From eea64a1e8761608f4c9d32f7755eaec598f1324c Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 14 Nov 2025 14:55:34 +0100
Subject: [PATCH 1/2] offload fetching to client

---
 qp_qiime2/qp_qiime2.py | 46 ++----------------------------------------
 1 file changed, 2 insertions(+), 44 deletions(-)

diff --git a/qp_qiime2/qp_qiime2.py b/qp_qiime2/qp_qiime2.py
index 231aa39..c8fb1b9 100644
--- a/qp_qiime2/qp_qiime2.py
+++ b/qp_qiime2/qp_qiime2.py
@@ -194,41 +194,6 @@
 }
 
 
-def _fetch_files(qclient, ainfo):
-    """helper method to fetch all files of an artifact from Qiita main.
-
-    Parameters
-    ----------
-    qclient : qiita_client.QiitaClient
-        The Qiita server client
-    ainfo : ArtifactInfo
-        Information about Qiita artifact
-
-    Returns
-    -------
-    Same as input BUT filepaths are adapated after downloading files from
-    Qiita main to local IF protocol coupling != filesystem. Otherwise, no
-    change occurs.
-    """
-    if qclient._plugincoupling != 'filesystem':
-        if 'files' in ainfo.keys():
-            ainfo['files'] = {
-                filetype: [
-                    {
-                        k: qclient.fetch_file_from_central(v)
-                        if k == 'filepath' else v
-                        for k, v
-                        in file.items()}
-                    for file
-                    in ainfo['files'][filetype]]
-                for filetype
-                in ainfo['files'].keys()
-            }
-        return ainfo
-    else:
-        return ainfo
-
-
 def call_qiime2(qclient, job_id, parameters, out_dir):
     """helper method to call Qiime2
 
@@ -324,11 +289,6 @@ def call_qiime2(qclient, job_id, parameters, out_dir):
                     ainfo = qclient.get(
                         "/qiita_db/artifacts/%s/" % artifact_id)
 
-                    # If plugin coupling != 'filesystem' download all artifact
-                    # files from Qiita main to here and adapt filepaths
-                    # accordingly.
-                    ainfo = _fetch_files(qclient, ainfo)
-
                     if not q2plugin_is_process and ainfo['analysis'] is None:
                         msg = ('Artifact "%s" is not an analysis '
                                'artifact.' % val)
@@ -484,12 +444,10 @@ def call_qiime2(qclient, job_id, parameters, out_dir):
     if q2plugin == 'feature-classifier' and q2method == 'classify_sklearn':
         ainfo = qclient.get("/qiita_db/artifacts/%s/" %
                             parameters['The feature data to be classified.'])
-        biom_fp = qclient.fetch_file_from_central(
-            ainfo['files']['biom'][0]['filepath'])
+        biom_fp = ainfo['files']['biom'][0]['filepath']
         plain_text_fp = None
         if 'plain_text' in ainfo['files']:
-            plain_text_fp = qclient.fetch_file_from_central(
-                ainfo['files']['plain_text'][0]['filepath'])
+            plain_text_fp = ainfo['files']['plain_text'][0]['filepath']
         biom_table = load_table(biom_fp)
         fna_fp = join(out_dir, 'sequences.fna')
         with open(fna_fp, 'w') as f:

From 300f2729b61cd6d03a560b02df97f472d62a4ebf Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 14 Nov 2025 14:56:31 +0100
Subject: [PATCH 2/2] revert

---
 qp_qiime2/qp_qiime2.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/qp_qiime2/qp_qiime2.py b/qp_qiime2/qp_qiime2.py
index c8fb1b9..54c47c5 100644
--- a/qp_qiime2/qp_qiime2.py
+++ b/qp_qiime2/qp_qiime2.py
@@ -288,7 +288,6 @@ def call_qiime2(qclient, job_id, parameters, out_dir):
                     artifact_id = val
                     ainfo = qclient.get(
                         "/qiita_db/artifacts/%s/" % artifact_id)
-
                     if not q2plugin_is_process and ainfo['analysis'] is None:
                         msg = ('Artifact "%s" is not an analysis '
                                'artifact.' % val)