Merge pull request #4993 from guerler/replace_history_import

Replace history import form

client/galaxy/scripts/apps/analysis.js

@@ -13,6 +13,7 @@ import Tours from "mvc/tours";
 import GridView from "mvc/grid/grid-view";
 import GridShared from "mvc/grid/grid-shared";
 import Workflows from "mvc/workflow/workflow";
+import HistoryImport from "components/history-import.vue";
 import HistoryList from "mvc/history/history-list";
 import ToolFormComposite from "mvc/tool/tool-form-composite";
 import QueryStringParsing from "utils/query-string-parsing";
@@ -58,6 +59,7 @@ window.app = function app(options, bootstrapped) {
             "(/)workflows/create(/)": "show_workflows_create",
             "(/)histories(/)citations(/)": "show_history_citations",
             "(/)histories(/)rename(/)": "show_histories_rename",
+            "(/)histories(/)import(/)": "show_histories_import",
             "(/)histories(/)permissions(/)": "show_histories_permissions",
             "(/)histories(/)(:action_id)": "show_histories",
             "(/)datasets(/)list(/)": "show_datasets",
@@ -139,6 +141,13 @@ window.app = function app(options, bootstrapped) {
             );
         },
 
+        show_histories_import: function() {
+            var historyImportInstance = Vue.extend(HistoryImport);
+            var vm = document.createElement("div");
+            this.page.display(vm);
+            new historyImportInstance().$mount(vm);
+        },
+
         show_histories_permissions: function() {
             this.page.display(
                 new FormWrapper.View({

client/galaxy/scripts/components/history-import.vue

@@ -0,0 +1,63 @@
+<template>
+    <div class="ui-portlet-limited">
+        <div class="portlet-header">
+            <div class="portlet-title">
+                <i class="portlet-title-icon fa fa-upload"></i>
+                <span class="portlet-title-text"><b>Import a History from an Archive</b></span>
+            </div>
+        </div>
+        <div class="portlet-content">
+            <div v-if="errormessage" class="ui-message alert alert-danger">
+                {{ errormessage }}
+            </div>
+            <div class="portlet-body">
+                <form ref="form">
+                    <div class="ui-form-element">
+                        <div class="ui-form-title">Archived History URL</div>
+                        <input class="ui-input" type="text" name="archive_source"/>
+                    </div>
+                    <div class="ui-form-element">
+                        <div class="ui-form-title">Archived History file</div>
+                        <input type="file" name="archive_file"/>
+                    </div>
+                </form>
+            </div>
+            <div class="portlet-buttons">
+                <input class="btn btn-primary" type="button" value="Import History" @click="submit"/>
+            </div>
+        </div>
+    </div>
+</template>
+<script>
+export default {
+    data() {
+        return {
+            errormessage: null
+        }
+    },
+    methods: {
+        submit: function() {
+            $.ajax({
+                url: `${Galaxy.root}api/histories`,
+                data: new FormData(this.$refs.form),
+                cache: false,
+                contentType: false,
+                processData: false,
+                method: "POST"
+            })
+            .done(response => {
+                window.location = `${Galaxy.root}histories/list?message=${response.message}&status=success`
+            })
+            .fail(response => {
+                let message = response.responseJSON && response.responseJSON.err_msg;
+                this.errormessage = message || "Import failed for unkown reason.";
+            });
+        }
+    }
+};
+</script>
+<style>
+.ui-message {
+    display: block;
+}
+</style>

client/galaxy/scripts/mvc/history/options-menu.js

@@ -169,7 +169,8 @@ var menu = [
     },
     {
         html: _l("Import from File"),
-        href: "history/import_archive"
+        href: "histories/import",
+        target: "_top"
     }
 ];
 

client/galaxy/style/less/ui.less

@@ -507,7 +507,7 @@
     position: relative;
     clear: both;
     width: auto;
-    height: 100%;
+    height: auto;
     .portlet-header {
         background: @form-heading-bg;
         border-bottom: solid @form-border 1px;
@@ -550,8 +550,8 @@
             width       : 100%;
         }
         .portlet-buttons {
-            margin-top: @ui-margin-vertical;
-            margin-bottom: @ui-margin-vertical;
+            margin-top: @ui-margin-vertical-large;
+            margin-bottom: @ui-margin-vertical-large;
             > .btn {
                 margin-right: 5px;
             }

