added units

aalbino2 · Jan 14, 2025 · ebb2254 · ebb2254
1 parent 90e17aa
commit ebb2254
Show file tree

Hide file tree

Showing 10 changed files with 160 additions and 5 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -28,6 +28,7 @@ license = { file = "LICENSE" }
 dependencies = [
     "nomad-lab>=1.3.0",
     "python-magic-bin; sys_platform == 'win32'",
+    "pdi-nomad-plugin",
 ]
 
 [project.urls]
@@ -116,6 +117,7 @@ parser_one_entry_point = "nomad_aa_plugin.parsers:parser_one_entry_point"
 parser_two_entry_point = "nomad_aa_plugin.parsers:parser_two_entry_point"
 parser_three_entry_point = "nomad_aa_plugin.parsers:parser_three_entry_point"
 parser_four_entry_point = "nomad_aa_plugin.parsers:parser_four_entry_point"
+parser_five_entry_point = "nomad_aa_plugin.parsers:parser_five_entry_point"
 
 app_entry_point = "nomad_aa_plugin.apps:app_entry_point"
 

diff --git a/src/nomad_aa_plugin/parsers/__init__.py b/src/nomad_aa_plugin/parsers/__init__.py
@@ -82,3 +82,24 @@ def load(self):
         '__has_comment': '#',
     },
 )
+
+
+class MyParserFiveEntryPoint(ParserEntryPoint):
+    parameter: int = Field(0, description='Custom configuration parameter')
+
+    def load(self):
+        from nomad_aa_plugin.parsers.parser import MyParserFive 
+
+        return MyParserFive(**self.dict())
+
+
+parser_five_entry_point = MyParserFiveEntryPoint(
+    name='MyParserFive',
+    description='My parser entry point configuration.',
+    mainfile_name_re=r'.+\.csv',
+    mainfile_mime_re="(?:text/plain|text/csv)",  # 'text/plain',  
+    mainfile_contents_dict={
+        '__has_all_keys': ['ValueFive', 'ValueFive2'],
+        '__has_comment': '#',
+    },
+)
diff --git a/src/nomad_aa_plugin/parsers/parser.py b/src/nomad_aa_plugin/parsers/parser.py
@@ -11,6 +11,7 @@
         EntryArchive,
     )
 
+from nomad.units import ureg
 from nomad.datamodel.datamodel import EntryArchive
 from nomad.parsing import MatchingParser
 from nomad.parsing.parser import MatchingParser
@@ -64,12 +65,14 @@ def parse(
 
         child_archive.data = MyClassTwo()
         child_archive.data.my_name = f'{my_name}'
-        child_archive.data.my_class_one = []
 
-        child_archive.data.my_class_one.append(MyClassOne())
+        my_class_one_subsec = MyClassOne()
+        my_class_one_subsec.my_value = df_csv["ValueTwo"]
+        my_class_one_subsec.my_time = df_csv["ValueTwo2"]
 
-        child_archive.data.my_class_one[0].my_value = df_csv["ValueTwo"]
-        child_archive.data.my_class_one[0].my_time = df_csv["ValueTwo2"]
+        # check which args the function m_add_subsection accepts: packages/nomad-FAIR/nomad/metainfo/metainfo.py
+        # DO NOT use list.append() to add a subsection to a section!
+        child_archive.data.m_add_sub_section(MyClassTwo.my_class_one, my_class_one_subsec)
 
         create_archive(
             child_archive.m_to_dict(),
@@ -209,3 +212,56 @@ def parse(
         )
 
         archive.data = MyClassOne()
+
+
+class MyParserFive(MatchingParser):
+    def parse(
+        self,
+        mainfile: str, 
+        archive: EntryArchive,
+        logger,
+    ) -> None:
+
+        df_csv = pd.read_csv(mainfile, sep=',') #, decimal=',', engine='python')
+
+        archive.data = MyClassOne()
+
+        child_archive = EntryArchive()
+
+        my_name = "And"
+        filetype = 'yaml'
+
+        example_filename = f'{my_name}.archive.{filetype}'
+
+        child_archive.data = MyClassTwo()
+        child_archive.data.my_name = f'{my_name}'
+
+        my_class_one_subsec = MyClassOne()
+        # use .to_numpy() method to avoid the error: 
+        # Quantity cannot wrap upcast type <class 'pandas.core.series.Series'>
+        my_class_one_subsec.my_value = ureg.Quantity(
+            df_csv["ValueFive"].to_numpy(),
+            ureg('celsius'),
+        )
+        # use .to_numpy() method to avoid the error: 
+        # Quantity cannot wrap upcast type <class 'pandas.core.series.Series'>
+        my_class_one_subsec.my_time =  ureg.Quantity(
+            df_csv["ValueFive2"].to_numpy(),
+            ureg('minute'),
+        )
+
+        # use the syntax my_variable.to('hour').magnitude to convert the units
+
+        # check which args the function m_add_subsection accepts: packages/nomad-FAIR/nomad/metainfo/metainfo.py
+        # DO NOT use list.append() to add a subsection to a section!
+        child_archive.data.m_add_sub_section(MyClassTwo.my_class_one, my_class_one_subsec)
+
+        create_archive(
+            child_archive.m_to_dict(),
+            archive.m_context,
+            example_filename,
+            filetype,
+            logger,
+        )
+
+        archive.data = MyClassOne()
diff --git a/src/nomad_aa_plugin/schema_packages/schema_package.py b/src/nomad_aa_plugin/schema_packages/schema_package.py
@@ -62,16 +62,20 @@ class MyClassOne(PlotSection, EntryData):
     my_value = Quantity(
         type=float,
         shape=['*'],
+        unit = 'K',
         a_eln=ELNAnnotation(
             component='NumberEditQuantity',
+            defaultDisplayUnit='celsius',
         ),
     )
 
