From 624a86a4a24959905673ca2eee9bf20b31c8e139 Mon Sep 17 00:00:00 2001
From: jeff-cohere <jeff-cohere@users.noreply.github.com>
Date: Wed, 30 Oct 2024 17:24:09 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20kbase/dt?=
 =?UTF-8?q?spy@e54819e663f38b916103fa95e596d9a3336caabf=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 examples/filter_on_taxon_oid.py |  18 ++++++++++++++++--
 examples/index.html             |   6 +++---
 sitemap.xml.gz                  | Bin 127 -> 127 bytes
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/examples/filter_on_taxon_oid.py b/examples/filter_on_taxon_oid.py
index b8edbdd..29068a2 100644
--- a/examples/filter_on_taxon_oid.py
+++ b/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)
-
diff --git a/examples/index.html b/examples/index.html
index 16cc828..fa361ce 100644
--- a/examples/index.html
+++ b/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>
 
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
index e74d7be6e040d0cc1a3cd188f59f11af4fe8f8e9..059d349bbcde21502177107ec85f0da2b5f2f4af 100644
GIT binary patch
delta 13
Ucmb=gXP58h;9w|MoXB1Q02pEeXaE2J

delta 13
Ucmb=gXP58h;Al`)n8;oM02#ysl>h($