baseURI -> subject-base

lszeremeta · Mar 29, 2021 · 06b2741 · 06b2741
1 parent c1ef89c
commit 06b2741
Show file tree

Hide file tree

Showing 4 changed files with 16 additions and 16 deletions.
diff --git a/README.md b/README.md
@@ -93,7 +93,7 @@ In this case, your local directory `/home/user/input` has been mounted under `/a
                      [-mf MOLECULARFORMULA] [-w MOLECULARWEIGHT]
                      [-mw MONOISOTOPICMOLECULARWEIGHT] [-d DESCRIPTION]
                      [-dd DISAMBIGUATINGDESCRIPTION] [-img IMAGE] [-an ALTERNATENAME]
-                     [-sa SAMEAS] [-p {drugbank}] [-c] [-b BASEURI] [-vd VALUE_DELIMITER]
+                     [-sa SAMEAS] [-p {drugbank}] [-c] [-b SUBJECT_BASE] [-vd VALUE_DELIMITER]
                      [-l LIMIT]
                      file
 
@@ -135,9 +135,9 @@ Arguments for changing the default column names
 
 * `-p {drugbank}`, `--preset {drugbank}` apply presets for individual CSV sources to avoid setting individual options manually
 * `-c, --columns` use only columns with renamed names
-* `-b BASEURI`, `--baseURI BASEURI` base URI of molecule ('http://example.com/molecule#' by default)
+* `-b SUBJECT_BASE`, `--subject-base SUBJECT_BASE` subject base of molecule ('http://example.com/molecule#entity' by default)
 * `-vd VALUE_DELIMITER`, `--value-delimiter VALUE_DELIMITER` value delimiter (' | ' by default)
-* `-l LIMIT`, `--limit LIMIT` maximum number of results
+* `-l LIMIT`, `--limit LIMIT` maximum number of results (unlimited by default)
 
 Available options may vary depending on the version. To display all available options with their descriptions use ``molstruct -h``.
 

diff --git a/molstruct/__main__.py b/molstruct/__main__.py
@@ -68,11 +68,11 @@ def main():
     additional_settings.add_argument("-c", "--columns",
                                      help="use only columns with renamed names",
                                      action="store_true")
-    additional_settings.add_argument("-b", "--baseURI", type=str,
-                                     help="base URI of molecule ('" + n.BASE_URI_MOLECULE + "' by default)")
+    additional_settings.add_argument("-b", "--subject-base", type=str,
+                                     help="subject base of molecule ('" + n.SUBJECT_BASE + "' by default)")
     additional_settings.add_argument("-vd", "--value-delimiter", type=str,
                                      help="value delimiter ('" + n.VALUE_DELIMITER + "' by default)")
-    additional_settings.add_argument("-l", "--limit", type=int, help="maximum number of results")
+    additional_settings.add_argument("-l", "--limit", type=int, help="maximum number of results (unlimited by default)")
 
     args = parser.parse_args()
 
@@ -87,7 +87,7 @@ def main():
 
     # replace default base molecule URI
     if args.baseURI:
-        n.BASE_URI_MOLECULE = args.baseURI
+        n.SUBJECT_BASE = args.baseURI
 
     # replace default value delimiter
     if args.value_delimiter:

diff --git a/molstruct/names.py b/molstruct/names.py
@@ -3,8 +3,8 @@
 # default value delimiter
 VALUE_DELIMITER = ' | '
 
-# default base URI of molecule
-BASE_URI_MOLECULE = 'http://example.com/molecule#entity'
+# default subject base of molecule
+SUBJECT_BASE = 'http://example.com/molecule#entity'
 
 # column names
 COLUMNS = {'identifier': 'identifier',

diff --git a/molstruct/outputs.py b/molstruct/outputs.py
@@ -24,7 +24,7 @@ def jsonld(reader, limit):
     out_str += '  "@graph" : [\n'
     for row in reader:
         out_str += '  {\n'
-        out_str += '  "@id" : ' + json.dumps(n.BASE_URI_MOLECULE + str(i)) + ',\n'
+        out_str += '  "@id" : ' + json.dumps(n.SUBJECT_BASE + str(i)) + ',\n'
         out_str += '  "@type" : "https://schema.org/MolecularEntity",\n'
 
         for key, value in n.COLUMNS.items():
@@ -103,11 +103,11 @@ def rdfa(reader, limit):
   </head>
   <body vocab="http://schema.org/">''')
     for row in reader:
-        print('    <div typeof="schema:MolecularEntity" about="' + html.escape(n.BASE_URI_MOLECULE + str(
+        print('    <div typeof="schema:MolecularEntity" about="' + html.escape(n.SUBJECT_BASE + str(
             i), quote=True), end='')
 
-        if '#' in n.BASE_URI_MOLECULE:
-            print('" id="' + html.escape(n.BASE_URI_MOLECULE.rpartition('#')[-1] + str(i), quote=True), end='')
+        if '#' in n.SUBJECT_BASE:
+            print('" id="' + html.escape(n.SUBJECT_BASE.rpartition('#')[-1] + str(i), quote=True), end='')
 
         print('">')
 
@@ -142,11 +142,11 @@ def microdata(reader, limit):
   <body>''')
     for row in reader:
         print('    <div itemscope itemtype="http://schema.org/MolecularEntity" itemid="' + html.escape(
-            n.BASE_URI_MOLECULE + str(
+            n.SUBJECT_BASE + str(
                 i), quote=True), end='')
 
-        if '#' in n.BASE_URI_MOLECULE:
-            print('" id="' + html.escape(n.BASE_URI_MOLECULE.rpartition('#')[-1] + str(i), quote=True), end='')
+        if '#' in n.SUBJECT_BASE:
+            print('" id="' + html.escape(n.SUBJECT_BASE.rpartition('#')[-1] + str(i), quote=True), end='')
 
         print('">')