feat: Create v13.1.3 release builds

CHANGELOG.md

@@ -5,6 +5,19 @@ All notable changes to SODA will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v13.1.3 - 2024-02-29
+
+## Feature Addditions:
+
+- Announcements have been redesigned to convey updates and fixes clearly.
+- Added the ability to generate a copy of a dataset's manifest files locally within the organize datasets feature.
+- Updated the UI for GM/FFM subject metadata Species, Strain, and RRID selection, and changed the API endpoint to use SciCrunch's public API to search for RRIDs.
+
+## Bug fixes:
+
+- Fixed an issue in the `Organize datasets` feature when creating a new Pennsieve dataset that prevented SODA from finding the dataset in some cases.
+- Banner image selection popup has been patched to overlay above entire app.
+
 ## v.13.1.2 - 2024-02-15
 
 ## Bug fixes:

package.json

@@ -1,7 +1,7 @@
 {
   "name": "soda-for-sparc",
   "procductName": "SODA for SPARC",
-  "version": "13.1.2",
+  "version": "13.1.3",
   "description": "Keep Calm and Curate",
   "main": "./out/main/index.js",
   "author": "SODA Team",

src/main/index.js

@@ -134,6 +134,15 @@ ipcMain.on("orcid", (event, url) => {
   });
 });
 
+ipcMain.handle("open-folder-path-select", (event, pathSelectDialogText) => {
+  const path = dialog.showOpenDialogSync(mainWindow, {
+    properties: ["openDirectory"],
+    title: pathSelectDialogText,
+  });
+  let returnPath = path[0] ? path[0] : null;
+  return returnPath;
+});
+
 // passing in the spreadsheet data to pass to a modal
 // that will have a jspreadsheet for user edits
 ipcMain.handle("spreadsheet", (event, spreadsheet) => {

src/main/main.js

@@ -469,6 +469,7 @@ ipcMain.on("restart_app", async () => {
   log.info("quitAndInstall");
   autoUpdater.quitAndInstall();
 });
+
 // passing in the spreadsheet data to pass to a modal
 // that will have a jspreadsheet for user edits
 ipcMain.handle("spreadsheet", (event, spreadsheet) => {
@@ -518,6 +519,8 @@ ipcMain.handle("spreadsheet", (event, spreadsheet) => {
     }
   });
 });
+
+ipcMain.handle("");
 const wait = async (delay) => {
   return new Promise((resolve) => setTimeout(resolve, delay));
 };

src/main/strain.js

@@ -1,33 +1,12 @@
-import https from "https";
 import { ipcMain } from "electron";
-
-ipcMain.handle("getStrainData", async (event, rridInfo) => {
-  let data = await new Promise((resolve, reject) => {
-    https.get(rridInfo, async (res) => {
-      let data = "";
-      let dataReady = false;
-      if (res.statusCode === 200) {
-        res.setEncoding("utf8");
-        res.on("data", (d) => {
-          data += d;
-        });
-        res.on("end", () => {
-          dataReady = true;
-        });
-
-        while (!dataReady) {
-          // wait for 1 second
-          await new Promise((r) => setTimeout(r, 1000));
-        }
-
-        resolve(data);
-      } else {
-        reject("Could not load strain");
-      }
-    });
+import axios from "axios";
+
+ipcMain.handle("getStrainData", async (event, rrid) => {
+  let organismResponse = await axios.get(`https://scicrunch.org/resolver/${rrid}.json`, {
+    headers: {
+      "Content-Type": "application/json",
+      apiKey: "2YOfdcQRDVN6QZ1V6x3ZuIAsuypusxHD",
+    },
   });
-
-  // let xmlSerializer = new XMLSerializer();
-  // let serialized =  xmlSerializer.serializeToString(data)
-  return data;
+  return organismResponse.data;
 });

src/pyflask/curate/curate.py

@@ -3201,10 +3201,23 @@ def main_curate_function(soda_json_structure):
                         selected_dataset_id = ds["content"]["id"]
 
 
-                    # whether we are generating a new dataset or merging, we want the dataset information for later steps
-                    r = requests.get(f"{PENNSIEVE_URL}/datasets/{selected_dataset_id}", headers=create_request_headers(get_access_token()))
-                    r.raise_for_status()
-                    myds = r.json()
+                    # check that dataset was created with a limited retry (for some users the dataset isn't automatically accessible)
+                    attempts = 0
+                    while(attempts < 3):
+                        try: 
+                            # whether we are generating a new dataset or merging, we want the dataset information for later steps
+                            r = requests.get(f"{PENNSIEVE_URL}/datasets/{selected_dataset_id}", headers=create_request_headers(get_access_token()))
+                            r.raise_for_status()
+                            myds = r.json()
+                            break
+                        except Exception as e:
+                            attempts += 1 
+                            # check if final attempt
+                            if attempts >= 2:
+                                # raise the error to the user
+                                raise e
+                            time.sleep(10)
+
 
                     ps_upload_to_dataset(soda_json_structure, ps, myds)
         except Exception as e:

src/pyflask/startup/minimumApiVersion.py

@@ -4,4 +4,4 @@ def get_api_version():
     """
     Returns the version of the API
     """
-    return {'version': os.getenv('API_VERSION', "13.1.2")}
+    return {'version': os.getenv('API_VERSION', "13.1.3")}

src/renderer/src/assets/css/main.css

@@ -177,7 +177,8 @@ button[data-id="bf_list_roles_team"] {
 button[data-id="guided-select-pennsieve-dataset-to-resume"],
 button[data-id="bf_list_users_pi"],
 button[data-id="guided_bf_list_users_pi"],
-button[data-id="guided_bf_list_users_and_teams"] {
+button[data-id="guided_bf_list_users_and_teams"],
+button[data-id="common-strain-rrid-dropdown"] {
   border: 1px solid rgba(34, 36, 38, 0.15);
   border-radius: 7px;
   height: 35px;