From 0ceb33a8dbb2991e45aefc1d73c6a74578b31356 Mon Sep 17 00:00:00 2001
From: Megan Henning <meganhenning@flywheel.io>
Date: Tue, 19 Sep 2017 11:47:10 -0500
Subject: [PATCH 1/3] Add mimetype field to packfile obj save

---
 api/placer.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/api/placer.py b/api/placer.py
index 325558e90..72a4be8cf 100644
--- a/api/placer.py
+++ b/api/placer.py
@@ -507,6 +507,7 @@ def finalize(self):
             'modified': cgi_field.modified,
             'size':	 cgi_field.size,
             'hash':	 cgi_field.hash,
+            'mimetype': cgi_field.mimetype,
 
             'type': self.metadata['packfile']['type'],
 

From d73d430b0d8a434b60f3e3c52a3054d9b050df2e Mon Sep 17 00:00:00 2001
From: Megan Henning <meganhenning@flywheel.io>
Date: Tue, 19 Sep 2017 12:26:20 -0500
Subject: [PATCH 2/3] Add db update and tests

---
 bin/database.py                               | 24 ++++++++++++++++++-
 test/integration_tests/python/test_uploads.py |  6 +++++
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/bin/database.py b/bin/database.py
index 557032e89..0d9bce131 100755
--- a/bin/database.py
+++ b/bin/database.py
@@ -14,6 +14,7 @@
 import time
 
 from api import config
+from api import util
 from api.dao import containerutil
 from api.dao.containerstorage import ProjectStorage
 from api.jobs.jobs import Job
@@ -21,7 +22,7 @@
 from api.types import Origin
 from api.jobs import batch
 
-CURRENT_DATABASE_VERSION = 35 # An int that is bumped when a new schema change is made
+CURRENT_DATABASE_VERSION = 36 # An int that is bumped when a new schema change is made
 
 def get_db_version():
 
@@ -1189,6 +1190,27 @@ def upgrade_to_35():
     process_cursor(cursor, upgrade_to_35_closure)
 
 
+def upgrade_to_36_closure(acquisition):
+
+    for f in acquisition['files']:
+        if not f.get('mimetype'):
+            logging.debug('file with name {} did not have mimetype'.format(f['name']))
+            f['mimetype'] = util.guess_mimetype(f['name'])
+
+    result = config.db.acquisitions.update_one({'_id': acquisition['_id']}, {'$set': {'files': acquisition['files']}})
+    if result.modified_count != 1:
+        raise Exception('Acquisition file not updated')
+
+    return True
+
+
+def upgrade_to_36():
+    """
+    scitran/core issue #931 - mimetype not set on packfile uploads
+    """
+    cursor = config.db.acquisitions.find({'files.mimetype': None})
+    process_cursor(cursor, upgrade_to_36_closure)
+
 
 
 ###
diff --git a/test/integration_tests/python/test_uploads.py b/test/integration_tests/python/test_uploads.py
index 394644165..eaacb866b 100644
--- a/test/integration_tests/python/test_uploads.py
+++ b/test/integration_tests/python/test_uploads.py
@@ -932,6 +932,12 @@ def test_packfile_upload(data_builder, file_form, as_admin, as_root, api_db):
         params={'token': token, 'metadata': metadata_json})
     assert r.ok
 
+    # make sure file was uploaded and mimetype and type are properly set
+    packfile = as_admin.get('/acquisitions').json()[0]['files'][0]
+    assert packfile['mimetype'] == 'application/zip'
+    assert packfile['type'] == 'test'
+
+
     # get another token (start packfile-upload)
     r = as_admin.post('/projects/' + project + '/packfile-start')
     assert r.ok

From fd7d378041a3452cb9202eabcedf87157a445d6f Mon Sep 17 00:00:00 2001
From: Megan Henning <meganhenning@flywheel.io>
Date: Tue, 19 Sep 2017 13:22:48 -0500
Subject: [PATCH 3/3] Only return acqs with files

---
 bin/database.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/database.py b/bin/database.py
index 0d9bce131..e01e6aad6 100755
--- a/bin/database.py
+++ b/bin/database.py
@@ -1208,7 +1208,7 @@ def upgrade_to_36():
     """
     scitran/core issue #931 - mimetype not set on packfile uploads
     """
-    cursor = config.db.acquisitions.find({'files.mimetype': None})
+    cursor = config.db.acquisitions.find({'files': { '$gt': [] }, 'files.mimetype': None})
     process_cursor(cursor, upgrade_to_36_closure)