Closed yoavnash closed 1 year ago
The line from data2rdf.annotation_pipeline import AnnotationPipeline generates the following error:
from data2rdf.annotation_pipeline import AnnotationPipeline
--------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) Cell In[4], line 1 ----> 1 from data2rdf.annotation_pipeline import AnnotationPipeline File /opt/conda/lib/python3.10/site-packages/data2rdf/annotation_pipeline.py:13 11 from data2rdf.excel_parser import ExcelParser 12 from data2rdf.mapper import Mapper, merge_same_as_individuals ---> 13 from data2rdf.rdf_generation import RDFGenerator 15 parser_choice = { 16 "csv": CSVParser, 17 "excel": ExcelParser, 18 } 21 class AnnotationPipeline: File /opt/conda/lib/python3.10/site-packages/data2rdf/rdf_generation.py:7 4 from rdflib import Graph 6 from data2rdf.annotation_confs import annotations ----> 7 from data2rdf.emmo_lib import emmo_utils 10 class RDFGenerator: 12 """ 13 Transforms the generic excel sheet to RDF 14 """ File /opt/conda/lib/python3.10/site-packages/data2rdf/emmo_lib/emmo_utils.py:6 2 import os 4 import pandas as pd ----> 6 unit_df = pd.read_csv( 7 os.path.join(os.path.dirname(os.path.abspath(__file__)), "emmo_units.csv"), 8 index_col=0, 9 ) 10 prefix_df = pd.read_csv( 11 os.path.join( 12 os.path.dirname(os.path.abspath(__file__)), "emmo_unit_prefixes.csv" 13 ), 14 index_col=0, 15 ) 18 def simple_unit_lookup(parsed_unit): File /opt/conda/lib/python3.10/site-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.<locals>._deprecate_kwarg.<locals>.wrapper(*args, **kwargs) 209 else: 210 kwargs[new_arg_name] = new_arg_value --> 211 return func(*args, **kwargs) File /opt/conda/lib/python3.10/site-packages/pandas/util/_decorators.py:331, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs) 325 if len(args) > num_allow_args: 326 warnings.warn( 327 msg.format(arguments=_format_argument_list(allow_args)), 328 FutureWarning, 329 stacklevel=find_stack_level(), 330 ) --> 331 return func(*args, **kwargs) File /opt/conda/lib/python3.10/site-packages/pandas/io/parsers/readers.py:950, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options) 935 kwds_defaults = _refine_defaults_read( 936 dialect, 937 delimiter, (...) 946 defaults={"delimiter": ","}, 947 ) 948 kwds.update(kwds_defaults) --> 950 return _read(filepath_or_buffer, kwds) File /opt/conda/lib/python3.10/site-packages/pandas/io/parsers/readers.py:605, in _read(filepath_or_buffer, kwds) 602 _validate_names(kwds.get("names", None)) 604 # Create the parser. --> 605 parser = TextFileReader(filepath_or_buffer, **kwds) 607 if chunksize or iterator: 608 return parser File /opt/conda/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1442, in TextFileReader.__init__(self, f, engine, **kwds) 1439 self.options["has_index_names"] = kwds["has_index_names"] 1441 self.handles: IOHandles | None = None -> 1442 self._engine = self._make_engine(f, self.engine) File /opt/conda/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1735, in TextFileReader._make_engine(self, f, engine) 1733 if "b" not in mode: 1734 mode += "b" -> 1735 self.handles = get_handle( 1736 f, 1737 mode, 1738 encoding=self.options.get("encoding", None), 1739 compression=self.options.get("compression", None), 1740 memory_map=self.options.get("memory_map", False), 1741 is_text=is_text, 1742 errors=self.options.get("encoding_errors", "strict"), 1743 storage_options=self.options.get("storage_options", None), 1744 ) 1745 assert self.handles is not None 1746 f = self.handles.handle File /opt/conda/lib/python3.10/site-packages/pandas/io/common.py:856, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options) 851 elif isinstance(handle, str): 852 # Check whether the filename is to be opened in binary mode. 853 # Binary mode does not support 'encoding' and 'newline'. 854 if ioargs.encoding and "b" not in ioargs.mode: 855 # Encoding --> 856 handle = open( 857 handle, 858 ioargs.mode, 859 encoding=ioargs.encoding, 860 errors=errors, 861 newline="", 862 ) 863 else: 864 # Binary mode 865 handle = open(handle, ioargs.mode) FileNotFoundError: [Errno 2] No such file or directory: '/opt/conda/lib/python3.10/site-packages/data2rdf/emmo_lib/emmo_units.csv'
By examining the folder /opt/conda/lib/python3.10/site-packages/data2rdf/emmo_lib/, this file is indeed missing:
/opt/conda/lib/python3.10/site-packages/data2rdf/emmo_lib/
The line
from data2rdf.annotation_pipeline import AnnotationPipeline
generates the following error:By examining the folder![image](https://user-images.githubusercontent.com/62147380/236252242-d1995c1b-ab16-4ebe-a8a5-9951ccf8ba26.png)
/opt/conda/lib/python3.10/site-packages/data2rdf/emmo_lib/
, this file is indeed missing: