Merge pull request #121 from ComPlat/100-new-powerxrd-reader

100 new powerxrd reader

Author: StarmanMartin

.github/workflows/pylint.yml

@@ -16,7 +16,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        pip install wheel setuptools pip pybind11 --upgrade
         pip install -r ./requirements/dev.txt
         pip install pylint
     - name: Analysing the code with pylint

.github/workflows/pytest.yml

@@ -9,20 +9,19 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r ./requirements/dev.txt
-        pip install pytest
-    - name: Build tests
-      run: |
-        python test_manager/__init__.py -t -g -tp
-    - name: Test the code with pytest
-      run: |
-        pytest ./test_manager/test_profiles.py
-        pytest ./test_manager/test_readers.py
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install wheel setuptools pip pybind11 --upgrade
+          pip install -r ./requirements/dev.txt
+          pip install pytest
+      - name: Build tests
+        run: |
+          python test_manager/__init__.py -t -g -tp
+      - name: Test the code with pytest
+        run: |
+          pytest .

converter_app/converters.py

@@ -1,4 +1,5 @@
 import copy
+import datetime
 import logging
 import os
 import re
@@ -364,15 +365,21 @@ def match_profile(cls, client_id, file_data):
         """
         converter = None
         matches = 0
-
+        latest_profile_uploaded = 0
         for profile in Profile.list(client_id):
             current_converter = cls(profile, file_data)
             current_matches = current_converter.match()
-
+            try:
+                profile_uploaded = datetime.datetime.fromisoformat(
+                    profile.as_dict['data']['metadata'].get('uploaded')).timestamp()
+            except (ValueError, TypeError):
+                profile_uploaded = 1
             logger.info('profile=%s matches=%s', profile.id, current_matches)
-
-            if current_matches is not False and current_matches > matches:
+            if (current_matches is not False and
+                    (current_matches > matches or current_matches == matches and
+                    profile_uploaded > latest_profile_uploaded)):
+                matches = max(matches, current_matches)
+                latest_profile_uploaded = profile_uploaded
                 converter = current_converter
-                matches = current_matches
 
         return converter

converter_app/models.py

@@ -163,7 +163,7 @@ def list(cls, client_id):
         profiles_path = Path(current_app.config['PROFILES_DIR']).joinpath(client_id)
 
         if profiles_path.exists():
-            for file_path in Path.iterdir(profiles_path):
+            for file_path in sorted(Path.iterdir(profiles_path)):
                 profile_id = str(file_path.with_suffix('').name)
                 profile_data = cls.load(file_path)
                 yield cls(profile_data, client_id, profile_id)

converter_app/readers/ascii.py

@@ -46,7 +46,7 @@ def prepare_tables(self):
                 row = row.replace('n.a.', '')
                 float_match = self.float_pattern.findall(row)
                 if float_match:
-                    float_match = [self.get_value(float_str) for float_str in float_match]
+                    float_match = [self.get_value(float_str.strip()) for float_str in float_match]
                     count = len(float_match)
 
                     if table['rows'] and count != previous_count:

converter_app/readers/helper/base.py

@@ -19,6 +19,15 @@ def __init__(self):
             'rows': []
         })
 
+    def add_metadata(self, key, value):
+        """
+        Add metadata to table
+        :param key: Key of the metadata
+        :param value: Value of the metadata
+        :return:
+        """
+        self['metadata'].add_unique(key, value)
+
     def __add__(self, other):
         raise NotImplementedError
 
@@ -47,7 +56,7 @@ class Reader:
     """
     Base reader. Any reader needs to extend this abstract reader.
     """
-    float_pattern = re.compile(r'(-?\d+[,.]*\d*[eE+\-\d]*)\S*')
+    float_pattern = re.compile(r'[-+]?[0-9]*[.,]?[0-9]+(?:[eE][-+]?[0-9]+)?\s*')
     float_de_pattern = re.compile(r'(-?[\d.]+,\d*[eE+\-\d]*)')
     float_us_pattern = re.compile(r'(-?[\d,]+.\d*[eE+\-\d]*)')
 
