def start_ampliseq_fixed_solution_download(design_id, meta, auth):
url = urlparse.urljoin(settings.AMPLISEQ_URL, "ws/tmpldesign/{0}/download/results".format(design_id))
monitor = FileMonitor(url=url, tags="ampliseq_template", status="Queued")
monitor.save()
t = tasks.download_something.apply_async(
(url, monitor.id), {"auth": auth},
link=tasks.ampliseq_zip_upload.subtask((meta,)))
def start_reference_download(url, reference):
monitor = FileMonitor(url=url, tags="reference")
monitor.save()
reference.file_monitor = monitor
reference.save()
try:
download_args = (url, monitor.id, settings.TEMP_PATH)
install_callback = tasks.install_reference.subtask((reference.id,))
t = tasks.download_something.apply_async(download_args, link=install_callback)
except Exception as err:
monitor.status = "System Error: " + str(err)
monitor.save()
def start_reference_download(url, reference):
monitor = FileMonitor(url=url, tags="reference")
monitor.save()
reference.file_monitor = monitor
reference.save()
try:
download_args = (url, monitor.id, settings.TEMP_PATH)
install_callback = tasks.install_reference.subtask((reference.id,))
t = tasks.download_something.apply_async(download_args, link=install_callback)
except Exception as err:
monitor.status = "System Error: " + str(err)
monitor.save()
def start_reference_download(url, reference, callback=None, reference_mask_filename=None):
monitor = FileMonitor(url=url, tags="reference")
monitor.save()
reference.status = "downloading"
reference.file_monitor = monitor
reference.save()
try:
download_args = (url, monitor.id, settings.TEMP_PATH)
install_callback = tasks.install_reference.subtask((reference.id, reference_mask_filename))
if callback:
install_callback.link(callback)
async_result = tasks.download_something.apply_async(download_args, link=install_callback)
return async_result
except Exception as err:
monitor.status = "System Error: " + str(err)
monitor.save()
def start_reference_download(url, reference, callback=None, reference_mask_filename=None):
monitor = FileMonitor(url=url, tags="reference")
monitor.save()
reference.status = "downloading"
reference.file_monitor = monitor
reference.save()
try:
download_args = (url, monitor.id, settings.TEMP_PATH)
install_callback = tasks.install_reference.subtask((reference.id, reference_mask_filename))
if callback:
install_callback.link(callback)
async_result = tasks.download_something.apply_async(download_args, link=install_callback)
return async_result
except Exception as err:
monitor.status = "System Error: " + str(err)
monitor.save()
def start_update_product(name, url, updateVersion, callback=None):
tagsInfo = "offCycleRel_{0}".format(updateVersion)
monitor = FileMonitor(name=name, url=url, tags=tagsInfo)
monitor.status = "downloading"
monitor.save()
return monitor.id
def start_update_product(name, url, updateVersion, callback=None):
tagsInfo = "offCycleRel_{0}".format(updateVersion)
monitor = FileMonitor(name=name, url=url, tags=tagsInfo)
monitor.status = "downloading"
monitor.save()
return monitor.id
def new_genome(request):
"""This is the page to create a new genome.
"""
if request.method == "POST":
# parse the data sent in
#required
name = request.POST.get('name', False)
short_name = request.POST.get('short_name', False)
fasta = request.POST.get('target_file', False)
version = request.POST.get('version', "")
notes = request.POST.get('notes', "")
#optional
read_exclude_length = request.POST.get('read_exclude_length', False)
#URL download
url = request.POST.get('url', False)
reference_path = os.path.join(settings.TEMP_PATH, fasta)
why_delete = ""
#if any of those were false send back a failed message
if not all((name, short_name, fasta)):
return render_to_json({"status": "Form validation failed", "error": True})
if not set(short_name).issubset("abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_"):
return render_to_json({"status": "The short name has invalid characters. The valid values are letters, numbers, and underscores.", "error": True})
#TODO: check to make sure the zip file only has one fasta or fa
if not url:
#check to ensure the size on the OS the same as the reported.
reported_file_size = request.POST.get('reported_file_size', False)
try:
uploaded_file_size = str(os.path.getsize(reference_path))
except OSError:
return render_to_json({"status": "The FASTA temporary files was not found", "error": True})
if reported_file_size != uploaded_file_size:
why_delete = "The file you uploaded differs from the expected size. This is due to an error uploading."
if not (fasta.lower().endswith(".fasta") or fasta.lower().endswith(".zip")):
why_delete = "The file you uploaded does not have a .fasta or .zip extension. It must be a plain text fasta file or a Zip compressed fasta."
is_zip = zipfile.is_zipfile(reference_path)
if is_zip:
zip_file = zipfile.ZipFile(reference_path, 'r')
files = zip_file.namelist()
# MAC OS zip is being compressed with __MACOSX folder Ex: '__MACOSX/', '__MACOSX/._contigs_2.fasta'.
# Filter out those files and Upload only FASTA file
files = [x for x in files if not 'MACOSX' in x]
zip_file.close()
else:
files = [fasta]
fasta_files = filter(lambda x: x.endswith('.fa') or x.endswith('.fasta'), files)
if len(fasta_files) != 1:
why_delete = "Error: upload must contain exactly one fasta file"
else:
target_fasta_file = fasta_files[0]
if why_delete:
try:
os.remove(reference_path)
except OSError:
why_delete += " The FASTA file could not be deleted."
logger.warning("User uploaded bad fasta file: " + str(why_delete))
return render_to_json({"status": why_delete, "error": True})
#Make an genome ref object
if ReferenceGenome.objects.filter(short_name=short_name, index_version=settings.TMAP_VERSION):
#check to see if the genome already exists in the database with the same version
return render_to_json({"status": "Failed - Genome with this short name and index version already exist.", "error": True})
ref_genome = ReferenceGenome()
ref_genome.name = name
ref_genome.short_name = short_name
ref_genome.version = version
ref_genome.notes = notes
ref_genome.status = "preprocessing"
ref_genome.enabled = False
ref_genome.index_version = settings.TMAP_VERSION
ref_genome.save()
logger.debug("Created new reference: %d/%s" % (ref_genome.pk, ref_genome))
temp_dir = tempfile.mkdtemp(suffix=short_name, dir=settings.TEMP_PATH)
temp_upload_path = os.path.join(temp_dir, fasta)
os.chmod(temp_dir, 0777)
os.rename(reference_path, temp_upload_path)
monitor = FileMonitor(
local_dir=temp_dir,
name=fasta
)
monitor.save()
ref_genome.file_monitor = monitor
ref_genome.reference_path = temp_upload_path
ref_genome.save()
index_task = tasks.build_tmap_index.subtask((ref_genome.id,), immutable=True)
if is_zip:
result = tasks.unzip_reference.apply_async(
args=(ref_genome.id, target_fasta_file),
link=index_task
)
else:
result = tasks.copy_reference.apply_async(
args=(ref_genome.id,),
link=index_task
)
ref_genome.status = "queued"
ref_genome.celery_task_id = result.task_id
ref_genome.save()
return render_to_json({"status": "The genome index is being created. This might take a while, check the status on the references tab. \
You are being redirected there now.", "error": False})
elif request.method == "GET":
ctx = RequestContext(request, {})
return render_to_response("rundb/configure/modal_references_new_genome.html", context_instance=ctx)
def new_genome(request):
"""This is the page to create a new genome.
