From 461f69f79727e535036057fcc69940899e731ff8 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 13:44:53 +0200
Subject: [PATCH 01/30] prepare another setting variable to store plugin
 coupling thightness

---
 qiita_client/plugin.py | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index 7ee87b4..36c37a2 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -136,13 +136,32 @@ def __init__(self, name, description, can_be_submitted_to_ebi,
 
 
 class BaseQiitaPlugin(object):
-    def __init__(self, name, version, description, publications=None):
+    def __init__(self, name, version, description, publications=None, plugincoupling='filesystem'):
         logger.debug('Entered BaseQiitaPlugin.__init__()')
         self.name = name
         self.version = version
         self.description = description
         self.publications = dumps(publications) if publications else ""
 
+        # Depending on your compute architecture, there are multiple options available how
+        # "thight" plugins are coupled to the central Qiita master/workers
+        # --- filesystem ---
+        # The default scenario is "filesystem", i.e. plugins as well as master/worker have
+        # unrestricted direct access to a shared filesystem, e.g. a larger volume / directory,
+        # defined in the server configuration as base_data_dir
+        # --- https ---
+        # A second scenario is that your plugins execute as independent jobs on another machine,
+        # e.g. as docker containers or other cloud techniques. Intentionally, you don't want to
+        # use a shared filesystem, but you have to make sure necessary input files are 
+        # provided to the containerized plugin before execution and resulting files are
+        # transfered back to the central Qiita master/worker. In this case, files are
+        # pulled / pushed through functions qiita_client.fetch_file_from_central and
+        # qiita_client.push_file_to_central, respectivey.
+        # Actually, all files need to be decorated with this function. The decision how
+        # data are transferred is then made within these two functions according to the
+        # "plugincoupling" setting.
+        self.plugincoupling = plugincoupling
+
         # Will hold the different commands
         self.task_dict = {}
 
@@ -178,7 +197,8 @@ def generate_config(self, env_script, start_script, server_cert=None):
             f.write(CONF_TEMPLATE % (self.name, self.version, self.description,
                                      env_script, start_script,
                                      self._plugin_type, self.publications,
-                                     server_cert, client_id, client_secret))
+                                     server_cert, client_id, client_secret,
+                                     self.plugincoupling))
 
     def _register_command(self, command):
         """Registers a command in the plugin
@@ -314,9 +334,11 @@ class QiitaTypePlugin(BaseQiitaPlugin):
     _plugin_type = "artifact definition"
 
     def __init__(self, name, version, description, validate_func,
-                 html_generator_func, artifact_types, publications=None):
+                 html_generator_func, artifact_types, publications=None,
+                 plugincoupling='filesystem'):
         super(QiitaTypePlugin, self).__init__(name, version, description,
-                                              publications=publications)
+                                              publications=publications,
+                                              plugincoupling=plugincoupling)
 
         logger.debug('Entered QiitaTypePlugin.__init__()')
         self.artifact_types = artifact_types
@@ -378,6 +400,7 @@ def register_command(self, command):
 START_SCRIPT = %s
 PLUGIN_TYPE = %s
 PUBLICATIONS = %s
+PLUGINCOUPLING = %s
 
 [oauth2]
 SERVER_CERT = %s

From fefc02b9c9ee654cdbc55d050da06d02c3866645 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 13:45:36 +0200
Subject: [PATCH 02/30] provide two functions to retrieve and push file content
 to qiita master

---
 qiita_client/qiita_client.py | 59 ++++++++++++++++++++++++++++++------
 1 file changed, 49 insertions(+), 10 deletions(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 553fae8..57954d7 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -6,6 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
+import os
 import time
 import requests
 import threading
@@ -253,13 +254,16 @@ def _fetch_token(self):
             # Timeout, etc. and logs them
             logger.debug(str(e))
 
-    def _request_oauth2(self, req, *args, **kwargs):
+    def _request_oauth2(self, req, rettype, *args, **kwargs):
         """Executes a request using OAuth2 authorization
 
         Parameters
         ----------
         req : function
             The request to execute
+        rettype : string
+            The return type of the function, either "json" or
+            if e.g. files are transferred "content"
         args : tuple
             The request args
         kwargs : dict
@@ -309,13 +313,16 @@ def _request_oauth2(self, req, *args, **kwargs):
                     r = req(*args, **kwargs)
         return r
 
-    def _request_retry(self, req, url, **kwargs):
+    def _request_retry(self, req, url, rettype='json', **kwargs):
         """Executes a request retrying it 2 times in case of failure
 
