add back old mapping tools

scripts/ontology_to_ontology_mapping_tool/README.md

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+## Ontology to Ontology Mapping Tool
+
+The Ontology Mapping tool was developed to facilitate the mapping between different cancer classification systems. We currently support mapping between OncoTree, ICD-O, NCIt, UMLS and HemeOnc systems.
+
+### Prerequisites
+The Ontology Mapping tool runs on python 3 and requires `pandas` and `requests` libraries. These libraries can be installed using
+```
+pip3 install pandas
+pip3 install requests
+ ```
+
+### Running the tool
+
+The tool can be run with the following command:
+```
+python <path/to/scripts/ontology_to_ontology_mapping_tool.py> --source-file <path/to/source/file> --target-file <path/to/target/file> --source-code <source_ontology_code> --target-code <target_ontology_code>
+```
+
+**Options**
+```
+ -i | --source-file: This is the source file path. The source file must contain one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header and it must contain codes corresponding to the Ontology System.
+ -o | --target-file: This is the path to the target file that will be generated. It will contain ontologies mapped from source code in <source-file> to <target-code>.
+ -s | --source-code: This is the source ontology code in <source-file>. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
+ -t | --target-code: This is the target ontology code that the script will attempt to map the source file ontology code to. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
+```
+
+**Note**
+- The source file should be tab delimited and should contain one of the ontology: ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header.
+- We currently are allowing only one ontology to another ontology mapping. In the future, we plan to extend the tool to support mapping to multiple ontology systems.

scripts/ontology_to_ontology_mapping_tool/file_comparison/README.md

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+## Ontology to Ontology Mapping Tool
+
+This tool helps compare existing OncoTree mapped ontologies against a reference OncoTree Codes file, and gives an output file named "missing_oncotree_codes.xlsx" that consist of a list of OncoTree codes that are missing from the inputted file. In order to use this tool, you must:
+1.	Download the 'refrence_oncotree_codes.xlsx' file 
+2.	Input an excel file that consists of OncoTree codes in column 1 and other ontology codes (UMLS, NCIT, SNOMED, ICDO Topography, HEMEONC, or ICDO Morphology) in the other columns. 
+
+This tool MUST consist of OncoTree codes in column 1 to compare the two files. The output file will only give OncoTree codes that are missing from the file you inputted.

scripts/ontology_to_ontology_mapping_tool/file_comparison/file_comparison.py

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+import pandas as pd
+import os
+
+file_a = pd.read_excel("reference_oncotree_codes.xlsx")
+oncotree_codes_a = file_a.iloc[:, 0].dropna()
+
+while True:
+    file_b = input("Enter name of the file in an Excel format ('.xlsx')")
+    if '.xlsx' not in file_b:
+        print("You forgot to add '.xlsx'. Please try again and add the required '.xlsx'.")
+    elif '.xlsx' in file_b:
+        if os.path.exists(file_b):
+            file_b = pd.read_excel(file_b)
+            file_b = file_b.astype(str)
+            file_b.replace({'': pd.NA}, inplace=True)
+            oncotree_codes_b = file_b.iloc[:, 0].dropna()
+
+            missing_codes = oncotree_codes_a[~oncotree_codes_a.isin(oncotree_codes_b)]
+
+            print("The following OncoTree codes from File A are NOT found in File B:")
+            for code in missing_codes:
+                print("-", code)
+
+
+            output_df = missing_codes
+            output_file_path = "missing_oncotree_codes.xlsx"
+            output_df.to_excel(output_file_path, index=False)
+        else:
+            print("This file does not exist in your folders. Try transferring the excel file into the same folder as where this code is in")