def run():
"""
Run page
"""
inforun = None
inforun_file = os.path.join(config_reader.config_dir, ".inforun")
if os.path.exists(inforun_file):
try:
with open(inforun_file, "r") as info:
inforun = json.loads(info.read())
except json.JSONDecodeError:
print("Unable to parse inforun file. Ignoring it.",
file=sys.stderr)
pass
tools = Tools().tools
tools_names = sorted(list(tools.keys()),
key=lambda x: (tools[x].order, tools[x].name))
tools_ava = {}
tools_options = {}
for tool_name, tool in tools.items():
tools_ava[tool_name] = 1 if tool.all_vs_all is not None else 0
tools_options[tool_name] = tool.options
if MODE == "webserver":
with Session.connect():
s_id = Session.new()
else:
upload_folder = Functions.random_string(20)
tmp_dir = config_reader.upload_folder
upload_folder_path = os.path.join(tmp_dir, upload_folder)
while os.path.exists(upload_folder_path):
upload_folder = Functions.random_string(20)
upload_folder_path = os.path.join(tmp_dir, upload_folder)
s_id = upload_folder
id_job = Functions.random_string(
5) + "_" + datetime.datetime.fromtimestamp(
time.time()).strftime('%Y%m%d%H%M%S')
if "id_job" in request.args:
id_job = request.args["id_job"]
email = ""
if "email" in request.args:
email = request.args["email"]
return render_template(
"run.html",
id_job=id_job,
email=email,
menu="run",
allowed_ext=ALLOWED_EXTENSIONS,
s_id=s_id,
max_upload_file_size=config_reader.max_upload_file_size,
example=config_reader.example_target != "",
target=os.path.basename(config_reader.example_target),
query=os.path.basename(config_reader.example_query),
tools_names=tools_names,
tools=tools,
tools_ava=tools_ava,
tools_options=tools_options,
version=VERSION,
inforun=inforun)
def get_tools_options(tool_name, chosen_options):
"""
Transform options chosen in javascript into parameters
:return: True is chosen options are valid + a string containing optional parameters to use with tool
:rtype: boolean, str
"""
tools = Tools().tools
if tool_name is None:
return True, None
tool = tools[tool_name] if tool_name in tools else None
tool_options = tool.options if tool is not None else None
# We filter options for the chosen tool.
tool_prefix = "tool-options-%s-" % tool_name
filtered_options = [
s[len(tool_prefix):].split("-") for s in chosen_options
if s.startswith(tool_prefix)
]
valid = True
options_params = None
try:
options_params = [
tool_options[int(o)]['entries'][int(e)]['value']
for o, e in filtered_options
]
except KeyError:
valid = False
except IndexError:
valid = False
return True, " ".join(options_params)
def run():
"""
Run page
"""
tools = Tools().tools
tools_names = sorted(list(tools.keys()),
key=lambda x: (tools[x].order, tools[x].name))
tools_ava = {}
for tool_name, tool in tools.items():
tools_ava[tool_name] = 1 if tool.all_vs_all is not None else 0
if MODE == "webserver":
with Session.connect():
s_id = Session.new()
else:
upload_folder = Functions.random_string(20)
tmp_dir = config_reader.upload_folder
upload_folder_path = os.path.join(tmp_dir, upload_folder)
while os.path.exists(upload_folder_path):
upload_folder = Functions.random_string(20)
upload_folder_path = os.path.join(tmp_dir, upload_folder)
s_id = upload_folder
id_job = Functions.random_string(
5) + "_" + datetime.datetime.fromtimestamp(
time.time()).strftime('%Y%m%d%H%M%S')
if "id_job" in request.args:
id_job = request.args["id_job"]
email = ""
if "email" in request.args:
email = request.args["email"]
return render_template(
"run.html",
id_job=id_job,
email=email,
menu="run",
allowed_ext=ALLOWED_EXTENSIONS,
s_id=s_id,
max_upload_file_size=config_reader.max_upload_file_size,
example=config_reader.example_target != "",
target=os.path.basename(config_reader.example_target),
query=os.path.basename(config_reader.example_query),
tools_names=tools_names,
tools=tools,
tools_ava=tools_ava,
version=VERSION)
def launch_analysis():
"""
Launch the job
"""
if MODE == "webserver":
try:
with Session.connect():
session = Session.get(s_id=request.form["s_id"])
except DoesNotExist:
return jsonify({
"success":
False,
"errors":
["Session has expired. Please refresh the page and try again"]
})
upload_folder = session.upload_folder
# Delete session:
session.delete_instance()
else:
upload_folder = request.form["s_id"]
id_job = request.form["id_job"]
email = request.form["email"]
file_query = request.form["query"]
file_query_type = request.form["query_type"]
file_target = request.form["target"]
file_target_type = request.form["target_type"]
tool = request.form["tool"] if "tool" in request.form else None
alignfile = request.form[
"alignfile"] if "alignfile" in request.form else None
alignfile_type = request.form[
