Merge pull request #12 from UMCUGenetics/release/v1.2.0

Release/v1.2.0
UMCUGenetics · Jun 10, 2024 · b193363 · b193363
2 parents 0e0e1c3 + dcf5b80
commit b193363
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Showing 5 changed files with 25 additions and 28 deletions.
diff --git a/README.md b/README.md
@@ -1 +1,18 @@
 # Clarity Portal
+
+## Install
+```bash
+python3.11 -m venv venv
+source venv/bin/activate
+pip install -r requirements.txt
+```
+
+## Development server
+```bash
+flask --app portal run --debug
+```
+
+## Production server
+```bash
+gunicorn -w 4 portal:app
+```
diff --git a/clarity_portal.py b/clarity_portal.py
diff --git a/clarity_portal.wsgi b/clarity_portal.wsgi
diff --git a/portal/forms.py b/portal/forms.py
@@ -30,7 +30,7 @@ class SubmitSampleForm(FlaskForm):
     parsed_samples = []
     sum_exome_count = 0
 
-    def validate(self):
+    def validate(self, extra_validators=[]):
         """Extra validation, used to validate submitted samples."""
         self.parsed_samples = []
         self.sum_exome_count = 0
@@ -154,7 +154,7 @@ class SubmitDXSampleForm(FlaskForm):
     parsed_samples = []
     sum_exome_count = 0
 
-    def validate(self):
+    def validate(self, extra_validators=[]):
         """Extra validation, used to validate submitted samples."""
         self.parsed_samples = {}
         self.parsed_worklist = {}
@@ -265,6 +265,7 @@ def validate(self):
         }
 
         for line in self.helix_worklist.data:
+            line = line.decode('utf-8')
             if not header:
                 header = line.rstrip().split(',')
                 for udf in udf_column:

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,6 @@
-Flask==1.0.2
+Flask==2.3.3
 Flask-Bootstrap==3.3.7.1
-Flask-Script==2.0.6
-Flask-WTF==0.14.2
-genologics==0.3.24
+Flask-WTF==1.2.1
+genologics==1.0.0
+gunicorn==21.2.0
+six==1.16.0