@@ -117,7 +126,7 @@ def get_tables(self) -> list[Table]:
                         'name': f'Column #{idx + start_len_c}'
                     } for idx, value in enumerate(table['rows'][0][start_len_c:])]
                     table['columns'] = sorted(table['columns'], key=lambda x: int(x['key']))
-                for k,v in enumerate(table['columns'][:should_len_c]):
+                for k, v in enumerate(table['columns'][:should_len_c]):
                     v['key'] = f'{k}'
 
             table['metadata']['rows'] = str(len(table['rows']))
@@ -168,13 +177,25 @@ def get_shape(self, row) -> list:
                 cell = str(cell).strip()
                 if cell in self.empty_values:
                     shape.append('')
-                elif self.float_pattern.match(cell):
+                elif self.float_pattern.fullmatch(cell):
                     shape.append('f')
                 else:
                     shape.append('s')
 
         return shape
 
+    def as_number(self, value: str) -> float | int:
+        """
+        Returns a numeric value if possible:
+
+        :raises ValueError: If not convertable
+        :param value: as string
+        :return: numeric value either int or float
+        """
+        if re.match(r'^[+-]?\d+$', value) is not None:
+            return int(value)
+        return float(self.get_value(value))
+
     def get_value(self, value: str) -> str:
         """
         Checks if values is a stringified float and makes it to a standard.

converter_app/readers/uxd_reader.py

@@ -0,0 +1,87 @@
+import logging
+
+from converter_app.models import File
+from converter_app.readers.helper.reader import Readers
+from converter_app.readers.helper.base import Reader
+
+logger = logging.getLogger(__name__)
+
+
+class UXDReader(Reader):
+    """
+    Reader for UDX files. Files from: Powder Diffraction -  Diffrac Plus
+
+    Test File: test_files/data_files/Powder Diffraction/Diffrac Plus/XCH-UXD/PD-01-02(2).UXD
+    """
+
+    identifier = 'uxd_reader'
+    priority = 10
+
+    def __init__(self, file: File):
+        super().__init__(file)
+        self._file_extensions = ['.uxd']
+        self._table = None
+        self._version = 2
+        self._max_table_length = 0
+
+    def check(self):
+        return self.file.suffix.lower() in self._file_extensions
+
+    def _read_data(self, line: str):
+        if self._version == 2:
+            try:
+                new_row = [self.as_number(x.strip()) for x in line.split(' ') if x != '']
+                if len(new_row) > 0:
+                    self._max_table_length = max(self._max_table_length, len(new_row))
+                    self._table['rows'].append(new_row)
+            except ValueError:
+                pass
+        elif self._version == 3:
+            try:
+                value = [self.as_number(x.strip()) for x in line.split('\t')]
+                self._table['rows'].append([value[0], value[1]])
+            except ValueError:
+                pass
+
+    def _add_metadata(self, key, val):
+        if self.float_pattern.fullmatch(val):
+            val = self.get_value(val)
+        self._table.add_metadata(key, val)
+
+    def prepare_tables(self):
+        tables = []
+        self._table = self.append_table(tables)
+        data_rows = []
+        for row in self.file.fp.readlines():
+            line = row.decode(self.file.encoding).rstrip()
+
+            if len(line) > 1 and (line[0] == '_' or line[0] == ';'):
+                self._table['header'].append(line)
+                if line[0] == '_' and line[1] != '+' and '=' in line:
+                    data = line.split('=')
+                    key = data[0].strip()[1:]
+                    value = data[1].strip().replace('\n', '')
+                    self._add_metadata(key, value)
+            else:
+                data_rows.append(line)
+        try:
+            self._version = int(self._table['metadata'].get('FILEVERSION'))
+        except ValueError:
+            self._version = 0
+
+        for row in data_rows:
+            self._read_data(row)
+
+        for row in self._table['rows']:
+            while len(row) < self._max_table_length:
+                row.append('')
+
+        if 'START' in self._table['metadata'] and 'STEPSIZE' in self._table['metadata']:
+            end = self.as_number(self._table['metadata']['START']) + (
+                        self.as_number(self._table['metadata']['STEPSIZE']) * (len(self._table['rows']) - 1))
+            self._table.add_metadata("END", end)
+
+        return tables
+
+
+Readers.instance().register(UXDReader)

