diff --git a/CHANGELOG.md b/CHANGELOG.md
index bd2a02040cdad31deb9738947269867e1209c9fc..44629bd9b80b9bfd6a8d6a991fe52c8ce5ed3919 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added ###
+- CFood that creates a Record for each line in a csv file
- `generic_analysis.py` allows to easily call scripts to perform analyses in
server side scripting [EXPERIMENTAL]
diff --git a/integrationtests/crawl.py b/integrationtests/crawl.py
index 79ed3b5ffe52d276677e2a7914f70923e5c9e70c..defed2cb4f5fb0a0f349898e555c5d25924e2f9b 100755
--- a/integrationtests/crawl.py
+++ b/integrationtests/crawl.py
@@ -34,7 +34,7 @@ from caosadvancedtools.crawler import FileCrawler
from caosadvancedtools.guard import INSERT, UPDATE
from caosadvancedtools.scifolder import (AnalysisCFood, ExperimentCFood,
PublicationCFood, SimulationCFood,
- SoftwareCFood)
+ SoftwareCFood, ResultTableCFood)
from example_hdf5cfood import ExampleH5CFood
@@ -91,6 +91,7 @@ if __name__ == "__main__":
interactive=False, hideKnown=False,
cfood_types=[ExperimentCFood, AnalysisCFood, SoftwareCFood,
PublicationCFood, SimulationCFood,
+ ResultTableCFood,
ExampleH5CFood
])
diff --git a/integrationtests/extroot/ExperimentalData/2010_TestProject/2019-02-03/result_table_DepthTest.csv b/integrationtests/extroot/ExperimentalData/2010_TestProject/2019-02-03/result_table_DepthTest.csv
new file mode 100644
index 0000000000000000000000000000000000000000..a29679afce78089f3cdd4e5e388262456668cd90
--- /dev/null
+++ b/integrationtests/extroot/ExperimentalData/2010_TestProject/2019-02-03/result_table_DepthTest.csv
@@ -0,0 +1,3 @@
+temperature [°C] ,depth
+234.4,3.0
+344.6,5.1
diff --git a/integrationtests/model.yml b/integrationtests/model.yml
index 6c68a86156c21c37abccee575de76486c44f3f06..9f7a62d1d0befbc7225353380c79db2f368c969c 100644
--- a/integrationtests/model.yml
+++ b/integrationtests/model.yml
@@ -19,6 +19,14 @@ SoftwareVersion:
binaries:
sourceCode:
Software:
+DepthTest:
+ obligatory_properties:
+ temperature:
+ datatype: DOUBLE
+ description: 'temp'
+ depth:
+ datatype: DOUBLE
+ description: 'temp'
Person:
obligatory_properties:
firstName:
diff --git a/integrationtests/test_crawler_with_cfoods.py b/integrationtests/test_crawler_with_cfoods.py
index 05bb581058a964d76ab78583cc290c348e8c4566..4efef87cef52e4a2a20a615afe210c32f52a276a 100755
--- a/integrationtests/test_crawler_with_cfoods.py
+++ b/integrationtests/test_crawler_with_cfoods.py
@@ -66,6 +66,17 @@ class CrawlerTest(unittest.TestCase):
datfile.description)
assert os.path.basename(datfile.path) == "datafile.dat"
+ # There should be two DepthTest Properties
+ depthtests = exp.get_property("DepthTest")
+ assert depthtests is not None
+ assert len(depthtests.value) == 2
+ depthtest = db.Record(id=depthtests.value[0])
+ depthtest.retrieve()
+ assert "DepthTest" in [p.name for p in depthtest.get_parents()]
+ assert 234.4 == depthtest.get_property("temperature").value
+ assert "°C" == depthtest.get_property("temperature").unit
+ assert 3.0 == depthtest.get_property("depth").value
+
# Should have a responsible person
self.assertIsNotNone(exp.get_property("responsible"))
person = db.Record(id=exp.get_property("responsible").value[0])
diff --git a/src/caosadvancedtools/scifolder/__init__.py b/src/caosadvancedtools/scifolder/__init__.py
index d7d67937b42ca23173fc93d4e704411f33d80bc4..cf753cfc0b72bf95e34edea1301b96ed18f040d0 100644
--- a/src/caosadvancedtools/scifolder/__init__.py
+++ b/src/caosadvancedtools/scifolder/__init__.py
@@ -3,3 +3,4 @@ from .experiment_cfood import ExperimentCFood
from .publication_cfood import PublicationCFood
from .simulation_cfood import SimulationCFood
from .software_cfood import SoftwareCFood
+from .result_table_cfood import ResultTableCFood
diff --git a/src/caosadvancedtools/scifolder/result_table_cfood.py b/src/caosadvancedtools/scifolder/result_table_cfood.py
new file mode 100644
index 0000000000000000000000000000000000000000..deaa2d00118659a9b177a05fe40b19a1793a16fb
--- /dev/null
+++ b/src/caosadvancedtools/scifolder/result_table_cfood.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+# encoding: utf-8
+#
+# Copyright (C) 2019 Henrik tom Wörden
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+import re
+
+import caosdb as db
+import pandas as pd
+from caosadvancedtools.cfood import (AbstractFileCFood, assure_has_description,
+ assure_has_parent, assure_has_property,
+ assure_object_is_in_list, get_entity)
