feat: update read metadata

ComPlat · Sep 5, 2023 · e0e21b0 · e0e21b0
1 parent a8aef77
commit e0e21b0
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Showing 22 changed files with 56 additions and 33 deletions.
diff --git a/chem_spectra/lib/composer/base.py b/chem_spectra/lib/composer/base.py
@@ -33,7 +33,7 @@ def coupling_string(js):
 
 
 class BaseComposer:
-    def __init__(self, core, auto_metadata=None):
+    def __init__(self, core):
         self.core = core
         self.title = None
         self.meta = None
@@ -43,7 +43,6 @@ def __init__(self, core, auto_metadata=None):
         self.refArea = 1
         self.refShift = 0
         self.prepare_itg_mpy()
-        self.auto_metadata = auto_metadata
 
     def __header_pk_common(self, category):
         return [
@@ -86,6 +85,7 @@ def __header_auto_metadata(self):
         return [
             '\n',
             TEXT_AUTO_METADATA,
+            '##$CSAUTOMETADATA=\n'
         ]
 
     def gen_headers_root(self):
@@ -294,10 +294,10 @@ def gen_simulation_info(self):
 
     def generate_auto_metadata(self):
         content = self.__header_auto_metadata()
-        if self.auto_metadata is None: return content
+        if self.core.auto_metadata is None: return content
 
-        for key, value in self.auto_metadata.items():
+        for key, value in self.core.auto_metadata.items():
             content.append(
-                '##{}={}\n'.format(key.upper(), value)
+                '{}={}\n'.format(key.upper(), value)
             )
         return content
diff --git a/chem_spectra/lib/composer/ni.py b/chem_spectra/lib/composer/ni.py
@@ -26,8 +26,8 @@
 
 
 class NIComposer(BaseComposer):
-    def __init__(self, core, auto_metadata=None):
-        super().__init__(core, auto_metadata)
+    def __init__(self, core):
+        super().__init__(core)
         self.title = core.fname
         self.meta = self.__compose()
 

diff --git a/chem_spectra/lib/converter/bagit/base.py b/chem_spectra/lib/converter/bagit/base.py
@@ -15,9 +15,9 @@ class BagItBaseConverter:
     def __init__(self, target_dir, params=False, fname=''):
         self.params = parse_params(params)
         if target_dir is None:
-            self.data, self.images, self.list_csv, self.combined_image, self.auto_metadata = None, None, None, None, None
+            self.data, self.images, self.list_csv, self.combined_image = None, None, None, None
         else:
-            self.data, self.images, self.list_csv, self.combined_image, self.auto_metadata = self.__read(target_dir, fname)
+            self.data, self.images, self.list_csv, self.combined_image = self.__read(target_dir, fname)
 
     def __read_metadata(self, target_dir):
         metadata_dir_path = os.path.join(target_dir, 'metadata/')
@@ -61,6 +61,10 @@ def __read(self, target_dir, fname):
         for file_name in list_file_names:
             jcamp_path = os.path.join(data_dir_path, file_name)
             base_cv = JcampBaseConverter(jcamp_path)
+            metadata = None
+            if file_name in auto_metadata:
+                metadata = auto_metadata[file_name]
+
             if base_cv.typ == 'MS':
                 mscv = JcampMSConverter(base_cv)
                 mscp = MSComposer(mscv)
@@ -73,6 +77,7 @@ def __read(self, target_dir, fname):
                 list_csv.append(tf_csv)
             else:
                 nicv = JcampNIConverter(base_cv)
+                if nicv.auto_metadata == None: nicv.auto_metadata = metadata
                 nicp = NIComposer(nicv)
                 list_composer.append(nicp)
                 tf_jcamp = nicp.tf_jcamp()
@@ -84,7 +89,7 @@ def __read(self, target_dir, fname):
 
         combined_image = self.__combine_images(list_composer)
 
