Merge pull request #1195 from briehl/spec-editor

TASK-1201 - Simple viewer for App Spec files

nbextensions/appCell2/appCell.js

@@ -42,7 +42,9 @@ define([
         if (!cell.metadata.kbase) {
             return false;
         }
-        if (cell.metadata.kbase.type === 'app2' || cell.metadata.kbase.type === 'app') {
+        if (cell.metadata.kbase.type === 'app2' ||
+            cell.metadata.kbase.type === 'app' ||
+            cell.metadata.kbase.type === 'devapp') {
             return true;
         }
         return false;
@@ -228,48 +230,53 @@ define([
             });
         }
 
-        function upgradeToAppCell(appSpec, appTag) {
+        /**
+         * appSpec = the appSpec structure
+         * appTag = a string, one of 'release', 'beta', 'dev'
+         * appType = a string, typically 'app', also 'devapp' for spec edit mode.
+         */
+        function upgradeToAppCell(appSpec, appTag, appType) {
             return Promise.try(function() {
-                    // Create base app cell
+                // Create base app cell
 
-                    // TODO: this should capture the entire app spec, so don't need
-                    // to carry appSpec around.
-                    spec = Spec.make({
-                        appSpec: appSpec
-                    });
+                // TODO: this should capture the entire app spec, so don't need
+                // to carry appSpec around.
+                spec = Spec.make({
+                    appSpec: appSpec
+                });
 
-                    var meta = {
-                        kbase: {
-                            type: 'app',
-                            attributes: {
-                                id: new Uuid(4).format(),
-                                status: 'new',
-                                created: (new Date()).toUTCString()
+                var meta = {
+                    kbase: {
+                        type: appType,
+                        attributes: {
+                            id: new Uuid(4).format(),
+                            status: 'new',
+                            created: (new Date()).toUTCString()
+                        },
+                        appCell: {
+                            app: {
+                                id: appSpec.info.id,
+                                gitCommitHash: appSpec.info.git_commit_hash,
+                                version: appSpec.info.ver,
+                                tag: appTag,
+                                // TODO: remove the spec from the cell metadata
+                                spec: appSpec
                             },
-                            appCell: {
-                                app: {
-                                    id: appSpec.info.id,
-                                    gitCommitHash: appSpec.info.git_commit_hash,
-                                    version: appSpec.info.ver,
-                                    tag: appTag,
-                                    // TODO: remove the spec from the cell metadata
-                                    spec: appSpec
-                                },
-                                params: null,
-                                output: {
-                                    byJob: {}
-                                }
+                            params: null,
+                            output: {
+                                byJob: {}
                             }
                         }
-                    };
-                    cell.metadata = meta;
+                    }
+                };
+                cell.metadata = meta;
 
-                    // Add the params
-                    utils.setCellMeta(cell, 'kbase.appCell.params', spec.makeDefaultedModel());
-                    // initializeParams(appSpec);
-                    // Complete the cell setup.
-                    return setupCell();
-                })
+                // Add the params
+                utils.setCellMeta(cell, 'kbase.appCell.params', spec.makeDefaultedModel());
+                // initializeParams(appSpec);
+                // Complete the cell setup.
+                return setupCell();
+            })
                 .then(function(cellStuff) {
                     // Initialize the cell to its default state.
                     // cellStuff.bus.emit('reset-to-defaults');

nbextensions/appCell2/main.js

@@ -155,18 +155,22 @@ define([
                     var setupData = payload.data;
                     var jupyterCellType = payload.type;
 
+                    if (setupData.type === 'app2') {
+                        setupData.type = 'app';
+                    }
+
                     if (jupyterCellType !== 'code' ||
-                        !setupData || 
-                        !(setupData.type === 'app2' || 
-                          setupData.type === 'app')) {
+                        !setupData ||
+                        !(setupData.type === 'app'  ||
+                          setupData.type === 'devapp')) {
                         return;
                     }
 
                     var appCell = AppCell.make({
                         cell: cell,
                         workspaceInfo: workspaceInfo
                     });
-                    appCell.upgradeToAppCell(setupData.appSpec, setupData.appTag)
+                    appCell.upgradeToAppCell(setupData.appSpec, setupData.appTag, setupData.type)
                         .catch(function(err) {
                             console.error('ERROR creating cell', err);
                             Jupyter.notebook.delete_cell(Jupyter.notebook.find_cell_index(cell));
@@ -218,4 +222,4 @@ define([
     };
 }, function(err) {
     console.error('ERROR loading appCell main', err);
-});
+});

nbextensions/appCell2/widgets/appCellWidget.js

@@ -2613,15 +2613,20 @@ define([
             // If the app has been run before...
             // The app reference is already in the app cell metadata.
             return Promise.try(function() {
+                if (utils.getCellMeta(cell, 'kbase.type') !== 'devapp') {
                     return getAppSpec();
-                })
+                }
+                return {};
+            })
                 .then(function(appSpec) {
                     // Ensure that the current app spec matches our existing one.
-                    var warning = checkSpec(appSpec);
-                    if (warning && warning.severity === 'warning') {
-                        if (warning.type === 'app-spec-mismatched-commit') {
-                            model.setItem('outdated', true);
-                            model.setItem('newAppName', warning.info.newAppName);
+                    if (appSpec && utils.getCellMeta(cell, 'kbase.type') !== 'devapp') {
+                        var warning = checkSpec(appSpec);
+                        if (warning && warning.severity === 'warning') {
+                            if (warning.type === 'app-spec-mismatched-commit') {
+                                model.setItem('outdated', true);
+                                model.setItem('newAppName', warning.info.newAppName);
+                            }
                         }
                     }
 

