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NPLinker · Sep 16, 2024 · e4fd800 · e4fd800
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diff --git a/dev/api/arranger/index.html b/dev/api/arranger/index.html
diff --git a/dev/api/scoring/index.html b/dev/api/scoring/index.html
diff --git a/dev/diagrams/arranger/index.html b/dev/diagrams/arranger/index.html
@@ -737,9 +737,18 @@
 </li>
 
         <li class="md-nav__item">
-  <a href="#gnps-antismash-and-bigscape" class="md-nav__link">
+  <a href="#gnps-and-antismash" class="md-nav__link">
     <span class="md-ellipsis">
-      GNPS, AntiSMASH and BigScape
+      GNPS and AntiSMASH
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#bigscape" class="md-nav__link">
+    <span class="md-ellipsis">
+      BigScape
     </span>
   </a>
 
@@ -1573,9 +1582,18 @@
 </li>
 
         <li class="md-nav__item">
-  <a href="#gnps-antismash-and-bigscape" class="md-nav__link">
+  <a href="#gnps-and-antismash" class="md-nav__link">
     <span class="md-ellipsis">
-      GNPS, AntiSMASH and BigScape
+      GNPS and AntiSMASH
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#bigscape" class="md-nav__link">
+    <span class="md-ellipsis">
+      BigScape
     </span>
   </a>
 
@@ -1627,14 +1645,14 @@ <h2 id="podp-project-metadata-json-file">PODP project metadata json file<a class
     A --&gt; |Yes| P{Does the file exist?}
     P --&gt; |No | P0[Download the file] --&gt; P1
     P --&gt; |Yes| P1[Validate the file]</code></pre>
-<h2 id="gnps-antismash-and-bigscape">GNPS, AntiSMASH and BigScape<a class="headerlink" href="#gnps-antismash-and-bigscape" title="Permanent link">&para;</a></h2>
+<h2 id="gnps-and-antismash">GNPS and AntiSMASH<a class="headerlink" href="#gnps-and-antismash" title="Permanent link">&para;</a></h2>
 <pre class="mermaid"><code>flowchart TD
     ConfigError[Dynaconf config validation error]
     DataError[Data validation error]
     UseIt[Use the data]
     Download[First remove existing data if relevent, then download or generate data]
 
-    A[GNPS, antiSMASH and BigSCape] --&gt; B{Pass Dynaconf config validation?}
+    A[GNPS or antiSMASH] --&gt; B{Pass Dynaconf config validation?}
     B --&gt;|No | ConfigError
     B --&gt;|Yes| G{Is the mode PODP?}
 
@@ -1644,6 +1662,28 @@ <h2 id="gnps-antismash-and-bigscape">GNPS, AntiSMASH and BigScape<a class="heade
     H --&gt; |No | DataError
     H --&gt; |Yes| UseIt 
 
+    G --&gt;|Yes, podp mode| G2{Does data dir exist?}
+    G2 --&gt; |No | Download
+    G2 --&gt; |Yes | J{Pass data validation?}
+    J --&gt;|No | Download --&gt; |try max 2 times| J
+    J --&gt;|Yes| UseIt</code></pre>
+<h2 id="bigscape">BigScape<a class="headerlink" href="#bigscape" title="Permanent link">&para;</a></h2>
+<pre class="mermaid"><code>flowchart TD
+    ConfigError[Dynaconf config validation error]
+    DataError[Data validation error]
+    UseIt[Use the data]
+    Download[First remove existing data if relevent, then download or generate data]
+
+    A[BigSCape] --&gt; B{Pass Dynaconf config validation?}
+    B --&gt;|No | ConfigError
+    B --&gt;|Yes| G{Is the mode PODP?}
+
+    G --&gt;|No, local mode| G1{Does data dir exist?}
+    G1 --&gt;|No | Download
+    G1 --&gt;|Yes| H{Pass data validation?}
+    H --&gt; |No | DataError
+    H --&gt; |Yes| UseIt 
+
     G --&gt;|Yes, podp mode| G2{Does data dir exist?}
     G2 --&gt; |No | Download
     G2 --&gt; |Yes | J{Pass data validation?}

diff --git a/dev/objects.inv b/dev/objects.inv
diff --git a/dev/search/search_index.json b/dev/search/search_index.json
diff --git a/dev/sitemap.xml b/dev/sitemap.xml
@@ -2,157 +2,157 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/install/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/logging/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/quickstart/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/antismash/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/arranger/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/bigscape/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/genomics/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/genomics_abc/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/genomics_utils/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/gnps/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/loader/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/metabolomics/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/metabolomics_abc/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/metabolomics_utils/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/mibig/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/nplinker/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/schema/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/scoring/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/scoring_abc/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/scoring_methods/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/scoring_utils/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/strain/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/strain_utils/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/api/utils/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/concepts/bigscape/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/concepts/config_file/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/concepts/gnps_data/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/concepts/working_dir_structure/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/diagrams/arranger/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
     <url>
          <loc>https://nplinker.github.io/nplinker/latest/diagrams/loader/</loc>
-         <lastmod>2024-09-12</lastmod>
+         <lastmod>2024-09-16</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>
diff --git a/dev/sitemap.xml.gz b/dev/sitemap.xml.gz