lib/galaxy/tools/imp_exp/imp_history_from_archive.xml

@@ -1,7 +1,7 @@
 <tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history">
   <type class="ImportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/>
-  <command interpreter="python">unpack_tar_gz_archive.py "${ str( $__ARCHIVE_SOURCE__ ).encode( 'base64' ) }" "${ str( $__DEST_DIR__ ).encode( 'base64' ) }" --$__ARCHIVE_TYPE__ --encoded</command>
+  <command>python '$__tool_directory__/unpack_tar_gz_archive.py' '${ str( $__ARCHIVE_SOURCE__ ).encode( 'base64' ) }' '${ str( $__DEST_DIR__ ).encode( 'base64' ) }' --$__ARCHIVE_TYPE__ --encoded</command>
   <inputs>
     <param name="__ARCHIVE_SOURCE__" type="text">
       <sanitizer sanitize="False"/>

lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py

@@ -49,7 +49,7 @@ def check_archive(archive_file, dest_dir):
     Ensure that a tar archive has no absolute paths or relative paths outside
     the archive.
     """
-    with tarfile.open(archive_file, mode='r:gz') as archive_fp:
+    with tarfile.open(archive_file, mode='r') as archive_fp:
         for arc_path in archive_fp.getnames():
             assert os.path.normpath(
                 os.path.join(
@@ -64,7 +64,7 @@ def unpack_archive(archive_file, dest_dir):
     """
     Unpack a tar and/or gzipped archive into a destination directory.
     """
-    archive_fp = tarfile.open(archive_file, mode='r:gz')
+    archive_fp = tarfile.open(archive_file, mode='r')
     archive_fp.extractall(path=dest_dir)
     archive_fp.close()
 

lib/galaxy/webapps/galaxy/api/histories.py

@@ -317,9 +317,16 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
 
         if "archive_source" in payload:
             archive_source = payload["archive_source"]
-            archive_type = payload.get("archive_type", "url")
+            archive_file = payload.get("archive_file")
+            if archive_source:
+                archive_type = payload.get("archive_type", "url")
+            elif hasattr(archive_file, "file"):
+                archive_source = payload["archive_file"].file.name
+                archive_type = "file"
+            else:
+                raise exceptions.MessageException("Please provide a url or file.")
             self.queue_history_import(trans, archive_type=archive_type, archive_source=archive_source)
-            return {}
+            return {"message": "Importing history from source '%s'. This history will be visible when the import is complete." % archive_source}
 
         new_history = None
         # if a history id was passed, copy that history

lib/galaxy/webapps/galaxy/buildapp.py

@@ -115,6 +115,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     webapp.add_client_route('/pages/edit')
     webapp.add_client_route('/histories/citations')
     webapp.add_client_route('/histories/list')
+    webapp.add_client_route('/histories/import')
     webapp.add_client_route('/histories/list_published')
     webapp.add_client_route('/histories/list_shared')
     webapp.add_client_route('/histories/rename')

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -1185,33 +1185,6 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         return self.get_ave_item_rating_data(trans.sa_session, history)
         # TODO: used in display_base.mako
 
-    @web.expose
-    # TODO: Remove require_login when users are warned that, if they are not
-    # logged in, this will remove their current history.
-    @web.require_login("use Galaxy histories")
-    def import_archive(self, trans, **kwargs):
-        """ Import a history from a file archive. """
-        # Set archive source and type.
-        archive_file = kwargs.get('archive_file', None)
-        archive_url = kwargs.get('archive_url', None)
-        archive_source = None
-        if hasattr(archive_file, 'file'):
-            archive_source = archive_file.file.name
-            archive_type = 'file'
-        elif archive_url:
-            archive_source = archive_url
-            archive_type = 'url'
-        # If no source to create archive from, show form to upload archive or specify URL.
-        if not archive_source:
-            form = web.FormBuilder(web.url_for(controller='history', action='import_archive'), "Import a History from an Archive", submit_text="Submit")
-            form.add_input("text", "Archived History URL", "archive_url", value="", error=None)
-            form.add_input("file", "Archived History File", "archive_file", value="", error=None)
-            return trans.show_form(form)
-        self.queue_history_import(trans, archive_type=archive_type, archive_source=archive_source)
-        return trans.show_message("Importing history from '%s'. \
-                                    This history will be visible when the import is complete" % archive_source)
-        # TODO: used in this file and index.mako
-
     @web.expose
     def export_archive(self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False, preview=False):
         """ Export a history to an archive. """

