class DataUploaderForm(Form):
"""
When we want to upload new data into the maps system. This form is used.
"""
name = CharField()
vcf_files = UploadField(extensions=['.vcf', '.vcf.gz'], required=True, label="Enriched VCF",\
help_text="Variant Call Formated sequence file enriched with resistance and location data.")
@staticmethod
def get_uploader_dir(pkey):
"""Returns the directory used to save uploaded data"""
return os.path.join(settings.MEDIA_ROOT, 'm_uploads', str(pkey).zfill(8))
def save(self, user):
"""
Save the data into the importer
"""
source = ImportSource.objects.create(
name=self.cleaned_data.get('name'),
uploader=user,
complete=False,
)
source.save()
path = self.get_uploader_dir(source.pk)
if not os.path.isdir(path):
os.makedirs(path)
files = list(list(self.cleaned_data['vcf_files'].values())[0])
for upload_file in files:
upload_file.conclude_upload(path, user)
ImportStrain.objects.create(import_source=source, upload_file=upload_file)
source.save()
return source
class UploadFastQSingleForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_FASTQ
doc_title = "Create FastQ Single-Ended Prediction"
doc = "Create a prediction from a single-ended FastQ genetic sequence file. This option involves a large file and takes more time to process that the VCF or manual options."
fastq_file = UploadField(
extensions=FASTQ_FILES,
required=True,
label="FastQ Files",
help_text=
"FastQ files containing the single sequence read. Multiple files can be selected, one fastq file per strain to compare."
)
ordered = 5
class UploadVcfForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_VCF
doc_title = "Create VCF Prediction"
doc = """Create a prediction from a variant call file in VCF format. Get more information about the <a href="http://samtools.github.io/hts-specs/VCFv4.2.pdf">VCF format here.</a>"""
vcf_file = UploadField(
extensions=VCF_FILES,
required=True,
label="VCF Files",
help_text=
"Variant Call Formated sequence data file. Multiple files can be selected, one vcf file per stain to compare."
)
ordered = 10
btn = 'primary'
class UploadFastQSingleForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_FASTQ
doc_title = "Single-Ended FastQ File"
doc_template = "predict/types/fastq_single.html"
doc = "Create a prediction from single-ended FastQ genetic sequence."
fastq_file = UploadField(
extensions=FASTQ_FILES,
required=True,
label="FastQ Files",
help_text=
"FastQ files containing the single sequence read. Multiple files can be selected, one fastq file per strain to compare."
)
ordered = 5
class UploadVcfForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_VCF
doc_title = "Varient Call File (VCF)"
doc_template = "predict/types/vcf.html"
doc = "Create a prediction from a variant call file in VCF format."
vcf_file = UploadField(
extensions=VCF_FILES,
required=True,
label="VCF Files",
help_text=
"Variant Call Formated sequence data file. Multiple files can be selected, one vcf file per stain to compare."
)
ordered = 10
btn = 'primary'
class UploadFastQPairForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_FASTQ2
doc_title = "Create FastQ Pair-Ended Prediction"
doc = "Create a prediction from a set of pair-ended FastQ genetic sequences. This option involves the largest files and takes more time to process that the VCF or manual options."
fastq_file = UploadField(
extensions=FASTQ_FILES,
buckets=[('file_one', "^(.+)[\._\- ][Rr]?1\.fastq(?:\.gz)?$",
"Forward FastQ Files", 'file_two'),
('file_two', "^(.+)[\._\- ][Rr]?2\.fastq(?:\.gz)?$",
"Backward FastQ Files", 'file_one')],
required=True,
label="FastQ Files",
help_text=
"FastQ file containing the forward and backward sequence. Multiple strains can be selected for comparison."
)
ordered = 6
class UploadFastQPairForm(UploadForm):
my_file_type = PredictDataset.FILE_TYPE_FASTQ2
doc_title = "Pair-Ended FastQ File"
doc_template = "predict/types/fastq_pair.html"
doc = "Create a prediction from a set of pair-ended FastQ genetic sequences."
fastq_file = UploadField(
extensions=FASTQ_FILES,
buckets=[('file_one', "^(.+)[\._\- ][Rr]?1\.(fastq|fq)(?:\.gz)?$",
"Forward FastQ Files", 'file_two'),
('file_two', "^(.+)[\._\- ][Rr]?2\.(fastq|fq)(?:\.gz)?$",
"Backward FastQ Files", 'file_one')],
required=True,
label="FastQ Files",
help_text=
"FastQ file containing the forward and backward sequence. Multiple strains can be selected for comparison."
)
ordered = 6