From 680357ef5f4b76716d366103fee5885db9fce23b Mon Sep 17 00:00:00 2001
From: greg <ghv2@psu.edu>
Date: Wed, 18 Nov 2020 11:24:29 -0500
Subject: [PATCH 1/3] Add the OpenSeadragon viewer for deep zoom images

---
 .../openseadragon/config/openseadragon.xml    |  19 ++++++
 .../openseadragon/static/logo.png             | Bin 0 -> 10490 bytes
 .../templates/openseadragon.mako              |  64 ++++++++++++++++++
 3 files changed, 83 insertions(+)
 create mode 100644 config/plugins/visualizations/openseadragon/config/openseadragon.xml
 create mode 100644 config/plugins/visualizations/openseadragon/static/logo.png
 create mode 100644 config/plugins/visualizations/openseadragon/templates/openseadragon.mako

diff --git a/config/plugins/visualizations/openseadragon/config/openseadragon.xml b/config/plugins/visualizations/openseadragon/config/openseadragon.xml
new file mode 100644
index 00000000000..269be91e01b
--- /dev/null
+++ b/config/plugins/visualizations/openseadragon/config/openseadragon.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="OpenSeadragon">
+    <description>Viewer for high-resolution zoomable images.</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">images.Jpg</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">images.Png</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">xml.Dzi</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">openseadragon.mako</entry_point>
+</visualization>
+
diff --git a/config/plugins/visualizations/openseadragon/static/logo.png b/config/plugins/visualizations/openseadragon/static/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..04626e5ef44c91d6174b4ce25dbf98cf18557dfa
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/config/plugins/visualizations/openseadragon/templates/openseadragon.mako b/config/plugins/visualizations/openseadragon/templates/openseadragon.mako
new file mode 100644
index 00000000000..340b7db72da
--- /dev/null
+++ b/config/plugins/visualizations/openseadragon/templates/openseadragon.mako
@@ -0,0 +1,64 @@
+<%
+    default_title = "OpenSeadragon Viewer"
+
+    # Use root for resource loading.
+    root = h.url_for("/static/")
+    app_root = root + "plugins/visualizations/openseadragon/static/"
+%>
+
+<!DOCTYPE HTML>
+<html>
+    <head>
+        <!-- OpenSeadragon Viewer is a web-based viewer for high-resolution zoomable images. -->
+        <title>${hda.name | h} | ${visualization_name}</title>
+
+        ## external scripts
+        ${h.javascript_link(app_root + "scripts/openseadragon.min.js")}
+    </head>
+    <body>
+        <!-- Div which will hold the Output -->
+        <div id="seadragon-viewer" style="width: 800px; height: 600px;"></div>
+        <script type="text/javascript">
+
+            // Galaxy hda stuff.
+            const hda_ext = "${hda.ext}";
+            const hda_id = "${trans.security.encode_id(hda.id)}";
+            // OpenSeadragon stuff.
+            const dzi_image_url = "${h.url_for(controller='/datasets', action='index')}/" + hda_id + "/display/";
+            const viewer_id = "seadragon-viewer";
+            const prefixUrl = "//openseadragon.github.io/openseadragon/images/";
+            const simple_image_url = "${h.url_for(controller='/datasets', action='index')}/" + hda_id + "/display";
+            const xmlns = "http://schemas.microsoft.com/deepzoom/2008";
+
+            if (hda_ext == 'jpg' || hda_ext == 'png') {
+                var viewer = OpenSeadragon({
+                    id: viewer_id,
+                    prefixUrl: prefixUrl,
+                    tileSources: {
+                        type: "image",
+                        url:  simple_image_url
+                    }
+                });
+            } else if (hda_ext == 'dzi') {
+                var viewer = OpenSeadragon({
+                    id: viewer_id,
+                    prefixUrl: prefixUrl,
+                    tileSources:   {
+                        Image: {
+                            xmlns:    xmlns,
+                            Url:      dzi_image_url,
+                            Format:   "${hda.metadata.format}",
+                            Overlap:  "${hda.metadata.overlap}",
+                            TileSize: "${hda.metadata.tile_size}",
+                            Size: {
+                                Height: "${hda.metadata.height}",
+                                Width:  "${hda.metadata.width}"
+                            }
+                        }
+                    }
+                });
+            }
+        </script>
+    </body>
+</html>
+

