Add ability to rewrite preset settings

lszeremeta · Apr 16, 2021 · f02facf · f02facf
1 parent 68a3cfe
commit f02facf
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Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -65,7 +65,7 @@ usage: molstruct [-h] [--version] -f {jsonldhtml,jsonld,rdfa,microdata} [-i IDEN
                  [-iu IUPACNAME] [-mf MOLECULARFORMULA] [-w MOLECULARWEIGHT]
                  [-mw MONOISOTOPICMOLECULARWEIGHT] [-d DESCRIPTION]
                  [-dd DISAMBIGUATINGDESCRIPTION] [-img IMAGE] [-an ALTERNATENAME]
-                 [-sa SAMEAS] [-p {drugbank-open}] [-c] [-s {iri,uuid,bnode}] [-b BASE]
+                 [-sa SAMEAS] [-p {drugbank-open} | -c] [-s {iri,uuid,bnode}] [-b BASE]
                  [-vd VALUE_DELIMITER] [-l LIMIT]
                  file
 ```
@@ -107,7 +107,7 @@ Arguments for changing the default column names
 ### Additional settings arguments
 
 * `-p {drugbank-open}`, `--preset {drugbank-open}` apply presets for individual CSV sources to avoid setting individual options manually ('drugbank-open' - [DrugBank CC0 Open Data dataset](https://go.drugbank.com/releases/latest#open-data))
-* `-c`, `--columns` use only columns with renamed names
+* `-c`, `--columns` use only columns with renamed names; not available when using a preset
 * `-s {iri,uuid,bnode}`, `--subject {iri,uuid,bnode}` molecule subject type ('iri' by default)
 * `-b BASE`, `--base BASE` molecule subject base for 'iri' subject type ('http://example.com/molecule#entity' by default)
 * `-vd VALUE_DELIMITER`, `--value-delimiter VALUE_DELIMITER` value delimiter (' | ' by default)

diff --git a/molstruct/__main__.py b/molstruct/__main__.py
@@ -63,11 +63,12 @@ def main():
                               help="sameAs column name ('" + n.COLUMNS['sameAs'] + "' by default), URL")
 
     additional_settings = parser.add_argument_group('Additional settings arguments')
-    additional_settings.add_argument("-p", "--preset", choices=['drugbank-open'],
-                                     help="apply presets for individual CSV sources to avoid setting individual options manually ('drugbank-open' - DrugBank CC0 Open Data dataset)")
-    additional_settings.add_argument("-c", "--columns",
-                                     help="use only columns with renamed names",
-                                     action="store_true")
+    additional_exclusive = additional_settings.add_mutually_exclusive_group()
+    additional_exclusive.add_argument("-p", "--preset", choices=['drugbank-open'],
+                                      help="apply presets for individual CSV sources to avoid setting individual options manually ('drugbank-open' - DrugBank CC0 Open Data dataset)")
+    additional_exclusive.add_argument("-c", "--columns",
+                                      help="use only columns with renamed names; not available when using a preset",
+                                      action="store_true")
     additional_settings.add_argument("-s", "--subject", choices=['iri', 'uuid', 'bnode'], default='iri',
                                      help="molecule subject type ('iri' by default)")
     additional_settings.add_argument("-b", "--base", type=str,
@@ -80,12 +81,11 @@ def main():
 
     # set presets
     if args.preset == 'drugbank-open':
-        args.value_delimiter = ' | '
-        args.columns = True
-        args.identifier = 'CAS'
-        args.name = 'Common name'
-        args.inChIKey = 'Standard InChI Key'
-        args.alternateName = 'Synonyms'
+        n.VALUE_DELIMITER = ' | '
+        n.COLUMNS['identifier'] = 'CAS'
+        n.COLUMNS['name'] = 'Common name'
+        n.COLUMNS['inChIKey'] = 'Standard InChI Key'
+        n.COLUMNS['alternateName'] = 'Synonyms'
 
     # replace default base molecule IRI
     if args.base: