From dd9d9f524fd166271d36fcd74eaa843579ad2c23 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 16 Sep 2024 16:31:31 +0200
Subject: [PATCH 1/2] update arranger diagrams

---
 docs/diagrams/arranger.md | 30 ++++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/docs/diagrams/arranger.md b/docs/diagrams/arranger.md
index ad037bfb..528920bc 100644
--- a/docs/diagrams/arranger.md
+++ b/docs/diagrams/arranger.md
@@ -28,7 +28,7 @@ flowchart TD
     P --> |Yes| P1[Validate the file]
 ```
 
-## GNPS, AntiSMASH and BigScape 
+## GNPS and AntiSMASH 
 ``` mermaid
 flowchart TD
     ConfigError[Dynaconf config validation error]
@@ -36,7 +36,7 @@ flowchart TD
     UseIt[Use the data]
     Download[First remove existing data if relevent, then download or generate data]
 
-    A[GNPS, antiSMASH and BigSCape] --> B{Pass Dynaconf config validation?}
+    A[GNPS or antiSMASH] --> B{Pass Dynaconf config validation?}
     B -->|No | ConfigError
     B -->|Yes| G{Is the mode PODP?}
     
@@ -53,6 +53,32 @@ flowchart TD
     J -->|Yes| UseIt
 ```
 
+## BigScape
+```mermaid
+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] --> B{Pass Dynaconf config validation?}
+    B -->|No | ConfigError
+    B -->|Yes| G{Is the mode PODP?}
+    
+    G -->|No, local mode| G1{Does data dir exist?}
+    G1 -->|No | Download
+    G1 -->|Yes| H{Pass data validation?}
+    H --> |No | DataError
+    H --> |Yes| UseIt 
+
+    G -->|Yes, podp mode| G2{Does data dir exist?}
+    G2 --> |No | Download
+    G2 --> |Yes | J{Pass data validation?}
+    J -->|No | Download --> |try max 2 times| J
+    J -->|Yes| UseIt
+```
+
+
 ## MIBiG Data
 MIBiG data is always downloaded automatically. Users cannot provide their own MIBiG data.
 

From 0d2bcf3b3d656094c4dcc17c4270a9efa29b94d4 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 16 Sep 2024 16:32:10 +0200
Subject: [PATCH 2/2] run bigscape for local mode if not provided

---
 src/nplinker/arranger.py | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/nplinker/arranger.py b/src/nplinker/arranger.py
index 24e0e56b..6f690e66 100644
--- a/src/nplinker/arranger.py
+++ b/src/nplinker/arranger.py
@@ -263,7 +263,9 @@ def _download_and_extract_antismash(self) -> None:
     def arrange_bigscape(self) -> None:
         """Arrange the BiG-SCAPE data.
 
-        For `local` mode, validate the BiG-SCAPE data.
+        For `local` mode, if the BiG-SCAPE data is provided by users, validate it and raise an error
+        if it is invalid. If the BiG-SCAPE data does not exist, run BiG-SCAPE to generate the
+        clustering file.
 
         For `podp` mode, if the BiG-SCAPE data does not exist, run BiG-SCAPE to generate the
         clustering file; if it exists but not valid, remove the data and re-run BiG-SCAPE to generate
@@ -281,16 +283,19 @@ def arrange_bigscape(self) -> None:
                 BiG-SCAPE data directory.
         - Check if the `data_sqlite.db` file exists in the BiG-SCAPE data directory.
         """
+        if self.config.mode == "local" and self.bigscape_dir.exists():
+            validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)
+            return
+
         pass_validation = False
-        if self.config.mode == "podp":
-            for _ in range(3):
-                try:
-                    validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)
-                    pass_validation = True
-                    break
-                except FileNotFoundError:
-                    shutil.rmtree(self.bigscape_dir, ignore_errors=True)
-                    self._run_bigscape()
+        for _ in range(3):
+            try:
+                validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)
+                pass_validation = True
+                break
+            except FileNotFoundError:
+                shutil.rmtree(self.bigscape_dir, ignore_errors=True)
+                self._run_bigscape()
 
         if not pass_validation:
             validate_bigscape(self.bigscape_dir, self.config.bigscape.cutoff)