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 database():
database_form = DatabaseForm()
if database_form.validate_on_submit():
data = database_form.data
query = data["query"]
res = []
each = {}
if data["select"] == "specie":
query_data = Specie.objects(kegg_id=query)
for item in query_data:
each["kegg_id"] = item.kegg_id
each["specie_name"] = item.specie_name
res.append(each)
return render_template("home/database.html", form=database_form, res=res, type="specie")
else:
query_data = SrrTask.objects(_id__icontains=query)
for item in query_data:
each["_id"] = item._id
each["kegg_id"] = item.kegg_id
each["method"] = item.method
res.append(each)
query_data2 = SrrTask.objects(kegg_id=query)
for item in query_data2:
each["_id"] = item._id
each["kegg_id"] = item.kegg_id
each["method"] = item.method
each["browse_link"] = item.browse_link
res.append(each)
return render_template("home/database.html", form=database_form, res=res, type="srr_task")
return render_template("home/database.html", form=database_form, res=None, type=None)
def specie_edit(_id=None):
specie_form = SpecieForm()
specie_query = Specie.objects.get_or_404(kegg_id=_id)
if specie_form.validate_on_submit():
data = specie_form.data
old_path = specie_query.gff_path
Specie.objects(kegg_id=_id).update_one(
set__specie_name=data["specie_name"])
Specie.objects(kegg_id=_id).update_one(set__gff_path=data["save_path"])
if not os.path.exists(data["save_path"]):
os.makedirs(data["save_path"])
os.system("mv " + old_path + " " + data["save_path"])
Specie.objects(kegg_id=_id).update_one(set__add_time=datetime.now())
flash("edit done !", "ok")
return redirect(url_for("admin.specie_edit", _id=_id))
return render_template("admin/specie_edit.html",
form=specie_form,
specie=specie_query)
def specie_add():
specie_form = SpecieForm()
if specie_form.validate_on_submit():
data = specie_form.data
f = specie_form.gff_file.data
filename = secure_filename(f.filename)
save_path = os.path.join(data["save_path"], "gff_file", filename)
if not os.path.exists(data["save_path"]):
os.system("mkdir " + data["save_path"])
if not os.path.exists(os.path.join(data["save_path"], "gff_file")):
os.system("mkdir " + os.path.join(data["save_path"], "gff_file"))
f.save(save_path)
new_specie = Specie(kegg_id=data["kegg_id"],
specie_name=data["specie_name"],
gff_path=data["save_path"],
add_time=datetime.now())
new_specie.get_genes_from_file(save_path)
new_specie.save()
flash("this specie is added !", "ok")
return redirect(url_for("admin.specie_add"))
return render_template("admin/specie_add.html", form=specie_form)
def validate_kegg_id(self, field):
kegg_id = field.data
kegg_id_count = Specie.objects(kegg_id=kegg_id).count()
if kegg_id_count > 0:
raise ValidationError("WRONG! This specie is already exist !")
def specie(page=None):
if page is None:
page = 1
page_data = Specie.objects().paginate(page=page, per_page=10)
return render_template("admin/specie.html", page_data=page_data)
def specie_gene(_id=None, page=None):
if page is None:
page = 1
specie_query = Specie.objects(kegg_id=_id).first()
page_data = specie_query.paginate_field("genes", page=page, per_page=50)
return render_template("admin/specie_gene.html", page_data=page_data)
def specie_del(_id=None):
Specie.objects(kegg_id=_id).delete()
flash("delete it done !", "ok")
return redirect(url_for("admin.specie"))