def task_id_edit(_id=None):
task_id_form = TaskIDForm()
task_id_query = TaskId.objects.get_or_404(_id=_id)
if task_id_form.validate_on_submit():
data = task_id_form.data
data_count = Specie.objects(srr_id=data["srr_id"]).count()
if data_count == 0:
TaskId.objects(task_id=_id).update_one(set__srr_id=data["srr_id"])
TaskId.objects(task_id=_id).update_one(set__email=data["email"])
TaskId.objects(task_id=_id).update_one(
set__task_time=datetime.now())
flash("edit done !", "ok")
return redirect(url_for("admin.task_id_edit", _id=_id))
elif data_count == 1 and task_id_query.srr_id != data["srr_id"]:
flash("this task is already exist !", "err")
return redirect(url_for("admin.task_id_edit", _id=_id))
elif data_count == 1 and task_id_query.srr_id == data["srr_id"]:
TaskId.objects(task_id=_id).update_one(set__email=data["email"])
TaskId.objects(task_id=_id).update_one(
set__task_time=datetime.now())
flash("edit done !", "ok")
return redirect(url_for("admin.task_id_edit", _id=_id))
return render_template("admin/task_id_edit.html",
form=task_id_form,
task_id=task_id_query)
def task_id_add():
task_id_form = TaskIDForm()
if task_id_form.validate_on_submit():
data = task_id_form.data
new_task_id = TaskId(task_id=str(uuid.uuid1()),
srr_id=data["srr_id"],
email=data["email"],
task_time=datetime.now())
new_task_id.save()
flash("this task is added !", "ok")
return redirect(url_for("admin.task_id_add"))
return render_template("admin/task_id_add.html", form=task_id_form)
def task_id(_id):
task_query = TaskId.objects(task_id=_id).first()
srr_id_query = task_query.srr_id
srr_task_query = SrrTask.objects.get_or_404(_id=srr_id_query)
each = {"_id": srr_task_query._id, "kegg_id": srr_task_query.kegg_id, "method": srr_task_query.method,
"operon": srr_task_query.operon_path, "jbrowse": srr_task_query.browse_link}
return render_template("home/task.html", each=each)
def validate_srr_id(self, field):
data = field.data
data_count = TaskId.objects(srr_id=data).count()
if data_count > 0:
raise ValidationError("the srr id is already exist !")
def task_id_del(_id=None):
TaskId.objects(task_id=_id).delete()
flash("delete it done !", "ok")
return redirect(url_for("admin.task_id"))
def task_id(page=None):
if page is None:
page = 1
page_data = TaskId.objects().paginate(page=page, per_page=10)
return render_template("admin/task_id.html", page_data=page_data)
def index():
submit_form = SubmitForm()
if submit_form.condition_add.data:
submit_form.condition.append_entry()
return render_template("home/index.html", form=submit_form)
i_iter = 0
for con in submit_form.condition.entries:
if con.condition_del.data:
submit_form.condition.entries.pop(i_iter)
return render_template("home/index.html", form=submit_form)
if con.repeat_add.data:
submit_form.condition.entries[i_iter].repeat.append_entry()
return render_template("home/index.html", form=submit_form)
j_iter = 0
for rep in con.repeat.entries:
if rep.repeat_del.data:
submit_form.condition.entries[i_iter].repeat.entries.pop(j_iter)
return render_template("home/index.html", form=submit_form)
j_iter = j_iter + 1
i_iter = i_iter + 1
auto = ""
if submit_form.kegg_auto.data:
auto = "y"
if submit_form.kegg_not_auto.data:
auto = "n"
if submit_form.validate_on_submit():
data = submit_form.data
srr_list = []
all_srr = []
for con in data["condition"]:
srr_list.append([])
for each in con["repeat"]:
srr_list[-1].append(each['srr'])
all_srr.append(each['srr'])
all_srr = sorted(all_srr)
srr_id = "-".join(all_srr)
data_count = SrrTask.objects(_id=srr_id).count()
if data_count == 1:
return redirect(url_for("home.srr_id", _id=srr_id))
new_task_id = TaskId(task_id=str(uuid.uuid1()), srr_id=srr_id, email=data["email"], task_time=datetime.now())
new_task_id.save()
if submit_form.gff_file.data is not None:
gff = submit_form.gff_file.data
gff_filename = secure_filename(gff.filename)
gff_path = os.path.join(path, data["kegg_id"], gff_filename)
if not os.path.exists(path):
os.system("mkdir " + path)
if not os.path.exists(os.path.join(path, data["kegg_id"])):
os.system("mkdir " + os.path.join(path, data["kegg_id"]))
gff.save(gff_path)
fna = submit_form.fna_file.data
fna_filename = secure_filename(fna.filename)
fna_path = os.path.join(path, data["kegg_id"], fna_filename)
if not os.path.exists(os.path.join(path, data["kegg_id"])):
os.system("mkdir " + os.path.join(path, data["kegg_id"]))
fna.save(fna_path)
kegg_id = data["kegg_id"]
soft = data["software_select"]
method = data["method_select"]
corr = data["correlation_select"]
executor.submit(operon_predict, srr_list, kegg_id, soft, method, corr, srr_id)
return redirect(url_for("home.wait"))
return render_template("home/index.html", form=submit_form, auto=auto)