From 8a55a486e38e01b55c70932c5dd2774939ba81bc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 9 Jan 2019 09:51:14 -0500
Subject: [PATCH] Simplify history import to fix extra_files and object store
 handling.

This usage counting this made sense in (a94bf20abfd15f21c3cc380ee92896d0f107bb23) but it is broken with the transition to object store compat (ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) an it is broken with extra files handling (9ea0fee48aa57361147e9145be8deaaafb2a0960).
---
 lib/galaxy/tools/imp_exp/__init__.py | 42 ++++++++++------------------
 1 file changed, 14 insertions(+), 28 deletions(-)

diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
index f1c73789cf1..d07c93e95e8 100644
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -101,16 +101,6 @@ class JobImportHistoryArchiveWrapper(UsesAnnotations):
                     provenance_attrs = load(open(provenance_file_name))
                     datasets_attrs += provenance_attrs
 
-                # Get counts of how often each dataset file is used; a file can
-                # be linked to multiple dataset objects (HDAs).
-                datasets_usage_counts = {}
-                for dataset_attrs in datasets_attrs:
-                    temp_dataset_file_name = \
-                        os.path.realpath(os.path.join(archive_dir, dataset_attrs['file_name']))
-                    if (temp_dataset_file_name not in datasets_usage_counts):
-                        datasets_usage_counts[temp_dataset_file_name] = 0
-                    datasets_usage_counts[temp_dataset_file_name] += 1
-
                 # Create datasets.
                 for dataset_attrs in datasets_attrs:
                     metadata = dataset_attrs['metadata']
@@ -150,26 +140,22 @@ class JobImportHistoryArchiveWrapper(UsesAnnotations):
                             os.path.realpath(os.path.abspath(os.path.join(archive_dir, dataset_attrs['file_name'])))
                         if not file_in_dir(temp_dataset_file_name, os.path.join(archive_dir, "datasets")):
                             raise MalformedContents("Invalid dataset path: %s" % temp_dataset_file_name)
-                        if datasets_usage_counts[temp_dataset_file_name] == 1:
-                            self.app.object_store.update_from_file(hda.dataset, file_name=temp_dataset_file_name, create=True)
+                        self.app.object_store.update_from_file(hda.dataset, file_name=temp_dataset_file_name, create=True)
 
-                            # Import additional files if present. Histories exported previously might not have this attribute set.
-                            dataset_extra_files_path = dataset_attrs.get('extra_files_path', None)
-                            if dataset_extra_files_path:
-                                try:
-                                    file_list = os.listdir(os.path.join(archive_dir, dataset_extra_files_path))
-                                except OSError:
-                                    file_list = []
+                        # Import additional files if present. Histories exported previously might not have this attribute set.
+                        dataset_extra_files_path = dataset_attrs.get('extra_files_path', None)
+                        if dataset_extra_files_path:
+                            try:
+                                file_list = os.listdir(os.path.join(archive_dir, dataset_extra_files_path))
+                            except OSError:
+                                file_list = []
 
-                                if file_list:
-                                    for extra_file in file_list:
-                                        self.app.object_store.update_from_file(
-                                            hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id,
-                                            alt_name=extra_file, file_name=os.path.join(archive_dir, dataset_extra_files_path, extra_file),
-                                            create=True)
-                        else:
-                            datasets_usage_counts[temp_dataset_file_name] -= 1
-                            shutil.copyfile(temp_dataset_file_name, hda.file_name)
+                            if file_list:
+                                for extra_file in file_list:
+                                    self.app.object_store.update_from_file(
+                                        hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id,
+                                        alt_name=extra_file, file_name=os.path.join(archive_dir, dataset_extra_files_path, extra_file),
+                                        create=True)
                         hda.dataset.set_total_size()  # update the filesize record in the database
 
                     # Set tags, annotations.