From 3d4f7b22b343914dc453e166349f65ba67d435b2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 28 Oct 2020 09:39:14 -0400
Subject: [PATCH 1/3] Galaxy schema rendering script.

Uses sqlite_schemadisp to generate images like the one at
https://galaxyproject.org/admin/internals/data-model/
---
 scripts/galaxy_schemadisp.py | 44 ++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 scripts/galaxy_schemadisp.py

diff --git a/scripts/galaxy_schemadisp.py b/scripts/galaxy_schemadisp.py
new file mode 100644
index 00000000000..d60702e40b6
--- /dev/null
+++ b/scripts/galaxy_schemadisp.py
@@ -0,0 +1,44 @@
+import os
+import sys
+from db_shell import *  # noqa
+
+gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
+sys.path.insert(1, os.path.abspath(os.path.join(gxy_root, 'lib')))
+
+from galaxy import model
+from sqlalchemy import MetaData
+from sqlalchemy.orm import class_mapper
+from sqlalchemy_schemadisplay import create_schema_graph, create_uml_graph
+
+if __name__ == "__main__":
+    gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
+    sqlitedb = os.path.join(gxy_root, 'database/universe.sqlite')
+    # Try to build a representation of what's in the sqlite database
+    if os.path.exists(sqlitedb):
+        graph = create_schema_graph(metadata=MetaData('sqlite:///' + sqlitedb),
+                                    show_datatypes=False,
+                                    show_indexes=False,
+                                    rankdir='LR',
+                                    concentrate=False)
+        print(f"Writing galaxy_universe.png, built from {sqlitedb}")
+        graph.write_png('galaxy_universe.png')
+    else:
+        print(f"No sqlitedb available at {sqlitedb}, skipping rendering")
+
+    # Build UML graph from loaded mapper
+    mappers = []
+    for attr in dir(model):
+        if attr[0] == '_':
+            continue
+        try:
+            cls = getattr(model, attr)
+            mappers.append(class_mapper(cls))
+        except Exception:
+            pass
+
+    graph = create_uml_graph(
+        mappers,
+        show_operations=False,
+    )
+    print("Writing galaxy_uml.png")
+    graph.write_png('galaxy_uml.png')  # write out the file

From dbc47ac083a779ebf1d69c1a28baacc24c0af50d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 12 Jan 2021 06:59:33 -0500
Subject: [PATCH 2/3] Import order fixes for schemadisp script

---
 scripts/galaxy_schemadisp.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/galaxy_schemadisp.py b/scripts/galaxy_schemadisp.py
index d60702e40b6..f755232c1b0 100644
--- a/scripts/galaxy_schemadisp.py
+++ b/scripts/galaxy_schemadisp.py
@@ -1,15 +1,17 @@
 import os
 import sys
+
 from db_shell import *  # noqa
 
 gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
 sys.path.insert(1, os.path.abspath(os.path.join(gxy_root, 'lib')))
 
-from galaxy import model
 from sqlalchemy import MetaData
 from sqlalchemy.orm import class_mapper
 from sqlalchemy_schemadisplay import create_schema_graph, create_uml_graph
 
+from galaxy import model
+
 if __name__ == "__main__":
     gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
     sqlitedb = os.path.join(gxy_root, 'database/universe.sqlite')

From e93627a4355c48b5b83522e5d3e2c7faf359d8ff Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 12 Jan 2021 13:48:17 +0100
Subject: [PATCH 3/3] Lint fixes, prompt for sqlalchemy_schemadisplay install

---
 scripts/galaxy_schemadisp.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/scripts/galaxy_schemadisp.py b/scripts/galaxy_schemadisp.py
index f755232c1b0..5410a92f8e6 100644
--- a/scripts/galaxy_schemadisp.py
+++ b/scripts/galaxy_schemadisp.py
@@ -2,14 +2,18 @@ import os
 import sys
 
 from db_shell import *  # noqa
+from sqlalchemy import MetaData
+from sqlalchemy.orm import class_mapper
+try:
+    from sqlalchemy_schemadisplay import create_schema_graph, create_uml_graph
+except ImportError:
+    print("please install sqlalchemy_schemadisplay to use this script (pip install sqlalchemy_schemadisplay)")
+    raise
+
 
 gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
 sys.path.insert(1, os.path.abspath(os.path.join(gxy_root, 'lib')))
 
-from sqlalchemy import MetaData
-from sqlalchemy.orm import class_mapper
-from sqlalchemy_schemadisplay import create_schema_graph, create_uml_graph
-
 from galaxy import model
 
 if __name__ == "__main__":