From 7649b73afd1104aba9704426f9679ce62235e9be Mon Sep 17 00:00:00 2001
From: greg <ghv2@psu.edu>
Date: Wed, 18 Nov 2020 15:43:26 -0500
Subject: [PATCH 2/3] Attempt to use the newer viz packaging approach

---
 client/gulpfile.js                                |  1 +
 .../visualizations/openseadragon/package.json     | 15 +++++++++++++++
 .../openseadragon/templates/openseadragon.mako    |  2 +-
 3 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 config/plugins/visualizations/openseadragon/package.json

diff --git a/client/gulpfile.js b/client/gulpfile.js
index c0d010cb852..015f572fda8 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -20,6 +20,7 @@ const PLUGIN_BUILD_IDS = [
     "mvpapp",
     "ngl",
     "openlayers",
+    "openseadragon",
     "pv",
 ];
 
diff --git a/config/plugins/visualizations/openseadragon/package.json b/config/plugins/visualizations/openseadragon/package.json
new file mode 100644
index 00000000000..25998b15792
--- /dev/null
+++ b/config/plugins/visualizations/openseadragon/package.json
@@ -0,0 +1,15 @@
+{
+    "name": "openseadragon",
+    "version": "2.4.2",
+    "license": "New BSD",
+    "dependencies": {
+        "backbone": "^1.3.3",
+        "bootstrap": "^3.3.7",
+        "jquery": "^3.3.1",
+        "parcel-bundler": "^1.4.1"
+    },
+    "scripts": {
+        "build": "parcel build src/openseadragon.min.js -d static/dist"
+    }
+}
+
diff --git a/config/plugins/visualizations/openseadragon/templates/openseadragon.mako b/config/plugins/visualizations/openseadragon/templates/openseadragon.mako
index 340b7db72da..52ad53f4bfc 100644
--- a/config/plugins/visualizations/openseadragon/templates/openseadragon.mako
+++ b/config/plugins/visualizations/openseadragon/templates/openseadragon.mako
@@ -13,7 +13,7 @@
         <title>${hda.name | h} | ${visualization_name}</title>
 
         ## external scripts
-        ${h.javascript_link(app_root + "scripts/openseadragon.min.js")}
+        ${h.javascript_link(app_root + "dist/openseadragon.min.js")}
     </head>
     <body>
         <!-- Div which will hold the Output -->

From f744bfa3abfa177f74fb9c84c131b0d306436c7f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Dec 2020 09:18:03 -0500
Subject: [PATCH 3/3] Tweak OSD plugin build, include images.

No need to bundle this since it's prebuilt -- this simply copies it
(including images and maps which were left out before) for staging,
which is faster and more complete.
---
 config/plugins/visualizations/openseadragon/package.json | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/config/plugins/visualizations/openseadragon/package.json b/config/plugins/visualizations/openseadragon/package.json
index 25998b15792..24914bf1fc4 100644
--- a/config/plugins/visualizations/openseadragon/package.json
+++ b/config/plugins/visualizations/openseadragon/package.json
@@ -3,13 +3,10 @@
     "version": "2.4.2",
     "license": "New BSD",
     "dependencies": {
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "jquery": "^3.3.1",
-        "parcel-bundler": "^1.4.1"
+        "cpy-cli": "^3.1.1",
+        "openseadragon": "^2.4.2"
     },
     "scripts": {
-        "build": "parcel build src/openseadragon.min.js -d static/dist"
+        "build": "cpy --cwd='node_modules/openseadragon/build/openseadragon' --parents './' '../../../../static/dist'"
     }
 }
-