id, 10) + 1}: ${
-                            self.workflow.nodes[step_id].name
-                        }<ul>${details}</ul></li>`;
-                    }
-                });
-                if (upgrade_message) {
-                    window.show_modal(
-                        "Issues loading this workflow",
-                        `Please review the following issues, possibly resulting from tool upgrades or changes.<p><ul>${upgrade_message}</ul></p>`,
-                        { Continue: hide_modal }
-                    );
-                } else {
-                    hide_modal();
-                }
-                self.showWorkflowParameters();
-            },
-            beforeSubmit: function(data) {
-                show_message("Loading workflow", "progress");
-            }
-        });
+        this.get_workflow_versions = function() {
+            let _workflow_version_dropdown = {};
+            let workflow_versions = JSON.parse(
+                $.ajax({
+                    url: `${Galaxy.root}api/workflows/${self.options.id}/versions`,
+                    async: false,
+                }).responseText
+            );
 
+            for (let i = 0; i < workflow_versions.length; i++) {
+                let current_wf = workflow_versions[i];
+                let version_text = `Version ${current_wf['version']}, ${current_wf['steps']} steps`;
+                let selected = false;
+                if (i == self.workflow.workflow_version) {
+                    version_text = `${version_text} (active)`;
+                    selected = true;
+                };
+                _workflow_version_dropdown[version_text] = {
+                    version: i,
+                    selected: selected,
+                }
+            }
+            return _workflow_version_dropdown
+        }
+
+        this.build_version_select = function() {
+            let versions = this.get_workflow_versions();
+            $("#workflow-version-switch").empty();
+            $.each(versions, function(k, v) {
+                $('#workflow-version-switch').append($('<option></option>').html(k).val(v.version).selected(v.selected));
+            });
+            $("#workflow-version-switch").on('change', function () {
+                $('#workflow-version-switch').unbind('change');
+                if (this.value != self.workflow.workflow_version) {
+                    if (self.workflow && self.workflow.has_changes) {
+                        let r = confirm("There are unsaved changes to your workflow which will be lost. Continue ?");
+                        if (r == false) {
+                            // We rebuild the version select list, to reset the selected version
+                            self.build_version_select();
+                            return
+                        }
+                    }
+                    self.load_workflow(self.options.id, this.value);
+                }
+            })
+        };
+
+        this.load_workflow = function load_workflow(id, version) {
+            this._workflowLoadAjax(id, version, {
+                success: function(data) {
+                    self.reset();
+                    self.workflow.from_simple(data, true);
+                    self.workflow.has_changes = false;
+                    self.workflow.fit_canvas_to_nodes();
+                    self.scroll_to_nodes();
+                    self.canvas_manager.draw_overview();
+                    // make_popupmenu($("#workflow-versions-switch"), self.get_workflow_versions());
+                    self.build_version_select();
+
+                    // Determine if any parameters were 'upgraded' and provide message
+                    var upgrade_message = "";
+                    _.each(data.steps, (step, step_id) => {
+                        var details = "";
+                        if (step.errors) {
+                            details += `<li>${step.errors}</li>`;
+                        }
+                        _.each(data.upgrade_messages[step_id], m => {
+                            details += `<li>${m}</li>`;
+                        });
+                        if (details) {
+                            upgrade_message += `<li>Step ${parseInt(step_id, 10) + 1}: ${
+                                self.workflow.nodes[step_id].name
+                            }<ul>${details}</ul></li>`;
+                        }
+                    });
+                    if (upgrade_message) {
+                        window.show_modal(
+                            "Issues loading this workflow",
+                            `Please review the following issues, possibly resulting from tool upgrades or changes.<p><ul>${upgrade_message}</ul></p>`,
+                            { Continue: hide_modal }
+                        );
+                    } else {
+                        hide_modal();
+                    }
+                    self.showWorkflowParameters();
+                },
+                error: function(response) {
+                        window.show_modal("Loading workflow failed.", response.err_msg, { Ok: function( response ){
+                        window.onbeforeunload = undefined;
+                        window.document.location = workflow_index;
+}})
+                },
+                beforeSubmit: function(data) {
+                    show_message("Loading workflow", "progress");
+                }
+            });
+        }
+
+        // Load workflow definition
+        this.load_workflow(self.options.id, self.options.version)
         if (window.make_popupmenu) {
             make_popupmenu($("#workflow-options-button"), {
                 Save: save_current_workflow,
@@ -530,7 +592,7 @@ export default Backbone.View.extend({
     copy_into_workflow: function(workflowId) {
         // Load workflow definition
         var self = this;
-        this._workflowLoadAjax(workflowId, {
+        this._workflowLoadAjax(workflowId, None, {
             success: function(data) {
                 self.workflow.from_simple(data, false);
                 // Determine if any parameters were 'upgraded' and provide message
@@ -584,11 +646,11 @@ export default Backbone.View.extend({
         cc.css({ left: left, top: top });
     },
 