     my_time = Quantity(
         type=float,
         shape=['*'],
+        unit = 's',
         a_eln=ELNAnnotation(
             component='NumberEditQuantity',
+            defaultDisplayUnit='minute',
         ),
     )
 

diff --git a/tests/data/myfile.newmainfilename b/tests/data/myfile.newmainfilename
diff --git a/tests/data/test_five.csv b/tests/data/test_five.csv
@@ -0,0 +1,18 @@
+Time,ValueFive,ValueFive2
+19.03.2018 13:01:47,3,1
+19.03.2018 13:02:02,4,2
+19.03.2018 13:02:17,5,3
+19.03.2018 13:02:32,6,4
+19.03.2018 13:02:47,7,5
+19.03.2018 13:03:02,8,6
+19.03.2018 13:03:17,9,7
+19.03.2018 13:03:32,10,8
+19.03.2018 13:03:47,11,9
+19.03.2018 13:04:02,12,10
+19.03.2018 13:04:17,13,11
+19.03.2018 13:04:32,14,12
+19.03.2018 13:04:47,15,13
+19.03.2018 13:05:02,16,14
+19.03.2018 13:05:17,17,15
+19.03.2018 13:05:32,18,16
+19.03.2018 13:05:47,19,17
diff --git a/tests/data/test_four.csv b/tests/data/test_four.csv
@@ -0,0 +1,18 @@
+Time,ValueFour,ValueFour2
+19.03.2018 13:01:47,3,1
+19.03.2018 13:02:02,4,2
+19.03.2018 13:02:17,5,3
+19.03.2018 13:02:32,6,4
+19.03.2018 13:02:47,7,5
+19.03.2018 13:03:02,8,6
+19.03.2018 13:03:17,9,7
+19.03.2018 13:03:32,10,8
+19.03.2018 13:03:47,11,9
+19.03.2018 13:04:02,12,10
+19.03.2018 13:04:17,13,11
+19.03.2018 13:04:32,14,12
+19.03.2018 13:04:47,15,13
+19.03.2018 13:05:02,16,14
+19.03.2018 13:05:17,17,15
+19.03.2018 13:05:32,18,16
+19.03.2018 13:05:47,19,17
diff --git a/tests/data/test.csv → tests/data/test_one.csv b/tests/data/test.csv → tests/data/test_one.csv
@@ -1,4 +1,4 @@
-Time,Value,Value2
+Time,ValueOne,ValueOne2
 19.03.2018 13:01:47,3,1
 19.03.2018 13:02:02,4,2
 19.03.2018 13:02:17,5,3

diff --git a/tests/data/test_three.csv b/tests/data/test_three.csv
@@ -0,0 +1,18 @@
+Time,ValueThree,ValueThree2
+19.03.2018 13:01:47,3,1
+19.03.2018 13:02:02,4,2
+19.03.2018 13:02:17,5,3
+19.03.2018 13:02:32,6,4
+19.03.2018 13:02:47,7,5
+19.03.2018 13:03:02,8,6
+19.03.2018 13:03:17,9,7
+19.03.2018 13:03:32,10,8
+19.03.2018 13:03:47,11,9
+19.03.2018 13:04:02,12,10
+19.03.2018 13:04:17,13,11
+19.03.2018 13:04:32,14,12
+19.03.2018 13:04:47,15,13
+19.03.2018 13:05:02,16,14
+19.03.2018 13:05:17,17,15
+19.03.2018 13:05:32,18,16
+19.03.2018 13:05:47,19,17
diff --git a/tests/data/test_two.csv b/tests/data/test_two.csv
@@ -0,0 +1,18 @@
+Time,ValueTwo,ValueTwo2
+19.03.2018 13:01:47,3,1
+19.03.2018 13:02:02,4,2
+19.03.2018 13:02:17,5,3
+19.03.2018 13:02:32,6,4
+19.03.2018 13:02:47,7,5
+19.03.2018 13:03:02,8,6
+19.03.2018 13:03:17,9,7
+19.03.2018 13:03:32,10,8
+19.03.2018 13:03:47,11,9
+19.03.2018 13:04:02,12,10
+19.03.2018 13:04:17,13,11
+19.03.2018 13:04:32,14,12
+19.03.2018 13:04:47,15,13
+19.03.2018 13:05:02,16,14
+19.03.2018 13:05:17,17,15
+19.03.2018 13:05:32,18,16
+19.03.2018 13:05:47,19,17