+from caosadvancedtools.read_md_header import get_header
+
+from ..cfood import assure_property_is, fileguide
+from .experiment_cfood import ExperimentCFood
+from .generic_pattern import date_pattern, date_suffix_pattern, project_pattern
+from .utils import parse_responsibles, reference_records_corresponding_to_files
+from .withreadme import DATAMODEL as dm
+from .withreadme import RESULTS, REVISIONOF, SCRIPTS, WithREADME, get_glob
+
+
+# TODO similarities with TableCrawler
+class ResultTableCFood(AbstractFileCFood):
+
+ # win_paths can be used to define fields that will contain windows style
+ # path instead of the default unix ones. Possible fields are:
+ # ["results", "revisionOf"]
+ win_paths = []
+ table_re = r"result_table_(?P<recordtype>.*).csv$"
+ property_name_re = re.compile(r"^(?P<pname>.+?)\s*(\[\s?(?P<unit>.*?)\s?\] *)?$")
+
+ @staticmethod
+ def name_beautifier(x): return x
+
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.table = pd.read_csv(fileguide.access(self.crawled_path))
+
+ @staticmethod
+ def get_re():
+ return (".*/ExperimentalData/"+project_pattern + date_pattern +
+ date_suffix_pattern + ResultTableCFood.table_re)
+
+ def create_identifiables(self):
+ self.recs = []
+ self.experiment, self.project = (
+ ExperimentCFood.create_identifiable_experiment(self.match))
+
+ for idx, row in self.table.iterrows():
+ rec = db.Record()
+ rec.add_parent(self.match.group("recordtype"))
+
+ for col in self.table.columns[:2]:
+ match = re.match(ResultTableCFood.property_name_re, col)
+
+ if match.group("unit"):
+ rec.add_property(match.group("pname"), row.loc[col], unit=match.group("unit"))
+ else:
+ rec.add_property(match.group("pname"), row.loc[col])
+ self.identifiables.append(rec)
+ self.recs.append(rec)
+
+ self.identifiables.extend([self.project, self.experiment])
+
+ def update_identifiables(self):
+ for ii, (idx, row) in enumerate(self.table.iterrows()):
+ for col in row.index:
+ match = re.match(ResultTableCFood.property_name_re, col)
+ assure_property_is(self.recs[ii], match.group("pname"), row.loc[col], to_be_updated=self.to_be_updated)
+ assure_property_is(self.experiment, self.match.group("recordtype"),
+ self.recs, to_be_updated=self.to_be_updated,
+ datatype=db.LIST(self.match.group("recordtype")))
diff --git a/unittests/test.csv b/unittests/test.csv
new file mode 100644
index 0000000000000000000000000000000000000000..a29679afce78089f3cdd4e5e388262456668cd90
--- /dev/null
+++ b/unittests/test.csv
@@ -0,0 +1,3 @@
+temperature [°C] ,depth
+234.4,3.0
+344.6,5.1
diff --git a/unittests/test_result_table_cfood.py b/unittests/test_result_table_cfood.py
new file mode 100644
index 0000000000000000000000000000000000000000..3341a2394cc9ef15ae172bb8992445d87c60d063
--- /dev/null
+++ b/unittests/test_result_table_cfood.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+
+"""
+test module for ResultTableCFood
+"""
+
+
+import os
+import re
+import unittest
+
+import caosdb as db
+from caosadvancedtools.scifolder.result_table_cfood import ResultTableCFood
+
+
+class CFoodTest(unittest.TestCase):
+ def test_re(self):
+ self.assertIsNotNone(re.match(ResultTableCFood.table_re, "result_table_Hallo.csv"))
+ self.assertEqual(re.match(ResultTableCFood.table_re, "result_table_Hallo.csv").group("recordtype"),
+ "Hallo")
+ self.assertIsNotNone(re.match(ResultTableCFood.table_re,
+ "result_table_Cool RecordType.csv"))
+ self.assertEqual(re.match(ResultTableCFood.table_re, "result_table_Cool RecordType.csv").group("recordtype"),
+ "Cool RecordType")
+ self.assertIsNone(re.match(ResultTableCFood.table_re, "result_tableCool RecordType.csv"))
+
+ self.assertIsNotNone(re.match(ResultTableCFood.property_name_re,
+ "temperature [C]"))
+ self.assertEqual(re.match(ResultTableCFood.property_name_re,
+ "temperature [C]").group("pname"),
+ "temperature")
+ self.assertEqual(re.match(ResultTableCFood.property_name_re,
+ "temperature [C]").group("unit"), "C")
+ self.assertEqual(re.match(ResultTableCFood.property_name_re,
+ "temperature [ C ]").group("unit"), "C")
+ self.assertEqual(re.match(ResultTableCFood.property_name_re,
+ "temperature").group("pname"), "temperature")
+
+ def test_ident(self):
+ rtc = ResultTableCFood(os.path.join(os.path.dirname(__file__), "test.csv"))
+ rtc.match = re.match(ResultTableCFood.get_re(),
+ "/ExperimentalData/2010_TestProject/2019-02-03_something/result_table_RT.csv")
+ rtc.create_identifiables()
+ rtc.update_identifiables()