Merge pull request #243 from ARGA-Genomes/rowFinder

Row Finder

Author: christopher-mangion

src/tools/rowFinder.py

@@ -0,0 +1,40 @@
+from lib.data.argParser import ArgParser
+from lib.processing.files import Step
+import pandas as pd
+
+if __name__ == '__main__':
+    parser = ArgParser(description="Get column examples of pre-Conversion files")
+    parser.addArgument("column", type=str, help="Column name to search")
+    parser.addArgument("values", type=str, nargs="*", help="Value to check for in column")
+    parser.addArgument('-c', '--chunksize', type=int, default=1024, help="File chunk size to read at a time")
+
+    sources, flags, args = parser.parseArgs()
+
+    for source in sources:
+        source._prepare(Step.PROCESSING, flags)
+        stageFile = source.processingManager.getLatestNodeFile() # Should be singular stage file before DwC
+
+        if not stageFile.exists():
+            print(f"File {stageFile.path} does not exist, please run all required downloading/processing.")
+            continue
+
+        if args.column not in stageFile.getColumns():
+            print(f"Column '{args.column}' does not exists in file")
+            continue
+
+        foundRows = []
+        for idx, df in enumerate(stageFile.readIterator(args.chunksize, on_bad_lines="skip"), start=1):
+            print(f"At chunk: {idx}", end="\r")
+
+            df = df[df[args.column].isin(args.values)]
+            if df.empty:
+                continue
+
+            foundRows.append(df)
+
+        if not foundRows:
+            print("\nNo rows found")
+            continue
+
+        print()
+        print(pd.concat(foundRows))