Patch some of the issues

.dockerignore

@@ -4,5 +4,6 @@ env
 .DS_Store
 app/__pycache__/
 *.env
+app/.env
 ETL
 predictions

app/app.py

@@ -12,6 +12,7 @@
 from functools import lru_cache
 import pickle
 import anndata
+import urllib.parse
 from dotenv import load_dotenv
 load_dotenv()
 
@@ -28,8 +29,8 @@
 base_url = os.environ.get('BASE_URL', 'data')
 ROOT_PATH = os.environ.get('ROOT_PATH', '/')
 BASE_PATH = os.environ.get('BASE_PATH', 'maayanlab.cloud')
-DEBUG = os.environ.get('DEBUG', True).lower() in ('true', '1', 't')
-UPDATE_STUDIES = os.environ.get('UPDATE_STUDIES', False).lower() in ('true', '1', 't')
+DEBUG = os.environ.get('DEBUG', 'true').lower() in ('true', '1', 't')
+UPDATE_STUDIES = os.environ.get('UPDATE_STUDIES', 'false').lower() in ('true', '1', 't')
 
 s3 = s3fs.S3FileSystem(anon=True, client_kwargs={'endpoint_url': endpoint})
 
@@ -86,7 +87,7 @@ def downloads():
 @app.route(f'{ROOT_PATH}/queryexpression', methods=['GET','POST'])
 def query_expression():
 
-    gene = request.form['gene']
+    gene = urllib.parse.quote(request.form['gene'], safe='')
 
     result = query_generanger(gene)
 
@@ -95,7 +96,7 @@ def query_expression():
 @app.route(f'{ROOT_PATH}/getgwas', methods=['GET','POST'])
 def get_gwas():
 
-    gene = request.form['gene']
+    gene = urllib.parse.quote(request.form['gene'], safe='')
 
     if gene == '':
         return {'GWAS_Catalog':[]}
@@ -106,7 +107,7 @@ def get_gwas():
 
 @app.route(f'{ROOT_PATH}/getkomp', methods=['GET','POST'])
 def get_mgi():
-    gene = request.form['gene']
+    gene = urllib.parse.quote(request.form['gene'], safe='')
     result = query_mgi(gene)
     return result
 
@@ -154,7 +155,7 @@ def getchea3():
 
 @app.route(f'{ROOT_PATH}/gettfs',  methods=['GET','POST'])
 def gettfs():
-	gene = request.form['gene']
+	gene = urllib.parse.quote(request.form['gene'], safe='')
 
 	if gene.strip() == '':
 		return {'data': []}
@@ -258,8 +259,8 @@ def dge():
 	perturb = response_json['perturb']
 	control = response_json['control']
 	method = response_json['method']
-	gse = response_json['gse']
-	species = response_json['species']
+	gse = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	norms = response_json['norms']
 	expr_file = '{base_url}/{species}/{gse}/{gse}_Expression.tsv'.format(species=species, gse=gse, base_url=base_url)
 	meta_file = '{base_url}/{species}/{gse}/{gse}_Metadata.tsv'.format(species=species, gse=gse, base_url=base_url)
@@ -276,14 +277,14 @@ def dge():
 def dgesingle():
 	response_json = request.get_json()
 	method = response_json['method']
-	gse = response_json['gse']
-	species = response_json['species']
+	gse = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	condition_group = response_json['conditiongroup']
 	cluster_group = response_json['diffcluster']
 
 	metajson = s3.open('{base_url}/{species}/{gse}/{gse}_metasep.json'.format(species=species, gse=gse, base_url=base_url),'r')
 	metadict = json.load(metajson)
-	base_expression_filename = metadict[condition_group]['filename']
+	base_expression_filename = urllib.parse.quote(metadict[condition_group]['filename'], safe='')
 	expr_file = '{base_url}/{species}/{gse}/{file}'.format(species=species, gse=gse, base_url=base_url, file=base_expression_filename)
 
 	data_dict = compute_dge_single(expr_file, method, 'Cluster', 'Cell_types',cluster_group, True)
@@ -304,16 +305,16 @@ def dgesingle():
 @app.route('/api/precomputed_dge',  methods=['GET','POST'])
 def fetch_precomputed_dge():
 	response_json = request.get_json()
-	sig = response_json['sig']
-	species = response_json['species']
+	sig = urllib.parse.quote(response_json['sig'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	dge_tab = get_precomputed_dge(sig, species)
 	return dge_tab.to_json(orient='index')
 
 @app.route('/api/precomputed_dge_options',  methods=['GET','POST'])
 def fetch_precomputed_dge_options():
 	response_json = request.get_json()
-	gse = response_json['gse']
-	species = response_json['species']
+	gse = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	return get_precomputed_dge_options(gse, species)
 
