Ensuring shared collection and gene list IDs return in the fetched li…

…sts of both

www/cgi/get_user_gene_carts.cgi

@@ -59,6 +59,8 @@ lib_path = os.path.abspath(os.path.join('..', '..', 'lib'))
 sys.path.append(lib_path)
 import geardb
 
+GENE_LIST_TYPES = ["unweighted-list", "weighted-list", "labeled-list"]
+
 def main():
     print('Content-Type: application/json\n\n')
 
@@ -96,9 +98,8 @@ def main():
 
     if group_by_type and not group_by_type == "false":
         # Group all cart results by their cart type and return
-        gctypes = ["unweighted-list", "weighted-list", "labeled-list"]
         gctypes_result = dict()
-        for cart_type in gctypes:
+        for cart_type in GENE_LIST_TYPES:
             subset_domain_carts = filter_by_cart_type(domain_carts, cart_type)
             subset_user_carts = filter_by_cart_type(user_carts, cart_type)
             subset_group_carts = filter_by_cart_type(group_carts, cart_type)
@@ -117,13 +118,16 @@ def main():
         print(json.dumps(gctypes_result, default=lambda o: o.__dict__))
         sys.exit(0)
 
-    if len(str(filter_cart_type)) > 0 and filter_cart_type != 'undefined':
+    if filter_cart_type and filter_cart_type in GENE_LIST_TYPES:
         domain_carts = filter_by_cart_type(domain_carts, filter_cart_type)
         user_carts = filter_by_cart_type(user_carts, filter_cart_type)
         group_carts = filter_by_cart_type(group_carts, filter_cart_type)
         recent_carts = filter_by_cart_type(recent_carts, filter_cart_type)
         shared_carts = filter_by_cart_type(shared_carts, filter_cart_type)
         public_carts = filter_by_cart_type(public_carts, filter_cart_type)
+    elif filter_cart_type and filter_cart_type not in GENE_LIST_TYPES:
+        # log warning that the cart type is not valid and return all carts
+        print("WARNING: Invalid cart type: " + filter_cart_type, file=sys.stderr)
 
     result = { 'domain_carts':domain_carts,
                 'group_carts':group_carts,

www/cgi/get_user_layouts.cgi

@@ -102,6 +102,7 @@ def main():
         result['user_layouts'] = geardb.LayoutCollection(include_datasets=bool_include_members).get_by_user(user)
         result['group_layouts'] =  geardb.LayoutCollection(include_datasets=bool_include_members).get_by_users_groups(user)
 
+    # NOTE: "null" values can happen but will be queried out in the SQL (unless there is a actual "null" share_id)
     if layout_share_id:
         result['shared_layouts'] = geardb.LayoutCollection(include_datasets=bool_include_members).get_by_share_id(layout_share_id)
 

www/include/dataset-collection-selector/dataset-collection-selector.js

@@ -76,16 +76,17 @@ document.addEventListener('DOMContentLoaded', () => {
 });
 
 /**
- * Fetches dataset collections from the API.
+ * Fetches dataset collections.
  *
- * @param {boolean} includeMembers - Whether to include members in the dataset collections.
+ * @param {string} [shareId=null] - The share ID of the dataset collection.
  * @returns {Promise<void>} - A promise that resolves when the dataset collections are fetched.
+ * @throws {Error} - If an error occurs during the fetch.
  */
-const fetchDatasetCollections = async (includeMembers=false) => {
-    const layoutShareId = selected_dc_share_id || null;
+const fetchDatasetCollections = async (shareId=null) => {
+    const layoutShareId = shareId || selected_dc_share_id || null;
 
     try {
-        dataset_collection_data = await apiCallsMixin.fetchDatasetCollections({includeMembers, layoutShareId});
+        dataset_collection_data = await apiCallsMixin.fetchDatasetCollections({includeMembers: false, layoutShareId});
 
         document.querySelector('#dropdown-dc').classList.remove('is-loading');
         document.querySelector('#dropdown-dc').classList.remove('is-disabled');

www/include/gene-collection-selector/gene-collection-selector.js

@@ -160,11 +160,13 @@ document.addEventListener('DOMContentLoaded', () => {
 
 /**
  * Fetches gene cart data from the server.
- * @returns {Promise<void>} A promise that resolves when the gene cart data is fetched.
+ *
+ * @param {string|null} shareId - The share ID of the gene list. Default is null.
+ * @returns {Promise<void>} - A promise that resolves when the gene cart data is fetched successfully.
  */
-const fetchGeneCartData = async () => {
+const fetchGeneCartData = async (shareId=null) => {
     try {
-        gene_cart_data = await apiCallsMixin.fetchGeneCarts({cartType: 'unweighted-list', includeMembers: false});
+        gene_cart_data = await apiCallsMixin.fetchGeneCarts({gcShareId: shareId, cartType: 'unweighted-list', includeMembers: false});
         document.querySelector('#dropdown-gene-lists').classList.remove('is-loading');
         document.querySelector('#dropdown-gene-lists').classList.remove('is-disabled');
 

www/include/pattern-collection-selector/pattern-collection-selector.js

@@ -246,13 +246,17 @@ const createPatternListItem = (item, cart) => {
     });
 }
 
