Deploying to gh-pages from @ e54819e 🚀

examples/filter_on_taxon_oid.py

@@ -1,6 +1,7 @@
 # This script searches the JGI Data Portal for files related to a given 
 # IMG taxon OID, printing out any related metadata.
 
+import argparse
 import dts
 import os
 
@@ -15,9 +16,22 @@
     'extra': 'project_id', # add project_id to returned metadata
 }
 
+# fetch search arguments from the command line
+parser = argparse.ArgumentParser(
+    prog='filter_on_taxon_oid.py',
+    description='''a small script that uses dtspy to search the JGI Data Portal
+for data associated with a given IMG taxon OID''',
+)
+parser.add_argument('--taxon_oid',
+    default = '2708742931',
+    help = 'an IMG taxon OID with which search results should be associated',
+    required = False,
+    type = int,
+)
+args = parser.parse_args()
+
 # do the search
 results = dts_client.search(database = 'jdp',
-                            query = '2708742931',
+                            query = f'{args.taxon_oid}',
                             specific = jdp_params)
 print(results)
-

examples/index.html

@@ -252,14 +252,14 @@
 
 <h1 id="example-scripts">Example scripts</h1>
 <ul>
-<li><a href="https://github.com/kbase/dtspy/blob/example-scripts/docs/examples/filter_on_taxon_oid.py">filter_on_taxon_id.py</a></li>
+<li><a href="https://github.com/kbase/dtspy/blob/main/docs/examples/filter_on_taxon_oid.py">filter_on_taxon_id.py</a></li>
 </ul>
 <p>This script searches for files in the JGI Data Portal related to a given IMG
 taxon OID, printing metadata for any results.</p>
 <ul>
-<li><a href="https://github.com/kbase/dtspy/blob/example-scripts/docs/examples/match_files_to_ids_in_spreadsheet.py">match_files_to_ids_in_spreadsheet.py</a></li>
+<li><a href="https://github.com/kbase/dtspy/blob/main/docs/examples/match_files_to_ids_in_spreadsheet.py">match_files_to_ids_in_spreadsheet.py</a></li>
 </ul>
-<p>This script extracts identifiers from a <a href="https://github.com/kbase/dtspy/blob/example-scripts/docs/examples/IMG.csv">spreadsheet</a>,
+<p>This script extracts identifiers from a <a href="https://github.com/kbase/dtspy/blob/main/docs/examples/IMG.csv">spreadsheet</a>,
 searches for related files, and writes another spreadsheet with relavent
 filenames and identifier information.</p>