         Parameters
         ----------
         req : function
             The request to execute
+        rettype : string
+            The return type of the function, either "json" (default) or
+            if e.g. files are transferred "content"
         url : str
             The url to access in the server
         kwargs : dict
@@ -323,7 +330,7 @@ def _request_retry(self, req, url, **kwargs):
 
         Returns
         -------
-        dict or None
+        dict or None or plain content IF rettype='content'
             The JSON information in the request response, if any
 
         Raises
@@ -358,7 +365,7 @@ def _request_retry(self, req, url, **kwargs):
         retries = MAX_RETRIES
         while retries > 0:
             retries -= 1
-            r = self._request_oauth2(req, url, verify=self._verify, **kwargs)
+            r = self._request_oauth2(req, rettype, url, verify=self._verify, **kwargs)
             r.close()
             # There are some error codes that the specification says that they
             # shouldn't be retried
@@ -374,7 +381,13 @@ def _request_retry(self, req, url, **kwargs):
                     "Message: %s" % (req.__name__, url, r.status_code, r.text))
             elif 0 <= (r.status_code - 200) < 100:
                 try:
-                    return r.json()
+                    if rettype is None or rettype == 'json':
+                        return r.json()
+                    else:
+                        if rettype == 'content':
+                            return r.content
+                        else:
+                            raise ValueError("return type rettype='%s' cannot be understand. Choose from 'json' (default) or 'content!" % rettype)
                 except ValueError:
                     return None
             stime = randint(MIN_TIME_SLEEP, MAX_TIME_SLEEP)
@@ -386,13 +399,16 @@ def _request_retry(self, req, url, **kwargs):
             "Request '%s %s' did not succeed. Status code: %d. Message: %s"
             % (req.__name__, url, r.status_code, r.text))
 
-    def get(self, url, **kwargs):
+    def get(self, url, rettype='json', **kwargs):
         """Execute a get request against the Qiita server
 
         Parameters
         ----------
         url : str
             The url to access in the server
+        rettype : string
+            The return type of the function, either "json" (default) or
+            if e.g. files are transferred "content"
         kwargs : dict
             The request kwargs
 
@@ -402,7 +418,7 @@ def get(self, url, **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.get()')
-        return self._request_retry(self._session.get, url, **kwargs)
+        return self._request_retry(self._session.get, url, rettype=rettype, **kwargs)
 
     def post(self, url, **kwargs):
         """Execute a post request against the Qiita server
@@ -420,7 +436,7 @@ def post(self, url, **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.post(%s)' % url)
-        return self._request_retry(self._session.post, url, **kwargs)
+        return self._request_retry(self._session.post, url, rettype='json', **kwargs)
 
     def patch(self, url, op, path, value=None, from_p=None, **kwargs):
         """Executes a JSON patch request against the Qiita server
@@ -479,7 +495,7 @@ def patch(self, url, op, path, value=None, from_p=None, **kwargs):
         # we made sure that data is correctly formatted here
         kwargs['data'] = data
 
-        return self._request_retry(self._session.patch, url, **kwargs)
+        return self._request_retry(self._session.patch, url, rettype='json', **kwargs)
 
     # The functions are shortcuts for common functionality that all plugins
     # need to implement.
@@ -502,7 +518,7 @@ def http_patch(self, url, **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.http_patch()')
-        return self._request_retry(self._session.patch, url, **kwargs)
+        return self._request_retry(self._session.patch, url, rettype='json', **kwargs)
 
     def start_heartbeat(self, job_id):
         """Create and start a thread that would send heartbeats to the server
@@ -714,3 +730,26 @@ def _process_files_per_sample_fastq(self, files, prep_info,
         prep_info = prep_info.filter(items=sample_names.keys(), axis=0)
 
         return sample_names, prep_info
+
+    def fetch_file_from_central(self, filepath):
+        logger.debug('Requesting file %s from qiita server.' % filepath)
+
+        # actual call to Qiita central to obtain file content
+        content = self.get('/cloud/fetch_file_from_central/' + filepath, rettype='content')
+
+        # create necessary directory locally
+        os.makedirs(os.path.dirname(filepath), exist_ok=True)
+
+        # write retrieved file content
+        with open(filepath, 'wb') as f:
+            f.write(content)
+
+        return filepath
+
+    def push_file_to_central(self, filepath):
+        logger.debug('Submitting file %s to qiita server.' % filepath)
+
+        self.post('/cloud/push_file_to_central/',
+            files={os.path.dirname(filepath): open(filepath, 'rb')})
+
+        return filepath
\ No newline at end of file

From a04beeb832586c69f45300cdf163f8a57c89dabb Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 16:29:40 +0200
Subject: [PATCH 03/30] add a configurable parameter to define plugincoupling
 for plugin

