Moving tools out of submodules (sorry!)

1 files changed, 0 insertions, 97 deletions

diff --git a/workflows/tools/normalize-yamlfa.py b/workflows/tools/normalize-yamlfa.py
deleted file mode 100755
index 55a8848..0000000
--- a/workflows/tools/normalize-yamlfa.py
+++ /dev/null
@@ -1,97 +0,0 @@
-# --- Normalize data
-# normalize-yamlfa.py [--yaml] --in ~/tmp/pubseq/state.json file(s)
-#
-# Example:
-#
-#    python3 ./workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --species ncbi_host_species.csv --specimen specimen.csv --validate
-
-import argparse
-import json
-import os
-import sys
-import types
-import normalize.mapping as mapping
-
-parser = argparse.ArgumentParser(description="""
-
-Normalize parameters in PubSeq JSON/YAML files. All entries in
-directory are parsed using the state.json file. It is possible
-to select a subset of IDs.
-
-This tool has two modes of operation. It can validate with the
---validate switch which stops at a warning and does no rewriting.
-This mode is typically used in troubleshooting.
-
-The other mode is --rewrite which rewrites the JSON files after
-making a backup (.bak) of the original. This mode updates files and
-won't stop - it is used for (automated) uploads.
-
-""")
-
-parser.add_argument('-s','--state', type=str, help='State file (JSON) as produced by transform2yamlfa', required=True)
-parser.add_argument('--species', type=str, help='Species mapping file')
-parser.add_argument('--specimen', type=str, help='Optional specimen mapping file')
-parser.add_argument('--validate', action='store_true', help='Validation mode - stops on warning')
-parser.add_argument('--rewrite', action='store_true', help='Rewrite mode - updates files')
-parser.add_argument('--yaml', action='store_true', help='Input YAML instead of JSON')
-parser.add_argument('id', nargs='*', help='optional id(s)')
-
-args = parser.parse_args()
-
-with open(args.state) as jsonf:
-    data = json.load(jsonf)
-
-dir = os.path.dirname(args.state)
-do_validate = args.validate
-do_rewrite = args.rewrite
-
-ids = args.id
-if not len(ids):
-    ids = list(data.keys())
-
-species = {}
-if args.species:
-    with open(args.species) as f:
-        for line in f:
-            name,uri = line.strip().split(',')
-            species[name] = uri
-else:
-    print("WARNING: no species mapping",file=sys.stderr)
-specimen = {}
-if args.specimen:
-    with open(args.specimen) as f:
-        for line in f:
-            name,uri = line.strip().split(',')
-            specimen[name] = uri
-else:
-    print("WARNING: no specimen mapping",file=sys.stderr)
-
-for id in ids:
-    if args.yaml:
-        raise Exception("YAML not yet supported")
-    fn = f"{dir}/{id}.json"
-    print(f"Reading {fn}",file=sys.stderr)
-    with open(fn) as f:
-        rec = types.SimpleNamespace(**json.load(f))
-        if do_validate:
-            print(rec)
-        rec.host,warning = mapping.host_species(rec.host,species)
-        if warning:
-            print("WARNING "+warning,file=sys.stderr)
-            rec.warnings.append(warning)
-        rec.sample,warning = mapping.specimen_source(rec.sample,specimen)
-        if warning:
-            print("WARNING "+warning,file=sys.stderr)
-            rec.warnings.append(warning)
-        print(rec)
-        if do_validate and warning:
-            print("bailing out in validation mode",file=sys.stderr)
-            sys.exit(2)
-        if do_rewrite:
-            if not os.path.exists(fn+".bak"): # make backup the first time
-                os.rename(fn,fn+".bak")
-            with open(fn, 'w') as outfile:
-                print(f"    Writing {fn}")
-                json.dump(rec.__dict__, outfile, indent=2)
-        else:
-            print(rec)