diff --git a/mutalyzer/sync.py b/mutalyzer/sync.py
index 82fd0c406ea19b51d549a6a06c91bc760bcb7689..0d0b51cf6ffc34136cbc2320a55e034096acdb9a 100644
--- a/mutalyzer/sync.py
+++ b/mutalyzer/sync.py
@@ -1,5 +1,7 @@
"""
Module for synchronizing the database with other Mutalyzer instances.
+
+Todo: add some logging to the output object.
"""
@@ -19,11 +21,18 @@ DEFAULT_CREATED_SINCE_DAYS = 7
class CacheSync(object):
"""
- Todo.
+ Synchronize the database cache with other Mutalyzer instances.
"""
def __init__(self, config, output, database):
"""
- Todo.
+ Instantiate the object.
+
+ @arg config: A configuration object.
+ @type config: mutalyzer.config.Config
+ @arg output: An output object.
+ @type output: mutalyzer.output.Output
+ @arg database: A database object.
+ @type database: mutalyzer.Db.Cache
"""
self._config = config
self._output = output
@@ -31,33 +40,57 @@ class CacheSync(object):
def local_cache(self, created_since=None):
"""
- Todo.
+ Get all entries in the local cache with creation date {created_since}
+ or later.
+
+ @kwarg created_since: Only entries with this creation date or later
+ are returned.
+ @type created_since: datatime.datetime
+
+ @return: List of cache entries.
+ @rtype: list(dictionary)
"""
if not created_since:
created_since = datetime.today() - \
timedelta(days=DEFAULT_CREATED_SINCE_DAYS)
- cache = self._database.getGBSince(created_since)
- entries = []
+ entries = self._database.getGBSince(created_since)
+ cache = []
- # For each entry, check if it is cached on our filesystem.
- # Todo: refactor
- for entry in cache:
- e = list(entry)
+ # Translate each entry to a dictionary and check if it is cached on
+ # our filesystem.
+ for entry in entries:
# Note that this way we only include Genbank files, not LRG files.
- file_name = '%s.gb.bz2' % entry[0]
- file_path = os.path.join(self._config.Retriever.cache, file_name)
- if os.path.isfile(file_path):
- e.append('%s.gb' % entry[0])
- else:
- e.append(None)
- entries.append(e)
-
- return entries
+ cached = None
+ if os.path.isfile(os.path.join(self._config.Retriever.cache,
+ '%s.gb.bz2' % entry[0])):
+ cached = '%s.gb' % entry[0]
+ cache.append({'name': entry[0],
+ 'gi': entry[1],
+ 'hash': entry[2],
+ 'chromosomeName': entry[3],
+ 'chromosomeStart': entry[4],
+ 'chromosomeStop': entry[5],
+ 'chromosomeOrientation': entry[6],
+ 'url': entry[7],
+ 'created': entry[8],
+ 'cached': cached}
+
+ return cache
def remote_cache(self, remote_wsdl, created_since=None):
"""
- Todo.
+ Get all entries in the remote cache with creation date {created_since}
+ or later.
+
+ @arg remote_wsdl: The url of the remote SOAP WSDL description.
+ @type remote_wsdl: string
+ @kwarg created_since: Only entries with this creation date or later
+ are returned.
+ @type created_since: datatime.datetime
+
+ @return: List of cache entries.
+ @rtype: list(dictionary)
"""
if not created_since:
created_since = datetime.today() - \
@@ -85,10 +118,30 @@ class CacheSync(object):
def sync_with_remote(self, remote_wsdl, url_template, created_since=None):
"""
- Todo.
+ Synchronize the local cache with the remote cache.
+
+ >>> wsdl = 'http://mutalyzer.nl/mutalyzer/services/?wsdl'
+ >>> template = 'http://mutalyzer.nl/mutalyzer/Reference/{file}'
+ >>> self.sync_with_remote(wsdl, template)
+ (14, 3)
+
+ @arg remote_wsdl: The url of the remote SOAP WSDL description.
+ @type remote_wsdl: string
+ @arg url_template: Formatting string containing a {file} occurence,
+ see examle usage above.
+ @string url_template: string
+ @kwarg created_since: Only remote entries with this creation date or
+ later are considered.
+ @type created_since: datatime.datetime
+
+ @return: The number of entries added to the local cache and the number
+ cache files downloaded from the remote site.
+ @rtype: tuple(int, int)
"""
remote_cache = self.remote_cache(remote_wsdl, created_since)
+ inserted = downloaded = 0
+
for entry in remote_cache:
if self._database.getHash(entry['name']):
continue
@@ -104,17 +157,23 @@ class CacheSync(object):
entry['chromosomeStop'],
entry['chromosomeOrientation'],
entry['url'])
- print 'inserting %s' % entry['name']
- if not entry['chromosomeName'] and not entry['url']:
- if entry['cached']:
- print 'downloading file from remote cache: %s' % (url_template % str(entry['cached']))
- self.store_remote_file(entry['name'], url_template % entry['cached'])
- else:
- print 'cannot download this file from remote cache'
+ inserted += 1
+ if not entry['chromosomeName'] and not entry['url'] \
+ and entry['cached']:
+ url = url_template.format(file=entry['cached'])
+ self.store_remote_file(entry['name'], url)
+ downloaded += 1
+
+ return inserted, downloaded
def store_remote_file(self, name, url):
"""
- Todo.
+ Download a remote file located at {url} and store it as {name}.
+
+ @arg name: Name to store the file under.
+ @type name: string
+ @arg url: Url to the remote file.
+ @type url: string
"""
if not re.match('^[\da-zA-Z\._-]+$', name):
return
@@ -125,5 +184,7 @@ class CacheSync(object):
handle.close()
# Store remote data
- retriever = Retriever.GenBankRetriever(self._config.Retriever, self._output, self._database)
+ retriever = Retriever.GenBankRetriever(self._config.Retriever,
+ self._output,
+ self._database)
retriever.write(data, name, 0)