Merge branch 'parser' into 'master'

ENH: initial version of a table-record conversion

See merge request bmp-caosdb/caosdb-advanced-user-tools!1

src/caosadvancedtools/table_converter.py

+#!/usr/bin/env python
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# 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/>.
+#
+# ** end header
+import argparse
+import re
+import sys
+
+import caosdb as db
+import pandas as pd
+
+
+def from_tsv(filename, recordtype):
+    """ parses a tsv file to a list of records """
+    df = pd.read_csv(filename, sep="\t")
+
+    return from_table(df, recordtype)
+
+
+def to_tsv(filename, container):
+    df = to_table(container)
+    df.to_csv(filename, sep="\t", index=False)
+
+
+def generate_property_name(prop):
+    if prop.unit is None:
+        return prop.name
+    else:
+        return "{} [{}]".format(prop.name, prop.unit)
+
+
+def to_table(container):
+    """ creates a table from the records in a container """
+
+    if len(container) == 0:
+        raise ValueError("Container is empty")
+    properties = set()
+
+    for rec in container:
+        properties.update([generate_property_name(p)
+                           for p in container[0].get_properties()])
+    df = pd.DataFrame(columns=list(properties))
+    rts = set([p.name for p in container[0].parents])
+
+    for ii, rec in enumerate(container):
+        if set([p.name for p in rec.parents]) != rts:
+            raise ValueError("Parents differ")
+
+        for p in rec.get_properties():
+
+            df.loc[ii, generate_property_name(p)] = p.value
+
+    return df
+
+
+def from_table(spreadsheet, recordtype):
+    """ parses a pandas DataFrame to a list of records """
+    records = db.Container()
+
+    for idx, row in spreadsheet.iterrows():
+        rec = db.Record()
+        rec.add_parent(name=recordtype)
+
+        for key, value in row.iteritems():
+            if (pd.notnull(value) and
+                    (not isinstance(value, str) or value.strip() != "")):
+                regexp = r"(.*)\[(.*)\].*"
+                match = re.match(regexp, key)
+
+                if match is not None:
+                    pname = match.group(1).strip()
+                    unit = match.group(2).strip()
+                    rec.add_property(name=pname, value=value, unit=unit)
+                else:
+                    rec.add_property(name=key, value=value)
+        records.append(rec)
+
+    return records
+
+
+if __name__ == "__main__":
+
+    p = argparse.ArgumentParser()
+    p.add_argument("-f", "--filename", help="The excel filename")
+    p.add_argument("--auth-token")
+    arg = p.parse_args(sys.argv[1:])
+
+    db.configure_connection(auth_token=arg.auth_token)
+
+    recordtype = "Experiment"
+
+    from_tsv(arg.filename, recordtype)

unittests/test.tsv

+temperature [*C]	greeting
+3.4	tach
+4.5	hi
+	hi
+4.5	

unittests/test_table_converter.py

+#!/usr/bin/env python
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# 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/>.
+#
+# ** end header
+import os
+import unittest
+from tempfile import NamedTemporaryFile
+
+import caosdb as db
+import pandas as pd
+from caosadvancedtools.table_converter import (from_table, from_tsv, to_table,
+                                               to_tsv)
+
+TEST_TABLE = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                          "test.tsv")
+
+
+class TableTest(unittest.TestCase):
+    def test_basic(self):
+        df = pd.read_csv(TEST_TABLE, sep="\t")
+        assert isinstance(from_table(df, "Measurement"), db.Container)
+
+    def test_empty(self):
+        c = db.Container()
+        self.assertRaises(ValueError, to_table, c)
+
+    def test_different_props(self):
+        r1 = db.Record()
+        r1.add_parent("no1")
+        r1.add_property("p1")
+        r2 = db.Record()
+        r2.add_parent("no1")
+        r2.add_property("p1")
+        r2.add_property("p2")
+        c = db.Container()
+        c.extend([r1, r2])
+        to_table(c)
+
+    def test_parents(self):
+        r1 = db.Record()
+        r1.add_parent("no1")
+        r2 = db.Record()
+        r2.add_parent("no2")
+        c = db.Container()
+        c.extend([r1, r2])
+        self.assertRaises(ValueError, to_table, c)
+
+
+class FromTsvTest(unittest.TestCase):
+    def test_basic(self):
+        from_tsv(TEST_TABLE, "Measurement")
+
+
+class ToTsvTest(unittest.TestCase):
+    def test_basic(self):
+        r = db.Record()
+        r.add_property("ha", 5)
+        r.add_parent("hu")
+        c = db.Container()
+        c.append(r)
+        to_tsv(NamedTemporaryFile().name, c)
+
+
+class IntegrationTest(unittest.TestCase):
+    """ converts  tsv to a container and back and compares origin with
+    result """
+    def test_backandforth(self):
+        cont = from_tsv(TEST_TABLE, "Measurement")
+        tempfile = NamedTemporaryFile(delete=False)
+        to_tsv(tempfile.name, cont)
+        with open(TEST_TABLE, "r") as no1, open(tempfile.name, "r") as no2:
+            assert no1.read() == no2.read()