+
 /**
- * Fetches patterns data asynchronously and executes a callback function.
- * @returns {Promise<void>} - A promise that resolves when the patterns data is fetched successfully.
+ * Fetches patterns data.
+ *
+ * @param {string|null} shareId - The gene list (pattern) share ID.
+ * @returns {Promise<void>} - A promise that resolves when the patterns data is fetched.
+ * @throws {Error} - If an error occurs during the fetch.
  */
-const fetchPatternsData = async () => {
+const fetchPatternsData = async (shareId=null) => {
     try {
-        patternsCartData = await apiCallsMixin.fetchGeneCarts({includeMembers: false});
+        patternsCartData = await apiCallsMixin.fetchGeneCarts({gcShareId: shareId, includeMembers: false});
 
         flatPatternsCartData = [...patternsCartData.domain_carts, ...patternsCartData.group_carts, ...patternsCartData.public_carts, ...patternsCartData.user_carts, ...patternsCartData.shared_carts, ...patternsCartData.recent_carts]
         document.getElementById('dropdown-pattern-lists').classList.remove('is-loading');

www/js/common.v2.js

@@ -981,7 +981,6 @@ const apiCallsMixin = {
         const {data} = await axios.post("cgi/get_users_layout_members.cgi", convertToFormData(payload));
         return data;
     },
-
     /**
      * Fetches dataset collections.
      *
@@ -991,12 +990,8 @@ const apiCallsMixin = {
      * @param {boolean} [options.includeMembers=true] - Whether to include collection members in output.
      * @returns {Promise<any>} - A promise that resolves to the fetched dataset collections.
      */
-    async fetchDatasetCollections({layoutShareId=null, noDomain=0, includeMembers=true}) {
-        const payload = {session_id: this.sessionId, layout_share_id: layoutShareId, no_domain: noDomain};
-
-        // is passed as string in the payload
-        payload.include_members = includeMembers ? 1 : 0;
-
+    async fetchDatasetCollections({layoutShareId=null, noDomain=0, includeMembers=true}={}) {
+        const payload = {session_id: this.sessionId, layout_share_id: layoutShareId, no_domain: noDomain, include_members: includeMembers ? 1 : 0};
         const {data} = await axios.post("cgi/get_user_layouts.cgi", convertToFormData(payload));
         return data;
     },
@@ -1119,19 +1114,15 @@ const apiCallsMixin = {
         return data;
     },
     /**
-     * Fetches gene carts based on the specified cart type.
-     * @param {string} cartType - The type of gene cart to fetch.
-     * @returns {Promise<any>} - A promise that resolves to the fetched gene carts data.
+     * Fetches gene carts.
+     * @param {Object} options - The options for fetching gene carts.
+     * @param {string|null} options.gcShareId - The share ID of the gene cart.
+     * @param {string|null} options.cartType - The type of the gene cart.
+     * @param {boolean} [options.includeMembers=true] - Whether to include members in the gene cart.
+     * @returns {Promise<Object>} The fetched gene carts.
      */
-    async fetchGeneCarts({cartType=null, includeMembers=true}) {
-        const payload = {session_id: this.sessionId};
-        if (cartType) {
-            payload.cart_type = cartType;
-        }
-
-        // is passed as string in the payload
-        payload.include_members = includeMembers ? 1 : 0;
-
+    async fetchGeneCarts({gcShareId=null, cartType=null, includeMembers=true}) {
+        const payload = {session_id: this.sessionId, cart_type: cartType, share_id: gcShareId, include_members: includeMembers ? 1 : 0};
         const {data} = await axios.post(`/cgi/get_user_gene_carts.cgi`, convertToFormData(payload));
         return data;
     },

www/js/dataset_explorer.js

@@ -2586,7 +2586,7 @@ const updateDatasetCollectionButtons = (collection=null) => {
 const updateDatasetCollections = async () => {
 
     // Fetch the dataset collections, which will update the dataset collection selector
-    await fetchDatasetCollections(false)
+    await fetchDatasetCollections()
 
     // Uses dataset-collection-selector.js variable
     const datasetCollectionData = dataset_collection_data;

www/js/expression.js

@@ -357,11 +357,13 @@ const handlePageSpecificLoginUIUpdates = async (event) => {
     // Wait until all pending API calls have completed before checking if we need to search
     document.getElementById("submit-expression-search").classList.add("is-loading");
     try {
+        const geneListShareId = getUrlParameter('gene_cart_share_id')
+
         // SAdkins note - Promise.all fails fast,
         // but Promise.allSettled waits until all resolve/reject and lets you know which ones failed
         const [cart_result, dc_result, org_result] = await Promise.all([
-            fetchGeneCartData(),
-            fetchDatasetCollections(false),
+            fetchGeneCartData(geneListShareId),
+            fetchDatasetCollections(layoutShareId),
             fetchOrganisms()
         ]);
     } catch (error) {

www/js/index.js

@@ -162,7 +162,7 @@ const handlePageSpecificLoginUIUpdates = async (event) => {
     document.getElementById("submit-expression-search").classList.add("is-loading");
     await Promise.all([
         fetchGeneCartData(),
-        fetchDatasetCollections(false)
+        fetchDatasetCollections()
     ]);
     document.getElementById("submit-expression-search").classList.remove("is-loading");
 

www/js/projection.js

@@ -137,14 +137,16 @@ const handlePageSpecificLoginUIUpdates = async (event) => {
     // Wait until all pending API calls have completed before checking if we need to search
     document.getElementById("submit-projection-search").classList.add("is-loading");
     try {
+        const pattern = getUrlParameter('projection_source', urlParams);
+
         // SAdkins note - Promise.all fails fast,
         // but Promise.allSettled waits until all resolve/reject and lets you know which ones failed
         const [cartResult, dcResult,] = await Promise.all([
-            fetchPatternsData(),
-            fetchDatasetCollections(false),
+            fetchPatternsData(pattern),
+            fetchDatasetCollections(layoutShareId),
         ]);
 
-        await parseDatasetCollectionURLParams();
+        parseDatasetCollectionURLParams();
         await parsePatternCartURLParams();
 
         // Should help with lining things up on index page