diff --git a/api/api.py b/api/api.py
index e8efc3156f3761f5d69ccbde96c7d4e9ae86ed23..355e78f0713acd4820c0613acf1ef2ba5b3f84ee 100644
--- a/api/api.py
+++ b/api/api.py
@@ -47,8 +47,8 @@ routes = [
]),
webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/tags', listhandler.ListHandler, methods=['POST'], name='tags_post', defaults={'list_name': 'tags'}),
webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/tags/<value:[^/]{3,24}>', listhandler.ListHandler, name='tags', defaults={'list_name': 'tags'}),
- webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/file', listhandler.FileListHandler, name='files_post', methods=['POST'], defaults={'list_name': 'files'}),
- webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/file/<filename:[^/]{3,60}>', listhandler.FileListHandler, name='files', defaults={'list_name': 'files'}),
+ webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/files', listhandler.FileListHandler, name='files_post', methods=['POST'], defaults={'list_name': 'files'}),
+ webapp2.Route(r'/api/<cont_name:[0-9a-z]{3,24}>/<cid:[0-9a-z]{3,24}>/files/<filename:[^/]{3,60}>', listhandler.FileListHandler, name='files', defaults={'list_name': 'files'}),
webapp2.Route(r'/api/<cont_name:collections|projects>/<cid:[0-9a-z]{3,24}>/permissions', listhandler.PermissionsListHandler, name='perms_post', methods=['POST'], defaults={'list_name': 'permissions'}),
webapp2.Route(r'/api/<cont_name:collections|projects>/<cid:[0-9a-z]{3,24}>/permissions/<site:[0-9a-z]{3,24}>/<_id:[\w\@\-\.]{3,60}>',
listhandler.PermissionsListHandler, name='perms', defaults={ 'list_name': 'permissions'}),
diff --git a/api/files.py b/api/files.py
index 24917eae1a6473b528e3009c0b936682a51df3cb..c05aa79e66af5ff16f0ede96445c3c3e35490163 100644
--- a/api/files.py
+++ b/api/files.py
@@ -22,7 +22,7 @@ class FileRequest(object):
The operations could be safely interleaved with other actions like permission checks or database updates.
"""
- def __init__(self, client_addr, filename, body, received_md5, metadata, tags, flavor):
+ def __init__(self, client_addr, filename, body, received_md5, metadata, tags):
self.client_addr = client_addr
self.filename = filename
self.body = body
@@ -31,7 +31,6 @@ class FileRequest(object):
self.tags = tags
self.mimetype = util.guess_mimetype(filename)
self.filetype = util.guess_filetype(filename, self.mimetype)
- self.flavor = flavor
def save_temp_file(self, tempdir_path):
self.tempdir_path = tempdir_path
@@ -137,8 +136,5 @@ class FileRequest(object):
except ValueError:
handler.abort(400, 'invalid "metadata" parameter')
body = handler.request.body_file
- flavor = handler.get_param('flavor', 'data') # TODO: flavor should go away
- if flavor not in ['data', 'attachment']:
- handler.abort(400, 'Query must contain flavor parameter: "data" or "attachment".')
md5 = handler.request.headers.get('Content-MD5')
- return cls(handler.request.client_addr, filename, body, md5, metadata, tags, flavor)
+ return cls(handler.request.client_addr, filename, body, md5, metadata, tags)
diff --git a/api/handlers/listhandler.py b/api/handlers/listhandler.py
index 9e0f092ca3f466871dabbb35a888bd2c374b5c3a..cf7e4b3b9a3d09e8a6c13b7dc5f6aeec1dcdb50b 100644
--- a/api/handlers/listhandler.py
+++ b/api/handlers/listhandler.py
@@ -28,7 +28,9 @@ def initialize_list_configurations():
'files': {
'storage': liststorage.ListStorage,
'permchecker': listauth.default_sublist,
- 'use_oid': True
+ 'use_oid': True,
+ 'mongo_schema_file': 'mongo/file.json',
+ 'input_schema_file': 'input/file.json'
},
'permissions': {
'storage': liststorage.ListStorage,
@@ -354,38 +356,34 @@ class FileListHandler(ListHandler):
file_request.save_temp_file(tempdir_path)
file_datetime = datetime.datetime.utcnow()
file_properties = {
- 'filename': file_request.filename,
- 'filesize': file_request.filesize,
- 'filehash': file_request.sha1,
- 'filetype': file_request.filetype,
- 'flavor': file_request.flavor,
- 'mimetype': file_request.mimetype,
+ 'name': file_request.filename,
+ 'size': file_request.filesize,
+ 'hash': file_request.sha1,
+ 'type': file_request.mimetype,
'tags': file_request.tags,
'metadata': file_request.metadata,
'created': file_datetime,
'modified': file_datetime,
- 'dirty': True
+ 'unprocessed': True
}
+ file_properties['tags'] = file_properties.get('tags', [])
dest_path = os.path.join(self.app.config['data_path'], str(_id)[-3:] + '/' + str(_id))
if not force:
method = 'POST'
else:
filepath = os.path.join(file_request.tempdir_path, filename)
for f in container['files']:
- if f['filename'] == filename:
- if file_request.check_identical(os.path.join(data_path, filename), f['filehash']):
+ if f['name'] == filename:
+ if file_request.check_identical(os.path.join(data_path, filename), f['hash']):
log.debug('Dropping %s (identical)' % filename)
os.remove(filepath)
self.abort(409, 'identical file exists')
else:
log.debug('Replacing %s' % filename)
- payload_validator(payload, 'PUT')
- payload.update(file_properties)
method = 'PUT'
break
else:
method = 'POST'
-
payload_validator(payload, method)
payload.update(file_properties)
result = keycheck(mongo_validator(permchecker(storage.exec_op)))(method, _id=_id, payload=payload)
diff --git a/api/schemas/input/file.json b/api/schemas/input/file.json
index 4295309f089918484905b37fcd04b4e6766820d9..7ad120129d140b62a5ba515103dee7f1c9e9bf58 100644
--- a/api/schemas/input/file.json
+++ b/api/schemas/input/file.json
@@ -2,13 +2,6 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
- "_id": {
- "maxLength": 32,
- "minLength": 2,
- "pattern": "^[0-9a-z][0-9a-z.@_-]{0,30}[0-9a-z]$",
- "title": "ID",
- "type": "string"
- },
"name": { "type": "string" },
"created": {"type": "string", "format": "date-time"},
"modified": {"type": "string", "format": "date-time"},
@@ -31,6 +24,5 @@
"type": "object"
}
},
- "required": ["_id"],
"additionalProperties": false
}
diff --git a/api/schemas/mongo/file.json b/api/schemas/mongo/file.json
index 93aba0ed2b0237b8ce9912ea3321fd018dcea260..2645ba7c76b14ab72c3033911d8f2d9ea7d3806e 100644
--- a/api/schemas/mongo/file.json
+++ b/api/schemas/mongo/file.json
@@ -2,7 +2,6 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
- "_id": { "type": "string"},
"name": { "type": "string" },
"created": {},
"modified": {},
@@ -25,6 +24,6 @@
"type": "object"
}
},
- "required": ["_id", "user", "text"],
+ "required": ["name", "created", "modified", "type", "size", "hash", "unprocessed"],
"additionalProperties": false
}
diff --git a/api/util.py b/api/util.py
index 7dfb20ebfa2e6d775ab271811cc6f9746d2f7aa8..57f1d6631db7463d17f4e900e1ce0d3dde6d6830 100644
--- a/api/util.py
+++ b/api/util.py
@@ -54,7 +54,7 @@ def parse_file(filepath, digest):
'filehash': digest,
'modality': dataset.nims_file_domain,
'datatypes': dataset.nims_file_kinds,
- 'flavor': 'data',
+ 'tags': ['data'],
}
datainfo = {
'acquisition_id': dataset.nims_acquisition_id,