converter_app/readers/xml_reader.py

@@ -0,0 +1,125 @@
+import logging
+
+import xml.etree.ElementTree as ET
+
+from converter_app.models import File
+from converter_app.readers.helper.reader import Readers
+from converter_app.readers.helper.base import Reader
+
+logger = logging.getLogger(__name__)
+
+
+class XMLReader(Reader):
+    """
+    Reader for XML files.
+    """
+
+    identifier = 'xml_reader'
+    priority = 10
+
+    def __init__(self, file: File):
+        super().__init__(file)
+        self._file_extensions = ['.xml']
+        self._table = None
+        self._data_tables = []
+        self._potential_data_tables = {}
+
+    def check(self):
+        return self.file.suffix.lower() in self._file_extensions
+
+    def _get_tag_name(self, node:  ET.Element):
+        return node.tag.split('}', 1)[-1]
+
+
+    def _filter_data_rows(self, node:  ET.Element, text: str, xml_path: str) -> bool:
+        text_array = [x for x in text.strip().split(' ') if x != '']
+        shape = self.get_shape(text_array)
+        if all(x == 'f' for x in shape) and len(shape) > 1:
+            self._data_tables.append(self._generate_data_table(shape, xml_path, text_array, node))
+            return True
+        return False
+
+    def _generate_data_table(self, shape: list[str], xml_path: str, text_array: list[str], node: ET.Element):
+        return {
+            'shape': ''.join(shape),
+            'path': xml_path,
+            'values': [self.as_number(x) for x in text_array],
+            'node': node
+        }
+
+    def handle_node(self, node:  ET.Element, xml_path: str, node_name: str):
+        """
+        This method can be overridden to handle special nodes separately.
+
+        :param node: XML node Object
+        :param xml_path: Path in global XML-file to this node
+        :param node_name: Name of the Node
+        """
+        pass
+
+    def _add_metadata(self, key: str, val: any, node: ET.Element):
+        m = self.float_pattern.fullmatch(val)
+        if key in self._potential_data_tables:
+            if m and  self._potential_data_tables[key] is not None:
+                self._potential_data_tables[key]['values'].append(self.as_number(val))
+                self._potential_data_tables[key]['shape'] += 'f'
+            else:
+                self._potential_data_tables[key] = None
+        elif m:
+            self._potential_data_tables[key] = self._generate_data_table(['f'], key, [val], node)
+        self._table.add_metadata(key, val)
+
+    def _read_node(self, node: ET.Element, xml_path: str = '#'):
+        for child in node:
+            text = child.text
+
+            try:
+                local_name = self._get_tag_name(child)
+                new_path = f'{xml_path}.{local_name}'
+            except ValueError:
+                new_path = 'Unknown'
+                local_name = ''
+
+            self.handle_node(child, xml_path, local_name)
+
+            if text is not None and not self._filter_data_rows(child, text, new_path):
+                self._add_metadata(new_path, text.strip(), node)
+            for k, v in child.attrib.items():
+                self._add_metadata(f'{new_path}.{k}', v, node)
+
+            self._read_node(child, new_path)
+
+    def prepare_tables(self):
+        tables = []
+        self._table = self.append_table(tables)
+        root = ET.XML(self.file.content)
+        self._read_node(root)
+        self._merge_tables(self._data_tables, tables)
+
+        potential_tables = [x for k, x in self._potential_data_tables.items() if len(x['values']) > 1]
+        potential_tables.sort(key= lambda x : len(x['values']))
+        self._merge_tables(potential_tables, tables)
+
+
+        return tables
+
+    def _merge_tables(self, data_tables: list, tables):
+        current_shape = ''
+        for table_col in data_tables:
+            if current_shape != table_col['shape']:
+                current_shape = table_col['shape']
+                self._table = self.append_table(tables)
+                self._table['rows'] = [[] for x in range(len(table_col['values']))]
+
+            tag_name = self._get_tag_name(table_col['node'])
+            self._table.add_metadata(f"COL #{len(self._table['rows'][0])}", tag_name)
+            self._table.add_metadata(f"COL #{len(self._table['rows'][0])} XML PATH", table_col['path'])
+
+            for i, v in enumerate(table_col['values']):
+                self._table['rows'][i].append(v)
+
+            for k, v in table_col['node'].attrib.items():
+                self._table.add_metadata(f'{tag_name}.{k}', v)
+
+
+Readers.instance().register(XMLReader)