-    _workflowLoadAjax: function(workflowId, options) {
+    _workflowLoadAjax: function(workflowId, version, options) {
         $.ajax(
             Utils.merge(options, {
                 url: this.urls.load_workflow,
-                data: { id: workflowId, _: "true" },
+                data: { id: workflowId, _: "true", version: version },
                 dataType: "json",
                 cache: false
             })

lib/galaxy/managers/workflows.py

@@ -368,7 +368,7 @@ class WorkflowContentsManager(UsesAnnotations):
 
         return workflow, missing_tool_tups
 
-    def workflow_to_dict(self, trans, stored, style="export"):
+    def workflow_to_dict(self, trans, stored, style="export", version=None):
         """ Export the workflow contents to a dictionary ready for JSON-ification and to be
         sent out via API for instance. There are three styles of export allowed 'export', 'instance', and
         'editor'. The Galaxy team will do its best to preserve the backward compatibility of the
@@ -377,22 +377,31 @@ class WorkflowContentsManager(UsesAnnotations):
         option describes the workflow in a context more tied to the current Galaxy instance and includes
         fields like 'url' and 'url' and actual unencoded step ids instead of 'order_index'.
         """
+        if version == '':
+            version = None
+        if version is not None:
+            version = int(version)
         if style == "editor":
-            return self._workflow_to_dict_editor(trans, stored)
+            wf_dict = self._workflow_to_dict_editor(trans, stored, version=version)
         elif style == "legacy":
-            return self._workflow_to_dict_instance(stored, legacy=True)
+            wf_dict = self._workflow_to_dict_instance(stored, legacy=True, version=version)
         elif style == "instance":
-            return self._workflow_to_dict_instance(stored, legacy=False)
+            wf_dict = self._workflow_to_dict_instance(stored, legacy=False, version=version)
         elif style == "run":
-            return self._workflow_to_dict_run(trans, stored)
+            wf_dict = self._workflow_to_dict_run(trans, stored, version=version)
         else:
-            return self._workflow_to_dict_export(trans, stored)
+            wf_dict = self._workflow_to_dict_export(trans, stored, version=version)
+        if version:
+            wf_dict['version'] = version
+        else:
+            wf_dict['version'] = len(stored.workflows) - 1
+        return wf_dict
 
-    def _workflow_to_dict_run(self, trans, stored):
+    def _workflow_to_dict_run(self, trans, stored, version=None):
         """
         Builds workflow dictionary used by run workflow form
         """
-        workflow = stored.latest_workflow
+        workflow = stored.get_internal_version(version)
         if len(workflow.steps) == 0:
             raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
         if attach_ordered_steps(workflow, workflow.steps):
@@ -476,8 +485,8 @@ class WorkflowContentsManager(UsesAnnotations):
         """
         return self._resource_mapper_function(trans=trans, stored_workflow=stored, workflow=workflow)
 
-    def _workflow_to_dict_editor(self, trans, stored):
-        workflow = stored.latest_workflow
+    def _workflow_to_dict_editor(self, trans, stored, version=None):
+        workflow = stored.get_internal_version(version)
         # Pack workflow data into a dictionary and return
         data = {}
         data['name'] = workflow.name
@@ -584,12 +593,12 @@ class WorkflowContentsManager(UsesAnnotations):
             data['steps'][step.order_index] = step_dict
         return data
 
-    def _workflow_to_dict_export(self, trans, stored=None, workflow=None):
+    def _workflow_to_dict_export(self, trans, stored=None, workflow=None, version=None):
         """ Export the workflow contents to a dictionary ready for JSON-ification and export.
         """
         if workflow is None:
             assert stored is not None
-            workflow = stored.latest_workflow
+            workflow = stored.get_internal_version(version)
 
         annotation_str = ""
         tag_str = ""
@@ -755,11 +764,11 @@ class WorkflowContentsManager(UsesAnnotations):
             data['steps'][step.order_index] = step_dict
         return data
 
-    def _workflow_to_dict_instance(self, stored, legacy=True):
+    def _workflow_to_dict_instance(self, stored, legacy=True, version=None):
         encode = self.app.security.encode_id
         sa_session = self.app.model.context
         item = stored.to_dict(view='element', value_mapper={'id': encode})
-        workflow = stored.latest_workflow
+        workflow = stored.get_internal_version(version)
         item['url'] = url_for('workflow', id=item['id'])
         item['owner'] = stored.user.username
         inputs = {}

lib/galaxy/model/__init__.py

@@ -3906,6 +3906,13 @@ class StoredWorkflow(HasTags, Dictifiable):
         self.latest_workflow_id = None
         self.workflows = []
 
+    def get_internal_version(self, version):
+        if version is None:
+            return self.latest_workflow
+        if len(self.workflows) <= version:
+            raise Exception("Version does not exist")
+        return list(reversed(self.workflows))[version]
+
     def copy_tags_from(self, target_user, source_workflow):
         # Override to only copy owner tags.
         for src_swta in source_workflow.owner_tags:

lib/galaxy/model/mapping.py

@@ -2224,7 +2224,8 @@ mapper(model.StoredWorkflow, model.StoredWorkflow.table, properties=dict(
     workflows=relation(model.Workflow,
         backref='stored_workflow',
         cascade="all, delete-orphan",
-        primaryjoin=(model.StoredWorkflow.table.c.id == model.Workflow.table.c.stored_workflow_id)),
+        primaryjoin=(model.StoredWorkflow.table.c.id == model.Workflow.table.c.stored_workflow_id),
+        order_by=-model.Workflow.id),
     latest_workflow=relation(model.Workflow,
         post_update=True,
         primaryjoin=(model.StoredWorkflow.table.c.latest_workflow_id == model.Workflow.table.c.id),

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -214,7 +214,18 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             style = "legacy"
         else:
             style = "instance"
-        return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style)
+        version = kwd.get('version')
+        return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)
+
+    @expose_api
+    def show_versions(self, trans, workflow_id, **kwds):
+        """
+        GET /api/workflows/{encoded_workflow_id}/versions
+
+        Lists all versions of this workflow.
+        """
+        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id)
+        return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]
 
     @expose_api
     def create(self, trans, payload, **kwd):
@@ -400,7 +411,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
 
         style = kwd.get("style", "export")
         download_format = kwd.get('format')
-        ret_dict = self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style)
+        version = kwd.get('version')
+        ret_dict = self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)
         if download_format == 'json-download':
             sname = stored_workflow.name
             sname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150]

lib/galaxy/webapps/galaxy/buildapp.py

@@ -446,6 +446,11 @@ def populate_api_routes(webapp, app):
                           controller='workflows',
                           action='workflow_dict',
                           conditions=dict(method=['GET']))
+    webapp.mapper.connect('show_versions',
+                          '/api/workflows/{workflow_id}/versions',
+                          controller='workflows',
+                          action='show_versions',
+                          conditions=dict(method=['GET']))
     # Preserve the following download route for now for dependent applications  -- deprecate at some point
     webapp.mapper.connect('workflow_dict',
                           '/api/workflows/download/{workflow_id}',

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -637,7 +637,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
 
     @web.expose
     @web.require_login("edit workflows")
-    def editor(self, trans, id=None):
+    def editor(self, trans, id=None, version=None):
         """
         Render the main workflow editor interface. The canvas is embedded as
         an iframe (necessary for scrolling to work properly), which is
@@ -653,10 +653,18 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             .order_by(desc(model.StoredWorkflow.table.c.update_time)) \
             .options(joinedload('latest_workflow').joinedload('steps')) \
             .all()
-        return trans.fill_template("workflow/editor.mako", workflows=workflows, stored=stored, annotation=self.get_item_annotation_str(trans.sa_session, trans.user, stored))
+        if version is None:
+            version = len(stored.workflows) - 1
+        else:
+            version = int(version)
+        return trans.fill_template("workflow/editor.mako",
+                                   workflows=workflows,
+                                   stored=stored,
+                                   version=version,
+                                   annotation=self.get_item_annotation_str(trans.sa_session, trans.user, stored))
 
     @web.json
-    def load_workflow(self, trans, id):
+    def load_workflow(self, trans, id, version=None):
         """
         Get the latest Workflow for the StoredWorkflow identified by `id` and
         encode it as a json string that can be read by the workflow editor
@@ -665,7 +673,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         stored = self.get_stored_workflow(trans, id, check_ownership=True, check_accessible=False)
         workflow_contents_manager = workflows.WorkflowContentsManager(trans.app)
-        return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor")
+        return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor", version=version)
 
     @web.expose
     @web.require_login("use workflows")

templates/webapps/galaxy/workflow/editor.mako

@@ -10,25 +10,25 @@
     self.active_view="workflow"
     self.overlay_visible=True
     self.editor_config = {
-        'id'      : trans.security.encode_id( stored.id ),
+        'id'      : trans.security.encode_id(stored.id),
         'urls'    : {
-            'tool_search'         : h.url_for( '/api/tools' ),
-            'get_datatypes'       : h.url_for( '/api/datatypes/mapping' ),
-            'load_workflow'       : h.url_for( controller='workflow', action='load_workflow' ),
-            'run_workflow'        : h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id)),
-            'rename_async'        : h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) ),
-            'annotate_async'      : h.url_for( controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id) ),
-            'get_new_module_info' : h.url_for( controller='workflow', action='get_new_module_info' ),
-            'workflow_index'      : h.url_for( '/workflows/list' ),
-            'save_workflow'       : h.url_for( controller='workflow', action='save_workflow' ),
-            'workflow_save_as'    : h.url_for( controller='workflow', action='save_workflow_as')
+            'tool_search'         : h.url_for('/api/tools'),
+            'get_datatypes'       : h.url_for('/api/datatypes/mapping'),
+            'load_workflow'       : h.url_for(controller='workflow', action='load_workflow'),
+            'run_workflow'        : h.url_for(controller='root', action='index', workflow_id=trans.security.encode_id(stored.id)),
+            'rename_async'        : h.url_for(controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id)),
+            'annotate_async'      : h.url_for(controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id)),
+            'get_new_module_info' : h.url_for(controller='workflow', action='get_new_module_info'),
+            'workflow_index'      : h.url_for('/workflows/list'),
+            'save_workflow'       : h.url_for(controller='workflow', action='save_workflow'),
+            'workflow_save_as'    : h.url_for(controller='workflow', action='save_workflow_as')
         },
         'workflows' : [{
-            'id'                  : trans.security.encode_id( workflow.id ),
-            'latest_id'           : trans.security.encode_id( workflow.latest_workflow.id ),
-            'step_count'          : len( workflow.latest_workflow.steps ),
-            'name'                : h.to_unicode( workflow.name )
-        } for workflow in workflows ]
+            'id'                  : trans.security.encode_id(workflow.id),
+            'latest_id'           : trans.security.encode_id(workflow.latest_workflow.id),
+            'step_count'          : len(workflow.latest_workflow.steps),
+            'name'                : h.to_unicode(workflow.name)
+        } for workflow in workflows]
     }
 %>
 </%def>
@@ -403,6 +403,10 @@
                 <label>Name:</label>
                 <span id="workflow-name" class="editable-text" title="Click to rename workflow">${h.to_unicode( stored.name ) | h}</span>
             </div>
+            <div id="workflow-version-area" class="form-row">
+                <label>Version:</label>
+            </div>
+            <select id="workflow-version-switch" href="#">Select version</select>
             ## Workflow tags.
             <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" />
             <div class="form-row">