From 709794f4c74bf09e3c883c126c49a4be1bc5d634 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <henrik@trineo.org>
Date: Thu, 17 Oct 2019 11:31:52 +0200
Subject: [PATCH] MAINT: fix test, allow non-interactive crawl, and docs
---
integrationtests/full_test/test_crawler.py | 4 +--
src/caosadvancedtools/cfood.py | 30 +++++++++++++++++++++-
2 files changed, 31 insertions(+), 3 deletions(-)
diff --git a/integrationtests/full_test/test_crawler.py b/integrationtests/full_test/test_crawler.py
index e4f559ed..d610d621 100755
--- a/integrationtests/full_test/test_crawler.py
+++ b/integrationtests/full_test/test_crawler.py
@@ -18,7 +18,7 @@ class CrawlerTest(unittest.TestCase):
# vanishing of the property
# thus an x is used here. Needs to be fixed.
exp = db.execute_query(
- "FIND Experiment with date=2019-02-03 and not identifier",
+ "FIND Experiment with date=2019-02-03 and identifier=empty_identifier",
unique=True)
# There should be a Project with name TestProject which is referenced
@@ -57,7 +57,7 @@ class CrawlerTest(unittest.TestCase):
# # first analysis # #
######################
ana = db.execute_query(
- "FIND Analysis with date=2019-02-03 and identifier='x'",
+ "FIND Analysis with date=2019-02-03 and identifier='empty_identifier'",
unique=True)
# There should be a Project with name TestProject which is referenced
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 94eada6f..d0bce391 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -175,7 +175,14 @@ class AbstractCFood(object):
def looking_for(self, crawled_file):
"""
- should set the instance variable Container with the identifiables
+ returns True if crawled_file can be added this CFood.
+
+ to be overwritten by subclasses.
+ Sometimes files belong to the CFood of created by another file. This
+ function can be used to define what files shall be 'attached'. E.g. the
+ data from an experiment should always contain a labnotes scan. Then a
+ subclass CFood for the experiment could be 'looking_for' this scan
+ using this function.
"""
return False
@@ -412,6 +419,27 @@ def get_ids_for_entities_with_names(entities):
class CMeal(object):
+ """
+ CMeal groups equivalent CFoods and allow their collected insertion.
+
+ Sometimes there is no one file that can be used to trigger the creation of
+ some Record. E.g. if a collection of images shall be referenced from one
+ Record that groups them, it is unclear which image should trigger the
+ creation of the Record.
+
+ CMeals are grouped based on the groups in the used regular expression. If,
+ in the above example, all the images reside in one folder, all groups
+ except that for the file name should match. The groups that shall match
+ need to be listed in the matching_groups class property. Subclasses will
+ overwrite this property.
+
+ The cook function of a cfood allows this class to work. Instead of directly
+ instantiating a CFood the cook function is used. If the CFood is also a
+ child of CMeal, it will be checked (using get_suitable_cfood) in the cook
+ function whether a new CFood should be created or if the file match should
+ be added to an existing one. In order to allow this all instances of a
+ CFood class are tracked in the existing_instances class member.
+ """
existing_instances = []
matching_groups = []
--
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