---
 qiita_client/plugin.py       | 27 +++++++++++++++--------
 qiita_client/qiita_client.py | 42 ++++++++++++++++++++++++------------
 2 files changed, 46 insertions(+), 23 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index 36c37a2..417efd0 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -136,7 +136,8 @@ def __init__(self, name, description, can_be_submitted_to_ebi,
 
 
 class BaseQiitaPlugin(object):
-    def __init__(self, name, version, description, publications=None, plugincoupling='filesystem'):
+    _ALLOWED_PLUGIN_COUPLINGS = ['filesystem', 'https']  # default must be first element
+    def __init__(self, name, version, description, publications=None, plugincoupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
         logger.debug('Entered BaseQiitaPlugin.__init__()')
         self.name = name
         self.version = version
@@ -160,6 +161,8 @@ def __init__(self, name, version, description, publications=None, plugincoupling
         # Actually, all files need to be decorated with this function. The decision how
         # data are transferred is then made within these two functions according to the
         # "plugincoupling" setting.
+        if plugincoupling not in self._ALLOWED_PLUGIN_COUPLINGS:
+            raise ValueError("valid plugincoupling values are ['%s'], but you provided %s" % ("', '".join(self._ALLOWED_PLUGIN_COUPLINGS), plugincoupling))
         self.plugincoupling = plugincoupling
 
         # Will hold the different commands
@@ -170,7 +173,7 @@ def __init__(self, name, version, description, publications=None, plugincoupling
             'QIITA_PLUGINS_DIR', join(expanduser('~'), '.qiita_plugins'))
         self.conf_fp = join(conf_dir, "%s_%s.conf" % (self.name, self.version))
 
-    def generate_config(self, env_script, start_script, server_cert=None):
+    def generate_config(self, env_script, start_script, server_cert=None, plugin_couling=_ALLOWED_PLUGIN_COUPLINGS[0]):
         """Generates the plugin configuration file
 
         Parameters
@@ -184,6 +187,9 @@ def generate_config(self, env_script, start_script, server_cert=None):
             If the Qiita server used does not have a valid certificate, the
             path to the Qiita certificate so the plugin can connect over
             HTTPS to it
+        plugin_coupling : str
+            Type of coupling of plugin to central for file exchange. 
+            Valid values are 'filesystem' and 'https'.
         """
         logger.debug('Entered BaseQiitaPlugin.generate_config()')
         sr = SystemRandom()
@@ -198,7 +204,7 @@ def generate_config(self, env_script, start_script, server_cert=None):
                                      env_script, start_script,
                                      self._plugin_type, self.publications,
                                      server_cert, client_id, client_secret,
-                                     self.plugincoupling))
+                                     plugin_couling))
 
     def _register_command(self, command):
         """Registers a command in the plugin
@@ -208,8 +214,7 @@ def _register_command(self, command):
         command: QiitaCommand
             The command to be added to the plugin
         """
-        logger.debug(
-            f'Entered BaseQiitaPlugin._register_command({command.name})')
+        logger.debug('Entered BaseQiitaPlugin._register_command(%s)' % command.name)
         self.task_dict[command.name] = command
 
     def _register(self, qclient):
@@ -271,7 +276,8 @@ def __call__(self, server_url, job_id, output_dir):
                               # this value will prevent underlying libraries
                               # from validating the server's cert using
                               # certifi's pem cache.
-                              ca_cert=config.get('oauth2', 'SERVER_CERT'))
+                              ca_cert=config.get('oauth2', 'SERVER_CERT'),
+                              plugincoupling=config.get('network', 'PLUGINCOUPLING'))
 
         if job_id == 'register':
             self._register(qclient)
@@ -335,7 +341,7 @@ class QiitaTypePlugin(BaseQiitaPlugin):
 
     def __init__(self, name, version, description, validate_func,
                  html_generator_func, artifact_types, publications=None,
-                 plugincoupling='filesystem'):
+                 plugincoupling=BaseQiitaPlugin._ALLOWED_PLUGIN_COUPLINGS[0]):
         super(QiitaTypePlugin, self).__init__(name, version, description,
                                               publications=publications,
                                               plugincoupling=plugincoupling)
@@ -400,9 +406,12 @@ def register_command(self, command):
 START_SCRIPT = %s
 PLUGIN_TYPE = %s
 PUBLICATIONS = %s
-PLUGINCOUPLING = %s
 
 [oauth2]
 SERVER_CERT = %s
 CLIENT_ID = %s
-CLIENT_SECRET = %s"""
+CLIENT_SECRET = %s
+
+[network]
+PLUGINCOUPLING = %s
+"""
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 57954d7..97a5069 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -183,7 +183,7 @@ class QiitaClient(object):
     get
     post
     """
-    def __init__(self, server_url, client_id, client_secret, ca_cert=None):
+    def __init__(self, server_url, client_id, client_secret, ca_cert=None, plugincoupling='filesystem'):
         self._server_url = server_url
         self._session = requests.Session()
 
