From 54700d20990bd68d272d250fd9b4d38edcf544bc Mon Sep 17 00:00:00 2001
From: Paul Lesack <paul.lesack@ubc.ca>
Date: Wed, 18 Sep 2024 15:36:16 -0700
Subject: [PATCH] Fixed bug with path column; dv_manifest_gen now handles
 recursion more like it should

---
 src/dataverse_utils/__init__.py               |  2 +-
 src/dataverse_utils/dataverse_utils.py        | 23 ++++++------
 .../scripts/dv_manifest_gen.py                | 36 ++++++++++---------
 3 files changed, 33 insertions(+), 28 deletions(-)

diff --git a/src/dataverse_utils/__init__.py b/src/dataverse_utils/__init__.py
index 8063eb8..a204956 100644
--- a/src/dataverse_utils/__init__.py
+++ b/src/dataverse_utils/__init__.py
@@ -5,5 +5,5 @@
 '''
 from dataverse_utils.dataverse_utils import *
 
-VERSION = (0,13,0)
+VERSION = (0,13,1)
 __version__ = '.'.join([str(x) for x in VERSION])
diff --git a/src/dataverse_utils/dataverse_utils.py b/src/dataverse_utils/dataverse_utils.py
index 3e46bf0..4681a24 100644
--- a/src/dataverse_utils/dataverse_utils.py
+++ b/src/dataverse_utils/dataverse_utils.py
@@ -118,18 +118,21 @@ def make_tsv(start_dir, in_list=None, def_tag='Data', # pylint: disable=too-many
     if kwargs.get('path'):
         headers.insert(1, 'path')
     outf = io.StringIO(newline='')
-    tsv_writer = csv.writer(outf, delimiter='\t',
-                            quoting=quotype
-                            )
+    tsv_writer = csv.DictWriter(outf, delimiter='\t',
+                                quoting=quotype,
+                                fieldnames=headers,
+                                extrasaction='ignore')
     if inc_header:
-        tsv_writer.writerow(headers)
+        tsv_writer.writeheader()
     for row in in_list:
-        desc = os.path.splitext(os.path.basename(row))[0]
-        if mime:
-            mtype = mimetypes.guess_type(row)[0]
-            tsv_writer.writerow([row, desc, def_tag, mtype])
-        else:
-            tsv_writer.writerow([row, desc, def_tag])
+        #the columns
+        r = {}
+        r['file'] = row
+        r['description'] = os.path.splitext(os.path.basename(row))[0]
+        r['mimetype'] = mimetypes.guess_type(row)[0]
+        r['tags'] = def_tag
+        r['path'] =  ''
+        tsv_writer.writerow(r)
     outf.seek(0)
     outfile = outf.read()
     outf.close()
diff --git a/src/dataverse_utils/scripts/dv_manifest_gen.py b/src/dataverse_utils/scripts/dv_manifest_gen.py
index 0e78855..465685f 100644
--- a/src/dataverse_utils/scripts/dv_manifest_gen.py
+++ b/src/dataverse_utils/scripts/dv_manifest_gen.py
@@ -6,6 +6,7 @@
 '''
 
 import argparse
+import glob
 import os
 import pathlib
 #pathlib new for Python 3.5
@@ -16,7 +17,7 @@
 
 import dataverse_utils as du
 
-VERSION = (0, 5, 0)
+VERSION = (0, 5, 1)
 __version__ = '.'.join([str(x) for x in VERSION])
 
 def parse() -> argparse.ArgumentParser():
@@ -100,27 +101,28 @@ def main() -> None:
     args.quote = quotype(args.quote)
     if  args.quote == -1:
         parser.error('Invalid quotation type')
-    f_list = []
 
-    if not args.files:
-        args.files = [str(x) for x in pathlib.Path('./').glob('*')]
-    if args.show_hidden:
-        args.files +=  [str(x) for x in pathlib.Path('./').glob('.*')]
-    for fil in args.files:
-        finder = pathlib.Path(fil).expanduser()
-        if args.recursive and finder.is_dir():
-            f_list += list(finder.rglob('*'))
+    f_list = []
+    for file in args.files:
+        if not args.recursive:
+            f_list += glob.glob(file,
+                      include_hidden=args.show_hidden)
         else:
-            f_list += list(finder.parent.glob(finder.name))
-    #Set comprehension strips out duplicates
-    #Strip out hidden files and directories
-    if args.show_hidden:
-        f_list = {str(x) for x in f_list if x.is_file()}
-    else:
-        f_list = {str(x) for x in f_list if x.is_file() and not re.search(r'^\.[Aa9-Zz9]*', str(x))}
+            f_list += glob.glob(file+'/**', recursive=True,
+                                include_hidden=args.show_hidden)
+    if not f_list and not args.files:
+        if not args.recursive:
+            f_list += glob.glob('./*', include_hidden=args.show_hidden)
+        else:
+            f_list += glob.glob('./**', recursive=True,
+                                include_hidden=args.show_hidden)
+    f_list = [pathlib.Path(_) for _ in f_list]
+    f_list = [_ for _ in f_list if _.stem != '' and _.exists() and _.is_file()]
     if not f_list:
+        #nothing to do
         print('Nothing matching these criteria. No manifest generated')
         sys.exit()
+
     if args.filename:
         du.dump_tsv(os.getcwd(), filename=args.filename,
                     in_list=f_list,