"""
def is_fasta(filename):
ext = os.path.splitext(filename)[1]
return ext.lower() in ['.fasta', '.fas', '.fa', '.seq']
if request.method == "POST":
# parse the data sent in
#required
name = request.POST.get('name', False)
short_name = request.POST.get('short_name', False)
fasta = request.POST.get('target_file', False)
version = request.POST.get('version', "")
notes = request.POST.get('notes', "")
#optional
read_exclude_length = request.POST.get('read_exclude_length', False)
#URL download
url = request.POST.get('url', False)
reference_path = os.path.join(settings.TEMP_PATH, fasta)
why_delete = ""
#if any of those were false send back a failed message
if not all((name, short_name, fasta)):
return render_to_json({
"status": "Form validation failed",
"error": True
})
if not set(short_name).issubset(
"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_"
):
return render_to_json({
"status":
"The short name has invalid characters. The valid values are letters, numbers, and underscores.",
"error": True
})
#TODO: check to make sure the zip file only has one fasta or fa
if not url:
#check to ensure the size on the OS the same as the reported.
reported_file_size = request.POST.get('reported_file_size', False)
try:
uploaded_file_size = str(os.path.getsize(reference_path))
except OSError:
return render_to_json({
"status": "The FASTA temporary files was not found",
"error": True
})
if reported_file_size != uploaded_file_size:
why_delete = "The file you uploaded differs from the expected size. This is due to an error uploading."
if not (is_fasta(fasta) or fasta.lower().endswith(".zip")):
why_delete = "The file you uploaded does not have a FASTA or ZIP extension. It must be a plain text a Zip compressed fasta file."
is_zip = zipfile.is_zipfile(reference_path)
if is_zip:
zip_file = zipfile.ZipFile(reference_path, 'r')
files = zip_file.namelist()
# MAC OS zip is being compressed with __MACOSX folder Ex: '__MACOSX/', '__MACOSX/._contigs_2.fasta'.
# Filter out those files and Upload only FASTA file
files = [x for x in files if not 'MACOSX' in x]
zip_file.close()
else:
files = [fasta]
fasta_files = filter(lambda x: is_fasta(x), files)
if len(fasta_files) != 1:
why_delete = "Error: upload must contain exactly one fasta file"
else:
target_fasta_file = fasta_files[0]
if why_delete:
try:
os.remove(reference_path)
except OSError:
why_delete += " The FASTA file could not be deleted."
logger.warning("User uploaded bad fasta file: " + str(why_delete))
return render_to_json({"status": why_delete, "error": True})
#Make an genome ref object
if ReferenceGenome.objects.filter(short_name=short_name,
index_version=settings.TMAP_VERSION):
#check to see if the genome already exists in the database with the same version
return render_to_json({
"status":
"Failed - Genome with this short name and index version already exist.",
"error": True
})
ref_genome = ReferenceGenome()
ref_genome.name = name
ref_genome.short_name = short_name
ref_genome.version = version
ref_genome.notes = notes
ref_genome.status = "preprocessing"
ref_genome.enabled = False
ref_genome.index_version = settings.TMAP_VERSION
ref_genome.save()
logger.debug("Created new reference: %d/%s" %
(ref_genome.pk, ref_genome))
temp_dir = tempfile.mkdtemp(suffix=short_name, dir=settings.TEMP_PATH)
temp_upload_path = os.path.join(temp_dir, fasta)
os.chmod(temp_dir, 0777)
os.rename(reference_path, temp_upload_path)
monitor = FileMonitor(local_dir=temp_dir, name=fasta)
monitor.save()
ref_genome.file_monitor = monitor
ref_genome.reference_path = temp_upload_path
ref_genome.save()
index_task = tasks.build_tmap_index.subtask((ref_genome.id, ),
immutable=True)
if is_zip:
result = tasks.unzip_reference.apply_async(
args=(ref_genome.id, target_fasta_file), link=index_task)
else:
result = tasks.copy_reference.apply_async(args=(ref_genome.id, ),
link=index_task)
ref_genome.status = "queued"
ref_genome.celery_task_id = result.task_id
ref_genome.save()
return render_to_json({
"status":
"The genome index is being created. This might take a while, check the status on the references tab. \
You are being redirected there now.",
"error": False
})
elif request.method == "GET":
ctx = RequestContext(request, {})
return render_to_response(
"rundb/configure/modal_references_new_genome.html",
context_instance=ctx)
