From cc9b962445908af19045ecd26ec00b915430c3ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <henrik@trineo.org>
Date: Thu, 17 Jan 2019 16:39:59 +0100
Subject: [PATCH] ENH: first test running
---
src/caosadvancedtools/cfood.py | 70 ++++++++++++++++++++++++++++++++
src/caosadvancedtools/crawler.py | 37 +++++++++++++++++
unittests/test_cfood.py | 18 ++++++++
3 files changed, 125 insertions(+)
create mode 100644 src/caosadvancedtools/cfood.py
create mode 100644 src/caosadvancedtools/crawler.py
create mode 100644 unittests/test_cfood.py
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
new file mode 100644
index 00000000..149fea52
--- /dev/null
+++ b/src/caosadvancedtools/cfood.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""does something"""
+
+import argparse
+from argparse import RawTextHelpFormatter
+import re
+import caosdb as db
+from datetime import datetime
+from caosdb.exceptions import TransactionError
+
+
+class CFood(object):
+ def __init__(self, pattern):
+ self.pattern = re.compile(pattern)
+
+ def treat_match(self, filename, match):
+ entities = self.create_identifiables(filename, match)
+ for key, ent in entities.items():
+ existing = find_existing(ent)
+ if existing is None:
+ print(key, "does not exist")
+ ent.insert()
+ print(key, "inserted")
+ entities[key] = ent
+ else:
+ print(key, "exists")
+ entities[key] = existing
+
+ self.update_identifiables(entities, filename, match)
+
+ def create_identifiables(self, filename, match):
+ entities = {}
+ entities["exp"] = db.Record()
+ #import IPython
+ #IPython.embed()
+ entities["exp"].add_parent(name="Experiment")
+ entities["exp"].add_property(name="species", value=match.group)
+
+ return entities
+
+ def update_identifiables(self, entities, filename, match):
+ entities["exp"].add_property(name="date",
+ value=datetime.today().isoformat())
+ db.Container().extend(entities.values).update()
+
+ @staticmethod
+ def find_existing(entity):
+ query_string = "FIND Record "+ entity.get_parents()[0].name
+ query_string += " with " + "and".join(["'" + p.name + "'='" + p.value +"'"
+ for p in entity.get_properties()])
+ print(query_string)
+ q = db.Query(query_string)
+ try:
+ r = q.execute(unique=True)
+ except TransactionError as er:
+ r = None
+ return r
+
+def get_parser():
+ parser = argparse.ArgumentParser(description=__doc__,
+ formatter_class=RawTextHelpFormatter)
+
+ return parser
+
+
+if __name__ == "__main__":
+ parser = get_parser()
+ args = parser.parse_args()
+
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
new file mode 100644
index 00000000..12947ba5
--- /dev/null
+++ b/src/caosadvancedtools/crawler.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""does something"""
+
+import argparse
+from argparse import RawTextHelpFormatter
+from cfood import CFood
+
+
+
+class Crawler(object):
+ def __init__(self, food):
+ self.food = food
+
+ def crawl(self):
+ filename="path/to/file"
+ for cfood in self.food:
+ match = cfood.pattern.match(filename)
+ if match is not None:
+ print("match")
+ cfood.treat_match(filename, match)
+
+
+def get_parser():
+ parser = argparse.ArgumentParser(description=__doc__,
+ formatter_class=RawTextHelpFormatter)
+
+ return parser
+
+
+if __name__ == "__main__":
+ parser = get_parser()
+ args = parser.parse_args()
+
+ f = CFood(pattern="(.*)to(.*)")
+ c = Crawler(food=[f])
+ c.crawl()
diff --git a/unittests/test_cfood.py b/unittests/test_cfood.py
new file mode 100644
index 00000000..4a4aa51f
--- /dev/null
+++ b/unittests/test_cfood.py
@@ -0,0 +1,18 @@
+import unittest
+from tempfile import NamedTemporaryFile
+
+import caosdb as db
+from caosadvancedtools.cfood import CFood
+
+
+
+class CFoodTest(unittest.TestCase):
+ def setUp(self):
+ self.exp = db.Record()
+ self.exp.add_parent(name="Experiment")
+ self.exp.add_property(name="species", value="microunicorn")
+ pass
+
+ def test_check_existence(self):
+ assert CFood.find_existing(self.exp) is None
+ pass
--
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