src/biokbase/narrative/appeditor.py

@@ -0,0 +1,46 @@
+from IPython.display import Javascript
+from jinja2 import Template
+from biokbase.narrative import clients
+import json
+
+
+def generate_app_cell(validated_spec=None, spec_tuple=None):
+    """Produces an invisible blob of JavaScript that inserts a new cell in the notebook,
+    and crams the validated_spec in it. It then removes itself, so it won't happen again
+    on page reload.
+
+    For the inputs, validated_spec > spec_tuple. That is, if validated_spec is present,
+    that's always used. if spec_tuple is there, and validated_spec is not, then the
+    tuple's used.
+
+    Also, the tuple should be (spec_json, display_yaml), all as strings.
+    """
+
+    if spec_tuple is not None and validated_spec is None:
+        nms = clients.get("narrative_method_store")
+        validated = nms.validate_method({
+            "id": "some_test_app",
+            "spec_json": spec_tuple[0],
+            "display_yaml": spec_tuple[1]
+        })
+        if validated.get('is_valid', 0) == 1:
+            validated_spec = validated['method_spec']
+        elif "errors" in validated and validated['errors']:
+            raise Exception(validated['errors'])
+
+    js_template = """
+        var outputArea = this,
+            cellElement = outputArea.element.parents('.cell'),
+            cellIdx = Jupyter.notebook.get_cell_elements().index(cellElement),
+            thisCell = Jupyter.notebook.get_cell(cellIdx),
+            spec_json = '{{spec}}',
+            cellData = {
+                type: 'devapp',
+                appTag: 'dev',
+                appSpec: JSON.parse(spec_json)
+            };
+        Jupyter.narrative.insertAndSelectCell('code', 'below', cellIdx, cellData);
+    """
+    js_code = Template(js_template).render(spec=json.dumps(validated_spec))
+
+    return Javascript(data=js_code, lib=None, css=None)

src/biokbase/narrative/tests/data/simple_display.yaml

@@ -0,0 +1,36 @@
+#
+# define display information
+#
+name: Test Simple Inputs
+tooltip: |
+    A simple test spec with a single input.
+screenshots: []
+
+icon: icon.png
+
+#
+# define a set of similar methods that might be useful to the user
+#
+suggestions:
+    apps:
+        related:
+            []
+        next:
+            []
+    methods:
+        related:
+            []
+        next:
+            []
+
+#
+# Configure the display and description of parameters
+#
+parameters :
+    simple_string :
+        ui-name : |
+            A String
+        short-hint : |
+            A description string.
+description : |
+    <p>This is a tiny, simple method intended for testing the Narrative's ability to parse and display specs.</p>

src/biokbase/narrative/tests/data/simple_spec.json

@@ -0,0 +1,46 @@
+{
+    "ver": "0.0.1",
+    "authors": [
+        "wjriehl"
+    ],
+    "contact": "help@kbase.us",
+    "visible": true,
+    "categories": ["active"],
+    "app_type": "editor",
+    "widgets": {
+        "input": null,
+        "output": null
+    },
+    "parameters": [
+        {
+            "id": "simple_string",
+            "optional": false,
+            "advanced": false,
+            "allow_multiple": false,
+            "default_values": [ "" ],
+            "field_type": "text",
+            "text_options": {
+            }
+        }
+    ],
+    "behavior": {
+        "service-mapping": {
+            "url": "",
+            "name": "NarrativeTest",
+            "method": "generic_test",
+            "input_mapping": [
+                {
+                    "input_parameter": "simple_string",
+                    "target_property": "simple_string"
+                }
+            ],
+            "output_mapping": [
+                {
+                    "service_method_output_path": [0,"simple_string"],
+                    "target_property": "simple_string"
+                }
+            ]
+        }
+    },
+    "job_id_output_field": "docker"
+}

src/biokbase/narrative/tests/test.cfg

@@ -34,6 +34,8 @@ job_info_file=data/job_test_data.json
 [specs]
 app_specs_file=data/app_specs.json
 type_specs_file=data/type_specs.json
+simple_spec_json=data/simple_spec.json
+simple_display_yaml=data/simple_display.yaml
 
 [app_tests]
 public_ws_name=wjriehl:1475006266615

src/biokbase/narrative/tests/test_appeditor.py

@@ -0,0 +1,32 @@
+"""
+Some tests for the App Editor module.
+"""
+import unittest
+from biokbase.narrative.appeditor import (
+    generate_app_cell
+)
+import json
+from util import TestConfig
+
+
+class AppEditorTestCase(unittest.TestCase):
+    @classmethod
+    def setUpClass(self):
+        config = TestConfig()
+        self.specs_list = config.load_json_file(config.get('specs', 'app_specs_file'))
+        self.spec_json = config.load_json_file(config.get('specs', 'simple_spec_json'))
+        with open(config.file_path(config.get('specs', 'simple_display_yaml'))) as f:
+            self.display_yaml = f.read()
+            f.close()
+
+    def test_gen_app_cell_post_validation(self):
+        js = generate_app_cell(validated_spec=self.specs_list[0])
+        self.assertIsNotNone(js)
+
+    def test_gen_app_cell_pre_valid(self):
+        js = generate_app_cell(spec_tuple=(json.dumps(self.spec_json), self.display_yaml))
+        self.assertIsNotNone(js)
+
+    def test_gen_app_cell_fail_validation(self):
+        with self.assertRaises(Exception):
+            generate_app_cell(spec_tuple=("{}", self.display_yaml))