TASK-1229 - UPA handler API

.travis.yml

@@ -11,12 +11,13 @@ env:
   - TRAVIS_NODE_VERSION="6.6.0"
 cache:
   directories:
-  - kbase-extension/static/ext_components
-  - node_modules
+    - kbase-extension/static/ext_components
+    - node_modules
+    - $HOME/.cache/pip
+
 branches:
   only:
     - develop
-    - staging
     - master
     - travis-firefox
 
@@ -27,6 +28,7 @@ before_install:
   - npm install -g bower
   - npm install -g grunt-cli
   - npm install -g karma-cli
+
 install:
   - pip install -r src/requirements.txt
 

kbase-extension/static/kbase/js/api/upa.js

@@ -0,0 +1,123 @@
+define([
+    'common/runtime'
+], function(Runtime) {
+    'use strict';
+
+    var UpaApi = function() {
+        var externalTag = '&';
+
+        /**
+         * Runs a regex that tests the given string to see if it's a valid upa.
+         * valid upas are of the form:
+         * ws/obj/ver or ws1/obj1/ver1;ws2/obj2/ver2;...
+         */
+        var isUpa = function(upa) {
+            return RegExp(/^\d+(\/\d+){2}(;\d+(\/\d+){2})*$/).test(upa);
+        };
+
+        var prepareUpaSerialization = function(upa) {
+            if (typeof upa !== 'string') {
+                // stringify the array version of an UPA, if that's what we have.
+                if (Array.isArray(upa)) {
+                    upa = upa.join(';');
+                }
+                else {
+                    throw {error: 'Can only serialize UPA strings or Arrays of UPA paths'};
+                }
+            }
+            if (!isUpa(upa)) {
+                throw {error: '"' + upa + '" is not a valid UPA. It may already have been serialized.'};
+            }
+            return upa;
+        };
+
+        /**
+         * @method
+         * @public
+         * Serializes an UPA - prepares it for storage as a part of Narrative cell metadata.
+         * This means a bit of a tweak to the UPA itself. Currently, we want to store it in a way
+         * that designates it as a serialized string, and gives an easy path to substitute the
+         * initial workspace part of the UPA with a different workspace.
+         * So it gets transformed from:
+         * ws1/obj1/ver1;ws2/obj2/ver2;...
+         * to
+         * [ws1]/obj1/ver1;ws2/obj2/ver2;...
+         *
+         * If the passed upa is not properly formatted, this will throw an Error.
+         */
+        var serialize = function(upa) {
+            upa = prepareUpaSerialization(upa);
+            return upa.replace(/^(\d+)\//, '[$1]/');
+        };
+
+        /**
+         * @public
+         * @method
+         *
+         * In the case of UPAs representing objects that are located in a different workspace all
+         * together (e.g. set items that aren't copied into the Narrative with the set container
+         * object), they get flagged with a special character. In that case, the UPA is maintained,
+         * but transformed into:
+         * &ws1/obj1/ver1;ws2/obj2/ver2;...
+         *
+         * This is an explicit method for handling that serialization. Deserialization of both is handled
+         * by the deserialize function.
+         *
+         * If the passed upa is not properly formatted, this will throw an Error.
+         */
+        var serializeExternal = function(upa) {
+            upa = prepareUpaSerialization(upa);
+            return externalTag + upa;
+        };
+
+        /**
+         * @public
+         * @method
+         * Deserializes a serialized UPA to one that is valid for use with the Workspace (or other
+         * services that consume Workspace objects).
+         * A serialized UPA is either of the form:
+         * [ws]/obj/ver;ws/obj/ver;...
+         * or
+         * &ws/obj/ver;ws/obj/ver
+         * In the [ws] case, the current workspace id replaces that whole token. In the &ws case,
+         * the & tag is removed.
+         */
+        var deserialize = function(serial) {
+            if (typeof serial !== 'string') {
+                throw {
+                    error: 'Can only deserialize UPAs from strings.'
+                };
+            }
+            var deserial;
+            if (serial[0] === externalTag) {
+                deserial = serial.substring(externalTag.length);
+            } else {
+                var wsId = Runtime.make().workspaceId();
+                if (!wsId) {
+                    throw {
+                        error: 'Currently loaded workspace is unknown! Unable to deserialize UPA.'
+                    };
+                }
+                deserial = serial.replace(/^\[\d+\]\//, Runtime.make().workspaceId() + '/');
+            }
+            if (!isUpa(deserial)) {
+                throw {
+                    error: 'Deserialized UPA: ' + deserial + ' is invalid!'
+                };
+            }
+            return deserial;
+        };
+
+
+        return {
+            serialize: serialize,
+            deserialize: deserialize,
+            serializeExternal: serializeExternal,
+            externalTag: externalTag,
+            isUpa: isUpa
+        };
+    };
+
+    return UpaApi;
+
+});

nbextensions/install.sh

@@ -11,13 +11,6 @@ export IPYTHONDIR=$narrdir/kbase-extension/ipython
 echo 'Root dir'
 echo ${dir}
 
-#jupyter nbextension disable appCell/main --sys-prefix
-#jupyter nbextension uninstall ${dir}/appCell --sys-prefix
-#jupyter nbextension install ${dir}/appCell --symlink --sys-prefix
-#jupyter nbextension enable appCell/main --sys-prefix
-
-#jupyter nbextension disable methodViewCell/main --sys-prefix
-#jupyter nbextension uninstall ${dir}/methodViewCell --sys-prefix
 jupyter nbextension install ${dir}/viewCell --symlink --sys-prefix
 jupyter nbextension enable viewCell/main --sys-prefix
 
@@ -38,9 +31,3 @@ jupyter nbextension enable advancedViewCell/main --sys-prefix
 
 jupyter nbextension install ${dir}/codeCell --symlink --sys-prefix
 jupyter nbextension enable codeCell/main --sys-prefix
-
-# jupyter nbextension disable codeCell/main --sys-prefix
-# jupyter nbextension install ${dir}/codeCell --symlink --sys-prefix
-
-#jupyter nbextension disable customView/main --sys-prefix
-#jupyter nbextension uninstall ${dir}/customView --sys-prefix

package.json

@@ -23,6 +23,7 @@
     "karma-coverage": "1.1.1",
     "karma-firefox-launcher": "1.0.0",
     "karma-jasmine": "1.0.2",
+    "karma-mocha-reporter": "^2.2.5",
     "karma-phantomjs-launcher": "1.0.1",
     "karma-requirejs": "1.0.0",
     "karma-safari-launcher": "1.0.0",

src/biokbase/narrative/clients.py

@@ -31,7 +31,7 @@ def __init_client(client_name):
         c = UserAndJobState(URLS.user_and_job_state)
     elif client_name == 'catalog':
         c = Catalog(URLS.catalog)
-    elif client_name == 'service':
+    elif client_name == 'service' or client_name == 'service_wizard':
         c = ServiceClient(URLS.service_wizard, use_url_lookup=True)
 
     else: