def clean(self):
file_type = self.cleaned_data.get('file_type', None)
fastq_type = self.cleaned_data.get('fastq_type')
# -----------------------------------------
# If this is a FastQ file, make sure the user
# has chosen a FastQ type
# -----------------------------------------
if file_type == FILE_TYPE_FASTQ and not fastq_type:
msg = "For FastQ files, please choose a FastQ type"
self.add_error('fastq_type', msg)
raise forms.ValidationError(msg)
# -----------------------------------------
# Check the dropbox metadata
# (This should be moved to an async or ajax call in another part of the code )
# -----------------------------------------
file_patterns = FilePatternHelper.get_file_patterns_for_dropbox(
file_type)
# Use the dropbox API to look at the files under this dropbox_url
#
(success, dbox_retriever_obj_or_err_msg) = get_dropbox_metadata_from_link(\
self.cleaned_data.get('dropbox_url'),\
file_patterns=file_patterns)
if success:
self.dropbox_retriever_object = dbox_retriever_obj_or_err_msg
#self.dropbox_metadata_info = dbox_retriever_obj_or_err_msg.matching_files_metadata
else:
#self.add_error('dropbox_url', dbox_metadata_or_err_msg)
raise forms.ValidationError(dbox_metadata_or_err_msg)
return self.cleaned_data
def clean(self):
file_type = self.cleaned_data.get('file_type', None)
fastq_type = self.cleaned_data.get('fastq_type')
# -----------------------------------------
# If this is a FastQ file, make sure the user
# has chosen a FastQ type
# -----------------------------------------
if file_type == FILE_TYPE_FASTQ and not fastq_type:
msg = "For FastQ files, please choose a FastQ type"
self.add_error('fastq_type', msg)
raise forms.ValidationError(msg)
# -----------------------------------------
# Check the dropbox metadata
# (This should be moved to an async or ajax call in another part of the code )
# -----------------------------------------
file_patterns = FilePatternHelper.get_file_patterns_for_dropbox(file_type)
# Use the dropbox API to look at the files under this dropbox_url
#
(success, dbox_retriever_obj_or_err_msg) = get_dropbox_metadata_from_link(\
self.cleaned_data.get('dropbox_url'),\
file_patterns=file_patterns)
if success:
self.dropbox_retriever_object = dbox_retriever_obj_or_err_msg
#self.dropbox_metadata_info = dbox_retriever_obj_or_err_msg.matching_files_metadata
else:
#self.add_error('dropbox_url', dbox_metadata_or_err_msg)
raise forms.ValidationError(dbox_metadata_or_err_msg)
return self.cleaned_data
def step2_check_file_matches(self):
"""
Does the dropbox metadata contain files that we're looking for?
"""
if self.err_found:
return False
assert isinstance(self.dropbox_link_metadata, dict),\
"Do not call this unless step 1, retrieval of Dropbox metadata is successful"
assert "is_dir" in self.dropbox_link_metadata,\
"Do not call this unless step 1, retrieval of Dropbox metadata is successful.\
(Metadata doesn't look good. Missing key 'is_dir')"
# -------------------------------------
# Handle a Dropbox link to a file?
# -------------------------------------
if self.dropbox_link_metadata['is_dir'] is False: # Yes, this is a file
self.is_directory_link = False
# Does it match?
fpath = self.dropbox_link_metadata['path']
if self.does_file_match_criteria(fpath):
self.matching_files_metadata.append(fpath)
return True
else:
file_msg = FilePatternHelper.get_file_patterns_err_msg(
self.file_patterns)
self.add_err_msg('No files match what we are looking for. %s' %
file_msg)
return False
# -------------------------------------
# Handle a Dropbox link to a directory?
# -------------------------------------
self.is_directory_link = True
# This is a directory, check each file
#
if not 'contents' in self.dropbox_link_metadata:
self.add_err_msg("The directory is empty. No 'contents' key")
return False
# Iterate through files
#
for file_info in self.dropbox_link_metadata['contents']:
if file_info[
'is_dir'] is True: # This is a subdirectory, keep going
continue
fpath = file_info['path'] # Assume the 'path' is always here
if self.does_file_match_criteria(fpath):
self.matching_files_metadata.append(fpath)
if len(self.matching_files_metadata) == 0:
self.add_err_msg('No files match what we are looking for. \
Please make sure you have at least one ".fastq" or ".vcf" file.')
return False
# We've got something
return True
def step2_check_file_matches(self):
"""
Does the dropbox metadata contain files that we're looking for?
"""
if self.err_found:
return False
assert isinstance(self.dropbox_link_metadata, dict),\
"Do not call this unless step 1, retrieval of Dropbox metadata is successful"
assert "is_dir" in self.dropbox_link_metadata,\
"Do not call this unless step 1, retrieval of Dropbox metadata is successful.\
(Metadata doesn't look good. Missing key 'is_dir')"
# -------------------------------------
# Handle a Dropbox link to a file?
# -------------------------------------
if self.dropbox_link_metadata['is_dir'] is False: # Yes, this is a file
self.is_directory_link = False
# Does it match?
fpath = self.dropbox_link_metadata['path']
if self.does_file_match_criteria(fpath):
self.matching_files_metadata.append(fpath)
return True
else:
file_msg = FilePatternHelper.get_file_patterns_err_msg(self.file_patterns)
self.add_err_msg('No files match what we are looking for. %s' % file_msg)
return False
# -------------------------------------
# Handle a Dropbox link to a directory?
# -------------------------------------
self.is_directory_link = True
# This is a directory, check each file
#
if not 'contents' in self.dropbox_link_metadata:
self.add_err_msg("The directory is empty. No 'contents' key")
return False
# Iterate through files
#
for file_info in self.dropbox_link_metadata['contents']:
if file_info['is_dir'] is True: # This is a subdirectory, keep going
continue
fpath = file_info['path'] # Assume the 'path' is always here
if self.does_file_match_criteria(fpath):
self.matching_files_metadata.append(fpath)
if len(self.matching_files_metadata) == 0:
self.add_err_msg('No files match what we are looking for. \
Please make sure you have at least one ".fastq" or ".vcf" file.')
return False
# We've got something
return True
def get_fastq_extension_type(self):
"""
For pair-ended FastQ files, figure out the extension
"""
return FilePatternHelper.get_fastq_extension_type(self.selected_files)
