def walk_database_query_picking_files(self):
for n in self.query:
item = Item(join(self.root, n.accession, n.filepath), self.root)
if getattr(n,'checksum',None):
item.remote_hash = n.checksum
if getattr(n,'size',None):
item.remote_size = n.size
if getattr(n,'mimetype',None):
item.remote_mimetype = n.mimetype
yield item
def copy_into_new_location(self):
self.copy_source_directory_tree_to_destination()
assert exists(dirname(self.destination))
shutil.copyfile(self.filepath, self.destination)
if exists(self.destination):
new = Item(self.destination)
self.destination_ownership(self.owner)
self.destination(self.group)
if new.find_sha256() == self.get_sha256():
return namedtuple("result","status message") \
("Good","")
else:
return namedtuple("result","status message") \
("Bad","source checksum and destination checksum mismatch")
else:
return namedtuple("result","status message") \
("Bad","destination could not be created")
def createMetaAccession(self):
metaAccessionDict = {}
for accession in self.accessions:
for item in accession.get_items():
# Clobber entries from previous accessions, keep the newest
metaAccessionDict[item.get_canonical_filepath()] = \
item.get_root_path()
metaAccessionList = []
for canonicalFilepath in metaAccessionDict:
metaAccessionList.append(
metaAccessionDict[canonicalFilepath] +
"/" + canonicalFilepath)
metaAccession = Batch()
for reconstructedFilePath in metaAccessionList:
metaAccession.add_item(Item(reconstructedFilePath))
return metaAccession
def __init__(self,path,root):
Item.__init__(self,path,root)
def main():
try:
parser = ArgumentParser(description="",epilog="")
parser.add_argument("record_number",help="",action="store")
parser.add_argument("file_list",help="",action="store")
args = parser.parse_args()
g = Grouping()
try:
files_list = open(args.file_list, 'r').readlines()
except:
stderr.write("cold not open file {flist}". \
format(flist = args.file_list))
return 1
for n_file in files_list:
fullpath_dir = dirname(n_file)
relpath_dir = relpath(fullpath_dir, '/media/repo/repository/tr/')
accession = relpath_dir.split('/')[0]
i = AccessionDirectory(join('/media/repo/repository/tr/',
accession),
'/media/repo/repository/tr/')
a = Item(n_file)
setattr(a,'accession',accession)
the_file_path = a.get_file_path().strip()
canonical_file_path = the_file_path.split(accession)[1].lstrip('/')
pattern = re_compile(r'(mvol)/(\w{4})/(\w{4})/(\w{4})')
matches = pattern.search(canonical_file_path)
if matches:
identifier = '-'.join([matches.group(1), matches.group(2),
matches.group(3), matches.group(4)])
files_required = generate_pattern_list(identifier)
n = g.does_it_need_a_new_item(identifier)
for tup in files_required:
pattern = re_compile(tup[1])
label = tup[0]
search = pattern.search(a.get_file_path())
if search:
check = True
is_page = False
for ppart in page_num_file_parts:
page_pattern = re_compile(ppart)
page_search = page_pattern. \
search(a.get_file_path())
if page_search:
is_page = True
n.add_page(a, label, page_search.group(1),
splitext(basename( \
a.get_file_path()))[0])
if not is_page:
n.add_representation(a, label)
g.sort_items()
else:
logging.error("could not match file {filename}". \
format(filename = the_file_path))
mvol_csv = "mvol-%s.csv" % args.record_number
main_csv = Output(mvol_csv)
main_csv.add_record(csv_headers)
for n in g.items:
if 'Thum' in n.identifier or 'tif' in n.identifier \
or 'test' in n.identifier:
continue
id_parts = n.identifier.split('-')
has_new_struct = 'N'
has_old_struct = 'N'
has_pdf = 'N'
has_pages = 'Y' if getattr(n,'pages',None) else 'N'
struct_objids = []
txt_objids = []
old_style = False
new_style = False
pdf = getattr(n, 'pdf', None)
new_mdata = getattr(n, 'struct', None)
old_mdata = getattr(n, 'txt', None)
if pdf:
has_pdf = 'Y'
else:
errors.get(n.identifier).append("missing {rep}". \
format(rep = rep))
if new_mdata and isinstance(new_mdata, list):
has_new_struct = 'Y'
struct_mdata_files = [x.get_file_path(). \
strip() for x in new_mdata]
elif new_mdata and isinstance(new_mdata, Item):
has_new_struct = 'Y'
struct_mdata_files = [new_mdata.get_file_path().strip()]
elif old_mdata and isinstance(old_mdata, list):
has_old_struct = 'Y'
struct_mdata_files = [x.get_file_path(). \
strip() for x in old_mdata]
elif old_mdata and isinstance(old_mdata, Item):
has_old_struct = 'Y'
struct_mdata_files = [old_mdata.get_file_path().strip()]
if struct_mdata_files:
for struct_mdata_file in struct_mdata_files:
try:
fp = open(struct_mdata_file,'r')
lines = fp.readlines()
lines = [x for x in lines if len(x.split('\t')) == 3]
relevant_lines = lines[1:]
objids = [x.replace('\t','').strip('\n') \
for x in relevant_lines]
page_difference = len(objids) - len(n.pages)
if has_new_struct == 'Y':
struct_objids = objids
elif has_old_struct == 'Y':
txt_objids = objids
except UnicodeDecodeError:
stderr.write("{mfile} couldn't be opened\n". \
format(mfile = struct_mdata_file))
record = [n.identifier, id_parts[0], id_parts[1],
id_parts[2], id_parts[3], ','.join(list(n.accessions)),
has_old_struct, has_new_struct, has_pdf,
has_pages, len(txt_objids),
len(struct_objids), len(n.pages)]
main_csv.add_record(record)
issue_csv_file_name = "%s-pages.csv" % n.identifier
issue_csv = Output(issue_csv_file_name)
issue_csv.add_record(page_csv_headers)
sorted_pages = sorted(n.pages)
for page in sorted_pages:
ocr_there = "Y" if getattr(page,'pos',None) or \
getattr(page,'alto',None) \
or getattr(p, 'xml',None) else "N"
jpeg_there = "Y" if getattr(page, 'jpeg',None) else "N"
tiff_there = "Y" if getattr(page, 'tiff',None) else "N"
try:
x = page.objectpage.split('_')[1].lstrip('0')
object_identifier = x.zfill(8)
except:
object_identifier = page.objectpage
page_record = [object_identifier,
page.objectpage, n.identifier,
ocr_there, jpeg_there, tiff_there]
issue_csv.add_record(page_record)
return 0
except KeyboardInterrupt:
return 131