"alignfile_type"] if "alignfile_type" in request.form else None
backup = request.form["backup"] if "backup" in request.form else None
backup_type = request.form[
"backup_type"] if "backup_type" in request.form else None
# Check form:
form_pass = True
errors = []
if alignfile is not None and alignfile_type is None:
errors.append(
"Server error: no alignfile_type in form. Please contact the support"
)
form_pass = False
if backup is not None and backup != "" and (backup_type is None
or backup_type == ""):
errors.append(
"Server error: no backup_type in form. Please contact the support")
form_pass = False
if backup is not None and backup != "":
alignfile = ""
file_query = ""
file_target = ""
else:
backup = None
if file_target == "":
errors.append("No target fasta selected")
form_pass = False
if tool is not None and tool not in Tools().tools:
errors.append("Tool unavailable: %s" % tool)
form_pass = False
if id_job == "":
errors.append("Id of job not given")
form_pass = False
if MODE == "webserver":
if email == "":
errors.append("Email not given")
form_pass = False
elif not re.match(r"^[\w.\-]+@[\w\-.]{2,}\.[a-z]{2,4}$", email):
errors.append("Email is invalid")
form_pass = False
# Form pass
if form_pass:
# Get final job id:
id_job = re.sub('[^A-Za-z0-9_\-]+', '', id_job.replace(" ", "_"))
id_job_orig = id_job
i = 2
while os.path.exists(os.path.join(APP_DATA, id_job)):
id_job = id_job_orig + ("_%d" % i)
i += 1
folder_files = os.path.join(APP_DATA, id_job)
os.makedirs(folder_files)
# Save files:
query = None
if file_query != "":
example = False
if file_query.startswith("example://"):
example = True
query_path = config_reader.example_query
query_name = os.path.basename(query_path)
file_query_type = "local"
else:
query_name = os.path.splitext(file_query.replace(
".gz", ""))[0] if file_query_type == "local" else None
if file_query_type == "local":
query_path = os.path.join(app.config["UPLOAD_FOLDER"],
upload_folder, file_query)
if os.path.exists(query_path):
if " " in file_query:
new_query_path = os.path.join(
app.config["UPLOAD_FOLDER"], upload_folder,
file_query.replace(" ", "_"))
shutil.move(query_path, new_query_path)
query_path = new_query_path
else:
errors.append("Query file not correct!")
form_pass = False
else:
query_path = file_query
query = Fasta(name=query_name,
path=query_path,
type_f=file_query_type,
example=example)
example = False
target = None
if file_target != "":
if file_target.startswith("example://"):
example = True
target_path = config_reader.example_target
target_name = os.path.basename(target_path)
file_target_type = "local"
else:
target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" \
else None
if file_target_type == "local":
target_path = os.path.join(app.config["UPLOAD_FOLDER"],
upload_folder, file_target)
if os.path.exists(target_path):
if " " in target_path:
new_target_path = os.path.join(
app.config["UPLOAD_FOLDER"], upload_folder,
file_target.replace(" ", "_"))
shutil.move(target_path, new_target_path)
target_path = new_target_path
else:
errors.append("Target file not correct!")
form_pass = False
else:
target_path = file_target
target = Fasta(name=target_name,
path=target_path,
type_f=file_target_type,
example=example)
if alignfile is not None and alignfile != "" and backup is not None:
Path(os.path.join(folder_files, ".align")).touch()
align = None
if alignfile is not None and alignfile != "":
alignfile_name = os.path.splitext(
alignfile)[0] if alignfile_type == "local" else None
alignfile_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, alignfile) \
if alignfile_type == "local" else alignfile
if alignfile_type == "local" and not os.path.exists(
alignfile_path):
errors.append("Alignment file not correct!")
form_pass = False
align = Fasta(name=alignfile_name,
path=alignfile_path,
type_f=alignfile_type)
bckp = None
if backup is not None:
backup_name = os.path.splitext(
backup)[0] if backup_type == "local" else None
backup_path = os.path.join(app.config["UPLOAD_FOLDER"], upload_folder, backup) \
if backup_type == "local" else backup
if backup_type == "local" and not os.path.exists(backup_path):
errors.append("Backup file not correct!")
form_pass = False
bckp = Fasta(name=backup_name,
path=backup_path,
type_f=backup_type)
if form_pass:
# Launch job:
job = JobManager(id_job=id_job,
email=email,
query=query,
target=target,
align=align,
backup=bckp,
mailer=mailer,
tool=tool)
if MODE == "webserver":
job.launch()
else:
job.launch_standalone()
return jsonify({
"success": True,
"redirect": url_for(".status", id_job=id_job)
})
if not form_pass:
return jsonify({"success": False, "errors": errors})