static/scripts/mvc/history/options-menu.js

@@ -1 +1 @@
-define("mvc/history/options-menu",["exports","mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(e,t,a,r,l,o){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}function u(e,t,a){return _.clone(y).filter(function(r){return!(e&&!r.anon)&&(!(!t&&r.purge)&&(r.href&&(r.href=a+r.href,r.target=r.target||"galaxy_main"),r.confirm&&(r.func=function(){confirm(r.confirm)&&(galaxy_main.location=r.href)}),!0))})}Object.defineProperty(e,"__esModule",{value:!0});var i=n(t),s=n(a),d=(n(r),n(l)),f=n(o),y=[{html:(0,d.default)("History Lists"),header:!0},{html:(0,d.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,d.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,d.default)("Current History"),header:!0,anon:!0},{html:(0,d.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,d.default)("Copy History"),func:function(){(0,s.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Share or Publish"),href:"history/sharing"},{html:(0,d.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,d.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,d.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,d.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,d.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,d.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,d.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,d.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really unhide all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Purge Deleted Datasets"),confirm:(0,d.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,d.default)("Downloads"),header:!0},{html:(0,d.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,d.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,d.default)("Other Actions"),header:!0},{html:(0,d.default)("Import from File"),href:"history/import_archive"}];f.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];$.each(e.models,function(e,a){var r=a.toJSON();r.activate&&t.push({html:(0,d.default)(r.config.title),anon:!0})}),t.length>0&&(t.unshift({html:(0,d.default)("Webhooks"),header:!0}),$.merge(y,t))}});e.default=function(e,t){var a=u(void 0===(t=t||{}).anonymous||t.anonymous,t.purgeAllowed||!1,Galaxy.root);return new i.default(e,a)}});
+define("mvc/history/options-menu",["exports","mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(e,t,a,r,l,o){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}function u(e,t,a){return _.clone(y).filter(function(r){return!(e&&!r.anon)&&(!(!t&&r.purge)&&(r.href&&(r.href=a+r.href,r.target=r.target||"galaxy_main"),r.confirm&&(r.func=function(){confirm(r.confirm)&&(galaxy_main.location=r.href)}),!0))})}Object.defineProperty(e,"__esModule",{value:!0});var i=n(t),s=n(a),d=(n(r),n(l)),f=n(o),y=[{html:(0,d.default)("History Lists"),header:!0},{html:(0,d.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,d.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,d.default)("Current History"),header:!0,anon:!0},{html:(0,d.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,d.default)("Copy History"),func:function(){(0,s.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Share or Publish"),href:"history/sharing"},{html:(0,d.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,d.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,d.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,d.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,d.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,d.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,d.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,d.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really unhide all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,d.default)("Really delete all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,d.default)("Purge Deleted Datasets"),confirm:(0,d.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,d.default)("Downloads"),header:!0},{html:(0,d.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,d.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,d.default)("Other Actions"),header:!0},{html:(0,d.default)("Import from File"),href:"histories/import",target:"_top"}];f.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];$.each(e.models,function(e,a){var r=a.toJSON();r.activate&&t.push({html:(0,d.default)(r.config.title),anon:!0})}),t.length>0&&(t.unshift({html:(0,d.default)("Webhooks"),header:!0}),$.merge(y,t))}});e.default=function(e,t){var a=u(void 0===(t=t||{}).anonymous||t.anonymous,t.purgeAllowed||!1,Galaxy.root);return new i.default(e,a)}});