def approve():
# Check if user has logged in
if g.user is not None:
if request.method == 'GET':
print("approve")
# query mongo
# pass json to the template
db = get_db()
collection = db[
current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
transformations = collection.transformations.find(
{"status": "submitted"})
transformations_data = []
try:
for data_tuple in transformations:
data = dict()
data['status'] = data_tuple.get('status')
data['transformation_type'] = data_tuple.get(
'transformationType')
data['name'] = data_tuple.get('transformationId')
transformations_data.append(data)
except pymongo.errors.ServerSelectionTimeoutError as err:
print(err)
return render_template('publish/approve.html',
columns=transformations_data)
else:
form_dic = request.form.to_dict()
transformation_id = form_dic.get('transformationId')
if transformation_id:
db = get_db()
collection = db[
current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
transformations = collection.transformations.find(
{"status": "submitted"})
transformations_data = []
for data_tuple in transformations:
data_name = data_tuple.get('transformationId')
if data_name == transformation_id:
collection.transformations.update_one(
{'transformationId': transformation_id},
{'$set': {
'status': 'approved'
}})
else:
data = dict()
data['status'] = data_tuple.get('status')
data['transformation_type'] = data_tuple.get(
'transformationType')
data['name'] = data_tuple.get('transformationId')
transformations_data.append(data)
return render_template('publish/approve.html',
columns=transformations_data)
return redirect(url_for('auth.login'))
def jsonList(type):
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
retVal = []
for toolInfo in collection.tools.find({"tooltype": type}):
retVal.append(singleToolInfo(str(ObjectId(toolInfo['_id'])), db))
return json.dumps(
retVal, default=json_util.default) # Not sure this is json formatted
def transformation_form():
if g.user is not None:
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
tools = collection.tools.find({}, {"title": 1})
return render_template('pages/post_transformation_form.html',
tools=tools)
return redirect(url_for('auth.login'))
def softwares():
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
tools = collection.tools.find()
raise HTTPException()
return render_template('pages/softwares.html',
tools=tools,
getIcon=getIcon)
def hasIcons(softwares):
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
for tool_name in softwares:
tool = collection.tools.find_one({"title": tool_name})
if (tool):
gridFSIcon = gridfs.GridFS(collection, "icons")
fs = gridFSIcon.find_one({"metadata.tool_id": str(tool["_id"])})
if fs:
return True
return False
def getIcon(tool_name):
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
tool = collection.tools.find_one({"title": tool_name})
image = ""
if (tool):
gridFSIcon = gridfs.GridFS(collection, "icons")
fs = gridFSIcon.find_one({"metadata.tool_id": str(tool["_id"])})
if fs:
base64_data = codecs.encode(fs.read(), 'base64')
image = base64_data.decode('utf-8')
return image
def home():
# example: /?software=Cell+Profiler
software = request.args.get('software')
db = get_db()
collection = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
if software:
transformations = collection.transformations.find(
{"dependencies": software})
else:
transformations = collection.transformations.find(
{"status": "approved"})
return render_template('pages/home.html',
transformations=transformations,
getIcon=getIcon,
hasIcons=hasIcons)
def search():
try:
db = get_db()
database = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
# text search for transformationId & description
transformation = database.transformations.find(
{"$text": {
"$search": request.args.get("search")
}})
except Exception as e:
print("Exception")
raise
return render_template('pages/home.html',
transformations=transformation,
getIcon=getIcon,
hasIcons=hasIcons)
def view_transformation(transformation_id):
try:
db = get_db()
database = db[current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
transformation = database.transformations.find_one(
{"_id": ObjectId(transformation_id)})
alltransformations = database.transformations.find({"transformationId":
transformation["transformationId"] }).sort("version", -1).\
collation(Collation(locale='en_US', numericOrdering=True))
except Exception as e:
print("Exception")
raise
return render_template('pages/view_transformation.html',
originalTransformation=transformation,
transformations=alltransformations,
getIcon=getIcon,
replaceEmptyString=replaceEmptyString)
def post_transformation():
# Check if user has logged in or anonymous submission is allowed
if g.user is not None or current_app.config["ANONYMOUS_SUBMISSION"].lower(
) == "true":
if request.method == 'POST':
transformation_type = request.form['radioOptions']
try:
if request.form['create'] == "json":
info_json = request.form['info_json']
dict_info_json = json.loads(info_json)
source_code_url = None
docker_image_name = None
for repo in dict_info_json["repository"]:
if repo["repType"] == "git":
source_code_url = repo["repUrl"]
if repo["repType"] == "docker":
docker_image_name = repo["repUrl"]
dict_info_json["url"] = source_code_url
dict_info_json["dockerImageName"] = docker_image_name
dict_info_json.pop("repository")
dict_info_json.pop("@context")
else:
dict_info_json = request.form.to_dict(flat=False)
single_fields = [
"name", "version", "author", "description",
"dockerImageName", "url"
]
for f in single_fields:
dict_info_json[f] = dict_info_json[f][0]
if transformation_type == "extractor":
dict_info_json["contexts"][0] = json.loads(
dict_info_json["contexts"][0])
dict_info_json["process"] = json.loads(
dict_info_json["process"])
else:
dict_info_json["input_formats"] = dict_info_json[
"input_formats"][0].replace(" ", "").split(",")
dict_info_json["output_formats"] = dict_info_json[
"output_formats"][0].replace(" ", "").split(",")
db = get_db()
database = db[
current_app.config['TRANSFORMATIONS_DATABASE_NAME']]
dict_info_json["transformationId"] = dict_info_json.pop("name")
dict_info_json["externalServices"] = dict_info_json.pop(
"external_services")
dict_info_json["transformationType"] = transformation_type
dict_info_json["status"] = "submitted"
dict_info_json["created"] = datetime.datetime.utcnow()
dict_info_json["updated"] = datetime.datetime.utcnow()
print(dict_info_json)
# Prior to insert, check the name and version if they already exist then error out, otherwise insert
query_result_id = database.transformations.find_one({
"transformationId":
dict_info_json["transformationId"],
"version":
dict_info_json["version"]
})
if query_result_id:
return redirect(
url_for('pages.update_transformation',
transformation_id=query_result_id["_id"]))
result_id = database.transformations.insert(dict_info_json)
print(transformation_type + " added. ID: " + str(result_id))
return redirect(
url_for('pages.view_transformation',
transformation_id=result_id))
except ValueError as e:
raise ValueError("Invalid JSON.")
except json.JSONDecodeError as e:
raise json.JSONDecodeError("Unable to decode the JSON")
except KeyError as ke:
raise KeyError(
"There is a missing necessary section of the extractor info"
)
return render_template('pages/post_transformation.html')
return redirect(url_for('auth.login'))