-        return list_files, list_images, list_csv, combined_image, auto_metadata
+        return list_files, list_images, list_csv, combined_image
 
     def get_base64_data(self):
         if self.data is None:

diff --git a/chem_spectra/lib/converter/fid/base.py b/chem_spectra/lib/converter/fid/base.py
@@ -77,6 +77,7 @@ def __set_properties(self):
         self.solv_peaks = []
         self.is_dept = self.__is_dept()
         self.__read_solvent()
+        self.auto_metadata = None
 
     def __is_em_wave(self):
         return self.typ in ['INFRARED', 'RAMAN', 'UVVIS']

diff --git a/chem_spectra/lib/converter/jcamp/base.py b/chem_spectra/lib/converter/jcamp/base.py
@@ -37,6 +37,7 @@ def __init__(self, path, params=False):
         self.solv_peaks = []
         self.is_dept = self.__is_dept()
         self.__read_solvent()
+        self.auto_metadata = self.__read_auto_metadata()
 
     def __read(self, path):
         return ng.jcampdx.read(path, show_all_data=True, read_err='ignore')
@@ -221,3 +222,15 @@ def __is_dept(self):
                 return True
 
         return False
+
+    def __read_auto_metadata(self):
+        target = self.dic.get('$CSAUTOMETADATA', [])
+        if target:
+            target = [t for t in target[0].split('\n')]
+            result = {}
+            for value in target:
+                splited = value.split('=')
+                if len(splited) > 1:
+                    result[splited[0]] = splited[1]
+            return result
+        return None
diff --git a/chem_spectra/lib/converter/jcamp/ms.py b/chem_spectra/lib/converter/jcamp/ms.py
@@ -25,6 +25,7 @@ def __init__(self, base):
         self.fname = base.fname
         self.runs, self.spectra, self.auto_scan = self.__read_mz_ml()
         self.datatables = self.__set_datatables()
+        self.auto_metadata = base.auto_metadata
 
     def __set_params(self, params):
         exact_mz = params.get('mass', 0) if params else 0

diff --git a/chem_spectra/lib/converter/jcamp/ni.py b/chem_spectra/lib/converter/jcamp/ni.py
@@ -71,6 +71,7 @@ def __init__(self, base):
         self.__read_integration_from_file()
         self.__read_multiplicity_from_file()
         self.__read_voltammetry_data_from_file()
+        self.auto_metadata = base.auto_metadata
 
     def __thres(self):
         dt = self.datatype

diff --git a/tests/fixtures/result/edit/edit_meta_13C-DEPT135 b/tests/fixtures/result/edit/edit_meta_13C-DEPT135
@@ -78,6 +78,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/edit/edit_meta_1H b/tests/fixtures/result/edit/edit_meta_1H
@@ -85,6 +85,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/edit/edit_meta_IR b/tests/fixtures/result/edit/edit_meta_IR
@@ -85,6 +85,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/im/im_meta_13C-DEPT135 b/tests/fixtures/result/im/im_meta_13C-DEPT135
@@ -56,4 +56,5 @@ $$ === CHEMSPECTRA PEAK TABLE EDIT ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
-##END=
+##$CSAUTOMETADATA=
+##END=
diff --git a/tests/fixtures/result/im/im_meta_1H b/tests/fixtures/result/im/im_meta_1H
@@ -147,6 +147,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/im/im_meta_IR b/tests/fixtures/result/im/im_meta_IR
@@ -143,6 +143,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/meta_13C-CPD b/tests/fixtures/result/meta_13C-CPD
@@ -95,6 +95,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/meta_13C-DEPT135 b/tests/fixtures/result/meta_13C-DEPT135
@@ -60,4 +60,5 @@ $$ === CHEMSPECTRA PEAK TABLE EDIT ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
diff --git a/tests/fixtures/result/meta_1H b/tests/fixtures/result/meta_1H
@@ -140,6 +140,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/meta_IR b/tests/fixtures/result/meta_IR
@@ -143,6 +143,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/meta_SVS-790A_13C b/tests/fixtures/result/meta_SVS-790A_13C
@@ -193,6 +193,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/fixtures/result/ps/ps_meta_IR b/tests/fixtures/result/ps/ps_meta_IR
@@ -146,6 +146,7 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 
 
 $$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
 ##END=
 
 ##END=

diff --git a/tests/lib/composer/test_base_composer.py b/tests/lib/composer/test_base_composer.py
@@ -22,15 +22,18 @@ def test_base_composer_generate_auto_metadata_headers(jcamp_file_1h):
     assert headers == [
       '\n',
       '$$ === CHEMSPECTRA AUTO METADATA ===\n',
+      '##$CSAUTOMETADATA=\n',
     ]
 
