From efce8dc07f3a53c53a611996c628397d7c33e526 Mon Sep 17 00:00:00 2001
From: Piotr <rivinek@gmail.com>
Date: Thu, 25 Sep 2014 20:53:23 +0200
Subject: [PATCH] [#69] Added begging of function for connection all together,
 decorator for params and func to get regex which need to be fixed to
 concatenate lists

---
 src/shmir/data/models.py         |  4 +++
 src/shmir/decorators.py          | 13 +++++++++
 src/shmir/designer/connection.py | 45 ++++++++++++++++++++++++++++++++
 3 files changed, 62 insertions(+)
 create mode 100644 src/shmir/designer/connection.py

diff --git a/src/shmir/data/models.py b/src/shmir/data/models.py
index 724ae54..371db35 100644
--- a/src/shmir/data/models.py
+++ b/src/shmir/data/models.py
@@ -90,6 +90,10 @@ def generate_regexp_all(cls):
 
         db_session.commit()
 
+    @classmethod
+    def get_all_regexp(cls):
+        return [bone.regex for bone in db_session.query(cls).all()]
+
     @classmethod
     def get_mirna(cls, name=None):
         if name:
diff --git a/src/shmir/decorators.py b/src/shmir/decorators.py
index a7de003..1160727 100644
--- a/src/shmir/decorators.py
+++ b/src/shmir/decorators.py
@@ -10,6 +10,7 @@
 import json
 
 from shmir.utils import json_error
+from shmir.designer import errors
 
 
 def require_json(require_data=True, required_data_words=None,
@@ -63,3 +64,15 @@ def jsonify(f):
     def wrapped(*args, **kwargs):
         return dumps(f(*args, **kwargs))
     return wrapped
+
+
+def param(name, g_type, description, default=None, required=False):
+    def wrapper(func):
+        def wrapped(**kwargs):
+            if not kwargs[name]:
+                if required:
+                    raise errors.InputException('{} is required'.format(name))
+                kwargs[name] = g_type(default)
+            return func(**kwargs)
+        return wrapped
+    return wrapper
diff --git a/src/shmir/designer/connection.py b/src/shmir/designer/connection.py
new file mode 100644
index 0000000..1ca0a92
--- /dev/null
+++ b/src/shmir/designer/connection.py
@@ -0,0 +1,45 @@
+from shmir import cache
+from shmir.data import (
+    models,
+    ncbi_api,
+)
+from shmir.decorators import param
+from shmir.designer.validators import calculate_gc_content
+
+
+def create_cache_key(*args):
+    return ':'.join(args)
+
+
+@param('transcript_name', str, 'Name of transcript', required=True)
+@param('min_gc', int, 'Minimum of GC content', default=40)
+@param('max_gc', int, 'Maximum of GC content', default=60)
+@param('max_offtarget', int, 'Maximum offtarget, minimum is 0', default=10)
+@param('mirna_name', str, 'miRNA name of Backbone', default=None)
+@param(
+    'stymulators', bool, 'Bool if immuno stimulators are wanted', default=False
+)
+def connection(
+    transcript_name, min_gc, max_gc, max_offtarget, mirna_name, stymulators
+):
+    sequence = '?'
+    cg_content = calculate_gc_content(sequence)
+
+    cache_key = create_cache_key(
+        transcript_name,
+        cg_content,
+        mirna_name,
+        max_offtarget,
+        str(stymulators)
+    )
+
+    sequence = cache.get(cache_key)  # TODO: check if get take cache by key xD
+
+    if not sequence:
+        sequence = ncbi_api.get_mRNA(transcript_name)
+
+    backbones = models.Backbone.get_mirna(mirna_name)
+    if not isinstance(backbones, list):
+        backbones = [backbones]
+
+    all_regex = models.Backbone.get_all_regexp()