From 7911f44b67defede836ab34e2c6385ec90a64f7c Mon Sep 17 00:00:00 2001
From: nroehner <nicholasroehner@gmail.com>
Date: Thu, 21 Oct 2021 21:13:53 -0400
Subject: [PATCH] Updated to version 1.5.2 with additional download of
 sequences when downloading components from SynBioHub.

---
 features_to_circuits/__init__.py              |  2 +-
 sequences_to_features/__init__.py             |  2 +-
 .../sequences_to_features.py                  | 30 ++++++++++++++++++-
 setup.py                                      |  4 +--
 4 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/features_to_circuits/__init__.py b/features_to_circuits/__init__.py
index 61f3d48..4bec5b3 100644
--- a/features_to_circuits/__init__.py
+++ b/features_to_circuits/__init__.py
@@ -1,4 +1,4 @@
 # See https://www.python.org/dev/peps/pep-0440/ for info on version numbering
-__version__ = '1.5.1'
+__version__ = '1.5.2'
 
 from features_to_circuits.features_to_circuits import *
\ No newline at end of file
diff --git a/sequences_to_features/__init__.py b/sequences_to_features/__init__.py
index 655c207..e49b2df 100644
--- a/sequences_to_features/__init__.py
+++ b/sequences_to_features/__init__.py
@@ -1,4 +1,4 @@
 # See https://www.python.org/dev/peps/pep-0440/ for info on version numbering
-__version__ = '1.5.1'
+__version__ = '1.5.2'
 
 from sequences_to_features.sequences_to_features import *
\ No newline at end of file
diff --git a/sequences_to_features/sequences_to_features.py b/sequences_to_features/sequences_to_features.py
index 3282334..03bba56 100644
--- a/sequences_to_features/sequences_to_features.py
+++ b/sequences_to_features/sequences_to_features.py
@@ -198,8 +198,8 @@ class FeatureLibrary():
     def __init__(self, docs, require_sequence=True):
         self.features = []
         self.docs = docs
-        self.__updated_indices = set()
 
+        self.__updated_indices = set()
         self.__feature_map = {}
         self.__feature_dict = {}
         self.__name_to_idents = {}
@@ -1513,6 +1513,28 @@ def curate(feature_library, target_library, output_library, output_files, extend
 
                 target_library.docs[i].write(output_files[i])
 
+def download_sequences(doc, synbiohub):
+    for comp_definition in doc.componentDefinitions:
+        for seq_URI in comp_definition.sequences:
+            download_sequence = False
+
+            try:
+                doc.getSequence(seq_URI)
+            except RuntimeError:
+                download_sequence = True
+            except NotFoundError as exc:
+                if is_sbol_not_found(exc):
+                    download_sequence = True
+
+            if download_sequence:
+                try:
+                    synbiohub.pull(seq_URI, doc)
+                except NotFoundError as exc:
+                    if is_sbol_not_found(exc):
+                        logger.warning('Unable to download sequence %s, seq_URI)')
+                    else:
+                        raise
+
 def main(args=None):
     if args is None:
         args = sys.argv[1:]
@@ -1666,6 +1688,8 @@ def main(args=None):
             try:
                 synbiohub.pull(feature_URL, feature_doc)
 
+                download_sequences(feature_doc, synbiohub)
+
                 feature_docs.append(feature_doc)
             except NotFoundError as exc:
                 if is_sbol_not_found(exc):
@@ -1688,6 +1712,8 @@ def main(args=None):
                 try:
                     synbiohub.pull(target_URL, target_doc)
 
+                    download_sequences(target_doc, synbiohub)
+
                     target_docs.append(target_doc)
                 except NotFoundError as exc:
                     target_docs.append(None)
@@ -1741,6 +1767,8 @@ def main(args=None):
                     target_doc = sbol2.Document()
 
                     synbiohub.pull(target_URL, target_doc)
+
+                    download_sequences(target_doc, synbiohub)
                 except NotFoundError as exc:
                     if is_sbol_not_found(exc):
                         logger.warning('Unable to find target URL %s at %s', target_URL, sbh_URL)
diff --git a/setup.py b/setup.py
index abcab1e..5bb9596 100644
--- a/setup.py
+++ b/setup.py
@@ -12,13 +12,13 @@
 
 setup(
     name='SYNBICT',
-    version='1.5.1',
+    version='1.5.2',
     description='Synthetic Biology Curation Tools (SYNBICT)',
     long_description='Synthetic Biology Curation Tools (SYNBICT) is a Python tool suite for automation-assisted annotation, curation, and functional inference for genetic designs.',
     author='Nicholas Roehner',
     author_email='nicholasroehner@gmail.com',
     url='https://github.com/SD2E/SYNBICT',
-    download_url='https://github.com/SD2E/SYNBICT/archive/refs/tags/v1.4.tar.gz',
+    download_url='https://github.com/SD2E/SYNBICT/archive/refs/tags/v1.5.2.tar.gz',
     packages=find_packages(),
     install_requires=install_requires,
     classifiers=[