 def test_base_composer_generate_auto_metadata(jcamp_file_1h):
     base_converter = JcampBaseConverter(jcamp_file_1h)
     metadata = {"just a string": "just a string value"}
-    composer = BaseComposer(core=base_converter, auto_metadata=metadata)
+    base_converter.auto_metadata = metadata
+    composer = BaseComposer(core=base_converter)
     auto_metadata = composer.generate_auto_metadata()
     assert auto_metadata == [
       '\n',
       '$$ === CHEMSPECTRA AUTO METADATA ===\n',
-      '##JUST A STRING=just a string value\n'
+      '##$CSAUTOMETADATA=\n',
+      'JUST A STRING=just a string value\n'
     ]
diff --git a/tests/lib/composer/test_ni_composer.py b/tests/lib/composer/test_ni_composer.py
@@ -40,20 +40,23 @@ def test_init_ni_composer_success(jcamp_file_1h):
 
 def test_init_ni_composer_success_with_auto_metadata(jcamp_file_1h, auto_metadata_dic):
     base_converter = JcampBaseConverter(jcamp_file_1h)
+    base_converter.auto_metadata = auto_metadata_dic
     ni_converter = JcampNIConverter(base=base_converter)
-    ni_composer = NIComposer(core=ni_converter, auto_metadata=auto_metadata_dic)
+    ni_composer = NIComposer(core=ni_converter)
 
     assert ni_composer is not None
-    assert ni_composer.auto_metadata == auto_metadata_dic
+    assert ni_composer.core.auto_metadata == auto_metadata_dic
 
 def test_composer_auto_metadata(jcamp_file_1h, auto_metadata_dic):
     base_converter = JcampBaseConverter(jcamp_file_1h)
+    base_converter.auto_metadata = auto_metadata_dic
     ni_converter = JcampNIConverter(base=base_converter)
-    ni_composer = NIComposer(core=ni_converter, auto_metadata=auto_metadata_dic)
+    ni_composer = NIComposer(core=ni_converter)
 
     assert ni_composer is not None
     assert '$$ === CHEMSPECTRA AUTO METADATA ===\n' in ni_composer.meta
-    assert '##TEST_KEY=just a string value\n' in ni_composer.meta
+    assert '##$CSAUTOMETADATA=\n' in ni_composer.meta
+    assert 'TEST_KEY=just a string value\n' in ni_composer.meta
 
 def test_ni_composer_header(jcamp_file_1h):
     base_converter = JcampBaseConverter(jcamp_file_1h)

diff --git a/tests/lib/converter/bagit/test_bagit_base_converter.py b/tests/lib/converter/bagit/test_bagit_base_converter.py
@@ -27,7 +27,6 @@ def test_bagit_converter_failed():
     assert converter.images is None
     assert converter.list_csv is None
     assert converter.combined_image is None
-    assert converter.auto_metadata is None
 
 def test_bagit_convert_to_jcamp():
     with tempfile.TemporaryDirectory() as td:
@@ -118,8 +117,6 @@ def test_get_base64_data_succeed():
         converter = BagItConveter(td)
         list_base64 = converter.get_base64_data()
         assert len(list_base64) == 3
-        for base64Str in list_base64:
-            assert base64Str.endswith("=")
 
 def test_get_combined_image_failed():
     converter = BagItConveter(None)
@@ -134,16 +131,3 @@ def test_get_combined_image():
         converter = BagItConveter(td)
         combined_image = converter.combined_image
         assertFileType(combined_image, 'image/png')
-
-def test_get_metadata():
-    with open(aif_auto_metadata_path, 'r') as f:
-        expected_metadata = json.loads(f.read())
-
-    with tempfile.TemporaryDirectory() as td:
-        with zipfile.ZipFile(aif_layout_path, 'r') as z:
-            z.extractall(td)
-
-        converter = BagItConveter(td)
-        auto_metadata = converter.auto_metadata
-        assert auto_metadata is not None
-        assert auto_metadata == expected_metadata