 
@@ -322,15 +323,15 @@ def fetch_precomputed_dge_options():
 @app.route('/singleplots',  methods=['GET','POST'])
 def makesingleplots():
 	response_json = request.get_json()
-	gse = response_json['gse']
-	species = response_json['species']
+	gse = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	condition_group = response_json['conditiongroup']
 	print('in pca, tsne, umap singleplots function')
 	print(condition_group)
 	#metajson file that stores the group/condition pairing to point to the expression h5 file
 	metajson = s3.open('{base_url}/{species}/{gse}/{gse}_metasep.json'.format(species=species, gse=gse, base_url=base_url),'r')
 	metadict = json.load(metajson)
-	base_expression_filename = metadict[condition_group]['filename']
+	base_expression_filename =urllib.parse.quote(metadict[condition_group]['filename'], safe='')
 	#image path for pulling the distribution plot from s3
 	base_name_for_cell_type_dist = base_expression_filename.split('.h5')[0]
 	base_name_for_cell_type_dist = base_name_for_cell_type_dist + '.png'
@@ -375,8 +376,8 @@ def makesingleplots():
 def getclusterinfo():
 	#The json below holds information about the conditiongroup that we are looking at for this data as well the specific species. 
 	response_json = request.get_json()
-	gse = response_json['gse']
-	species = response_json['species']
+	gse = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	condition_group = response_json['conditiongroup']
 	metajson = s3.open('{base_url}/{species}/{gse}/{gse}_metasep.json'.format(species=species, gse=gse, base_url=base_url),'r')
 	metadict = json.load(metajson)
@@ -857,9 +858,8 @@ def plot_api(geo_accession):
 
 @app.route(f'{ROOT_PATH}/api/volcano', methods=['GET', 'POST'])
 def plot_volcano_api():
-	request.form
-	gene = request.form["gene"]
-	species = request.form["species"]
+	gene = urllib.parse.quote(request.form["gene"], safe='')
+	species = urllib.parse.quote(request.form["species"], safe='')
 	try:
 		json_item_plot = send_plot(species, gene)
 	except Exception as e:
@@ -913,10 +913,10 @@ def samples_api(geo_accession):
 def get_study_data():
 
 	response_json = request.get_json()
-	geo_accession = response_json['gse']
+	geo_accession = urllib.parse.quote(response_json['gse'], safe='')
 	control = response_json['control']
 	perturb = response_json['perturb']
-	species = response_json['species']
+	species = urllib.parse.quote(response_json['species'], safe='')
 
 	metadata_file = base_url + '/' + species + '/' + geo_accession + '/' + geo_accession + '_Metadata.tsv'
 	expression_file = base_url + '/' + species + '/' + geo_accession + '/' + geo_accession + '_Expression.tsv'
@@ -950,8 +950,8 @@ def get_study_data():
 @app.route(f'{ROOT_PATH}/api/bulksampvis',  methods=['GET', 'POST'])
 def visualize_samps():
 	response_json = request.get_json()
-	geo_accession = response_json['gse']
-	species = response_json['species']
+	geo_accession = urllib.parse.quote(response_json['gse'], safe='')
+	species = urllib.parse.quote(response_json['species'], safe='')
 	meta_df = base_url + '/' + species + '/' + geo_accession + '/' + geo_accession + '_Metadata.tsv'
 
 	meta_df = pd.read_csv(s3.open(meta_df), sep='\t', index_col=0)
@@ -984,7 +984,7 @@ def query_options():
 @app.route(f'{ROOT_PATH}/api/query_genes',  methods=['GET', 'POST'])
 def query_genes():
 	response_json = request.get_json()
-	g = response_json['gene']
+	g = urllib.parse.quote(response_json['gene'], safe='')
 	res = infer_gene(g)
 	return res
 

app/helpers.py

@@ -86,9 +86,9 @@ def enrichr_id(genes, desc=''):
 @lru_cache()
 def query_enricher(gene):
     ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/genemap'
-    query_string = '?json=true&setup=true&gene=%s'
+    params = dict(json='true', setup='true', gene=gene)
 
-    response = requests.get(ENRICHR_URL + query_string % gene)
+    response = requests.get(ENRICHR_URL, params=params)
     if not response.ok:
         raise Exception('Error finding gene')
 
@@ -126,12 +126,9 @@ def query_enricher_diabetes(genelist, description):
     listid = data["userListId"]
 
     ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/enrich'
-    query_string = '?userListId=%s&backgroundType=%s'
-    user_list_id = listid
     gene_set_library = 'Diabetes_Perturbations_GEO_2022'
-    response = requests.get(
-        ENRICHR_URL + query_string % (user_list_id, gene_set_library)
-    )
+    params = dict(userListId=listid, backgroundType=gene_set_library)
+    response = requests.get(ENRICHR_URL, params=params)
     if not response.ok:
         raise Exception('Error fetching enrichment results')
 
@@ -147,8 +144,9 @@ def query_enricher_diabetes(genelist, description):
 def query_komp(gene: str):
 
     gene = gene[0].upper() + (gene[1:]).lower()
-    KOMP_URL = "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=marker_symbol:" + gene
-    response = requests.get(KOMP_URL)
+    KOMP_URL = "https://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select"
+    params = dict(q="marker_symbol:" + gene)
+    response = requests.get(KOMP_URL, params=params)
     if not response.ok:
         raise Exception('Error analyzing retrieving information')
     data = json.loads(response.text)