add meta-query command

gwasstudio/cli/metadata/query.py

@@ -0,0 +1,25 @@
+import cloup
+
+from gwasstudio.mongo.models import EnhancedDataProfile
+
+help_doc = """
+Metadata query
+"""
+
+
+@cloup.command("meta_query", no_args_is_help=True, help=help_doc)
+@cloup.option(
+    "--key",
+    default=None,
+    help="query key",
+)
+@cloup.option(
+    "--value",
+    default=None,
+    help="query value",
+)
+def meta_query(key, value):
+    obj = EnhancedDataProfile()
+    objs = obj.query(**{key: value})
+    print(objs)
+    pass

gwasstudio/main.py

@@ -6,6 +6,7 @@
 # from gwasstudio.cli.export import export
 from gwasstudio.cli.info import info
 from gwasstudio.cli.metadata.ingest import meta_ingest
+from gwasstudio.cli.metadata.query import meta_query
 from gwasstudio.cli.metadata.view import meta_view
 
 # from gwasstudio.cli.ingest import ingest
@@ -92,6 +93,7 @@ def main():
     # cli_init.add_command(ingest)
     cli_init.add_command(meta_ingest)
     cli_init.add_command(meta_view)
+    cli_init.add_command(meta_query)
     logger.info("{} started".format(__appname__.capitalize()))
     cli_init(obj={})
 

gwasstudio/mongo/mixin.py

@@ -66,6 +66,22 @@ def view(self):
                 logger.debug(detail)
         return detail
 
+    def query(self, **kwargs):
+        """
+
+        :param kwargs:
+        :return:
+        """
+        docs = []
+        if len(kwargs) > 0:
+            with self.mec:
+                if "trait_desc" in kwargs.keys():
+                    docs = self.klass.objects(trait_desc__contains=kwargs.get("trait_desc")).as_pymongo()
+                else:
+                    docs = self.klass.objects(**kwargs).as_pymongo()
+                logger.debug("found {} documents".format(len(docs)))
+        return docs
+
     def modify(self, **kwargs):
         """
         Perform an atomic update of the document in the database and