minerva-author-ui@1.5.0 minerva-browser@3.15.5

labsyspharm · Jun 7, 2023 · cadad87 · cadad87
1 parent 77c7230
commit cadad87
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Showing 4 changed files with 23 additions and 13 deletions.
diff --git a/minerva-story/index.html b/minerva-story/index.html
@@ -10,7 +10,7 @@
 <body>
     <div id="minerva-browser" style="position: absolute; top: 0; left: 0; height: 100%; width: 100%;"> </div>
     <script defer src="https://use.fontawesome.com/releases/v5.2.0/js/all.js" integrity="sha384-4oV5EgaV02iISL2ban6c/RmotsABqE4yZxZLcYMAdG7FAPsyHYAPpywE9PJo+Khy" crossorigin="anonymous"></script>
-    <script src="https://cdn.jsdelivr.net/npm/minerva-browser@3.15.0/build/bundle.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/minerva-browser@3.15.5/build/bundle.js"></script>
   <script>
         window.viewer = MinervaStory.default.build_page({
           hideWelcome: true,

diff --git a/src/app.py b/src/app.py
@@ -110,17 +110,18 @@ def extract_story_json_stem(input_file):
 
 def yield_labels(opener, csv_file, chan_label, num_channels):
     label_num = 0
+    can_open_csv = False
     # First, try to load labels from CSV
-    if str(csv_file) != ".":
+    try:
         with open(csv_file, encoding="utf-8-sig") as cf:
             for row in csv.DictReader(cf):
                 if label_num < num_channels:
                     default = row.get("marker_name", str(label_num))
                     default = row.get("Marker Name", default)
                     yield chan_label.get(str(label_num), default)
                     label_num += 1
-    # Second, try to load labels from OME-XML
-    else:
+    except FileNotFoundError:
+        # Second, try to load labels from OME-XML
         for label in opener.load_xml_markers():
             yield label
             label_num += 1
@@ -1667,6 +1668,8 @@ def api_import():
                     saved = copy_saved_states(autosaved, saved)
 
             input_image_file = pathlib.Path(saved["in_file"])
+            if (data["missingpath"]):
+                input_image_file = pathlib.Path(data["missingpath"])
 
             if data["csvpath"]:
                 csv_file = pathlib.Path(data["csvpath"])
@@ -1683,14 +1686,17 @@ def api_import():
                 # This step could take up to a minute
                 response["masks"] = reload_all_mask_state_subsets(saved["masks"])
 
-            if "defaults" in saved:
-                response["defaults"] = saved["defaults"]
-
             response["waypoints"] = saved["waypoints"]
             response["groups"] = saved["groups"]
-            for group in saved["groups"]:
-                for chan in group["channels"]:
+
+            if "defaults" in saved:
+                response["defaults"] = saved["defaults"]
+                for chan in saved["defaults"]:
                     chan_label[str(chan["id"])] = chan["label"]
+            else:
+                for group in saved["groups"]:
+                    for chan in group["channels"]:
+                        chan_label[str(chan["id"])] = chan["label"]
         else:
             csv_file = pathlib.Path(data["csvpath"])
 
@@ -1721,7 +1727,8 @@ def api_import():
 
             (invalid, opener) = return_image_opener(str(input_image_file))
             if invalid or not opener:
-                return api_error(404, "Image file not found: " + str(input_image_file))
+                img_file = re.search("[^\\\/]*$", str(input_image_file))[0]
+                return api_error(404, "IMAGE ASK ERR: " + img_file)
 
             (num_channels, num_levels, width, height) = opener.get_shape()
 
@@ -1734,6 +1741,9 @@ def api_import():
             print(e)
             return api_error(500, "Invalid tiff file")
 
+        # Copy defaults to channel label dictionary
+        chan_defaults = response.get("defaults", []);
+
         try:
             labels = list(yield_labels(opener, csv_file, chan_label, num_channels))
         except Exception:
@@ -1760,7 +1770,7 @@ def api_import():
                 "marker_csv_file": str(csv_file),
                 "input_image_file": str(input_image_file),
                 "waypoints": response.get("waypoints", []),
-                "defaults": response.get("defaults"),
+                "defaults": response.get("defaults", []),
                 "sample_info": response.get(
                     "sample_info", {"rotation": 0, "name": "", "text": ""}
                 ),

diff --git a/src/save_exhibit_pyramid.py b/src/save_exhibit_pyramid.py
@@ -32,7 +32,7 @@ def json_to_html(exhibit):
         '    <body>\n'
         '        <div id="minerva-browser" style="position: absolute; top: 0; left: 0; height: 100%; width: 100%;"></div>\n'
         '        <script defer src="https://use.fontawesome.com/releases/v5.2.0/js/all.js" integrity="sha384-4oV5EgaV02iISL2ban6c/RmotsABqE4yZxZLcYMAdG7FAPsyHYAPpywE9PJo+Khy" crossorigin="anonymous"></script>\n'
-        '        <script src="https://cdn.jsdelivr.net/npm/minerva-browser@3.15.0/build/bundle.js"></script>\n'
+        '        <script src="https://cdn.jsdelivr.net/npm/minerva-browser@3.15.5/build/bundle.js"></script>\n'
         '        <script>\n'
         '         window.viewer = MinervaStory.default.build_page({\n'
                      f'exhibit: {exhibit},\n'

diff --git a/static/index.html b/static/index.html
@@ -1 +1 @@
-<!doctype html><html><head><title>Minerva Author</title><link rel="icon" href="images/favicon.png"><meta charset="UTF-8"><meta http-equiv="Cache-control" content="no-cache"/><meta name="description" content="Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views."><meta name="keywords" content="Minerva, microscopy, multiplexed, immunofluorescence, imaging, OME, LSP"><meta property="og:title" content="Minerva Author"/><meta property="og:type" content="website"/><meta property="og:url" content="https://author.minerva.im"/><meta property="og:image" content="https://author.minerva.im/images/Minerva-Author_HorizLogo_RGB.svg"/><script defer="defer" src="https://use.fontawesome.com/releases/v5.2.0/js/all.js" integrity="sha384-4oV5EgaV02iISL2ban6c/RmotsABqE4yZxZLcYMAdG7FAPsyHYAPpywE9PJo+Khy" crossorigin="anonymous"></script></head><body><div id="minerva"></div><script src="https://cdn.jsdelivr.net/npm/minerva-author-ui@1.4.0/build/bundle.cd18d7bf8c0adf1d053d.js"></script></body></html>
+<!doctype html><html><head><title>Minerva Author</title><link rel="icon" href="images/favicon.png"><meta charset="UTF-8"><meta http-equiv="Cache-control" content="no-cache"/><meta name="description" content="Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views."><meta name="keywords" content="Minerva, microscopy, multiplexed, immunofluorescence, imaging, OME, LSP"><meta property="og:title" content="Minerva Author"/><meta property="og:type" content="website"/><meta property="og:url" content="https://author.minerva.im"/><meta property="og:image" content="https://author.minerva.im/images/Minerva-Author_HorizLogo_RGB.svg"/><script defer="defer" src="https://use.fontawesome.com/releases/v5.2.0/js/all.js" integrity="sha384-4oV5EgaV02iISL2ban6c/RmotsABqE4yZxZLcYMAdG7FAPsyHYAPpywE9PJo+Khy" crossorigin="anonymous"></script></head><body><div id="minerva"></div><script src="https://cdn.jsdelivr.net/npm/minerva-author-ui@1.5.0/build/bundle.aa36dd10fcd586e82f39.js"></script></body></html>