From a9dc52644c5e5bc925a0f5fcc17480bae293d516 Mon Sep 17 00:00:00 2001
From: Gianmauro Cuccuru <gianmauro.cuccuru@fht.org>
Date: Mon, 21 Oct 2024 21:59:57 +0200
Subject: [PATCH] add meta-query command

---
 gwasstudio/cli/metadata/query.py | 25 +++++++++++++++++++++++++
 gwasstudio/main.py               |  2 ++
 gwasstudio/mongo/mixin.py        | 16 ++++++++++++++++
 3 files changed, 43 insertions(+)
 create mode 100644 gwasstudio/cli/metadata/query.py

diff --git a/gwasstudio/cli/metadata/query.py b/gwasstudio/cli/metadata/query.py
new file mode 100644
index 0000000..c66957d
--- /dev/null
+++ b/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
diff --git a/gwasstudio/main.py b/gwasstudio/main.py
index 77605d2..ddc51b4 100644
--- a/gwasstudio/main.py
+++ b/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={})
 
diff --git a/gwasstudio/mongo/mixin.py b/gwasstudio/mongo/mixin.py
index c3a8a50..0848a1b 100644
--- a/gwasstudio/mongo/mixin.py
+++ b/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