@@ -219,6 +219,8 @@ def __init__(self, server_url, client_id, client_secret, ca_cert=None):
         self._token = None
         self._fetch_token()
 
+        self._plugincoupling = plugincoupling
+
     def _fetch_token(self):
         """Retrieves an access token from the Qiita server
 
@@ -732,24 +734,36 @@ def _process_files_per_sample_fastq(self, files, prep_info,
         return sample_names, prep_info
 
     def fetch_file_from_central(self, filepath):
-        logger.debug('Requesting file %s from qiita server.' % filepath)
+        if self._plugincoupling == 'filesystem':
+            return filepath
+
+        if self._plugincoupling == 'https':
+            logger.debug('Requesting file %s from qiita server.' % filepath)
+
+            # actual call to Qiita central to obtain file content
+            content = self.get('/cloud/fetch_file_from_central/' + filepath, rettype='content')
 
-        # actual call to Qiita central to obtain file content
-        content = self.get('/cloud/fetch_file_from_central/' + filepath, rettype='content')
+            # create necessary directory locally
+            os.makedirs(os.path.dirname(filepath), exist_ok=True)
 
-        # create necessary directory locally
-        os.makedirs(os.path.dirname(filepath), exist_ok=True)
+            # write retrieved file content
+            with open(filepath, 'wb') as f:
+                f.write(content)
 
-        # write retrieved file content
-        with open(filepath, 'wb') as f:
-            f.write(content)
+            return filepath
 
-        return filepath
+        raise ValueError("File communication protocol '%s' as defined in plugins configuration is NOT defined." % self._plugincoupling)
 
     def push_file_to_central(self, filepath):
-        logger.debug('Submitting file %s to qiita server.' % filepath)
+        if self._plugincoupling == 'filesystem':
+            return filepath
+
+        if self._plugincoupling == 'https':
+            logger.debug('Submitting file %s to qiita server.' % filepath)
+
+            self.post('/cloud/push_file_to_central/',
+                files={os.path.dirname(filepath): open(filepath, 'rb')})
 
-        self.post('/cloud/push_file_to_central/',
-            files={os.path.dirname(filepath): open(filepath, 'rb')})
+            return filepath
 
-        return filepath
\ No newline at end of file
+        raise ValueError("File communication protocol '%s' as defined in plugins configuration is NOT defined." % self._plugincoupling)

From 8f9fbec689a8e631828c3e80da6661da7900795a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 16:39:46 +0200
Subject: [PATCH 04/30] codestyle

---
 qiita_client/plugin.py       | 56 ++++++++++++++++++++++--------------
 qiita_client/qiita_client.py | 38 +++++++++++++++++-------
 2 files changed, 62 insertions(+), 32 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index 417efd0..b0cc4c6 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -136,33 +136,44 @@ def __init__(self, name, description, can_be_submitted_to_ebi,
 
 
 class BaseQiitaPlugin(object):
-    _ALLOWED_PLUGIN_COUPLINGS = ['filesystem', 'https']  # default must be first element
-    def __init__(self, name, version, description, publications=None, plugincoupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
+    # default must be first element
+    _ALLOWED_PLUGIN_COUPLINGS = ['filesystem', 'https']
+
+    def __init__(self, name, version, description, publications=None,
+                 plugincoupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
         logger.debug('Entered BaseQiitaPlugin.__init__()')
         self.name = name
         self.version = version
         self.description = description
         self.publications = dumps(publications) if publications else ""
 
-        # Depending on your compute architecture, there are multiple options available how
-        # "thight" plugins are coupled to the central Qiita master/workers
+        # Depending on your compute architecture, there are multiple options
+        # available how "thight" plugins are coupled to the central
+        # Qiita master/workers
         # --- filesystem ---
-        # The default scenario is "filesystem", i.e. plugins as well as master/worker have
-        # unrestricted direct access to a shared filesystem, e.g. a larger volume / directory,
-        # defined in the server configuration as base_data_dir
+        # The default scenario is "filesystem", i.e. plugins as well as
+        # master/worker have unrestricted direct access to a shared filesystem,
+        # e.g. a larger volume / directory, defined in the server configuration
+        # as base_data_dir
         # --- https ---
-        # A second scenario is that your plugins execute as independent jobs on another machine,
-        # e.g. as docker containers or other cloud techniques. Intentionally, you don't want to
-        # use a shared filesystem, but you have to make sure necessary input files are 
-        # provided to the containerized plugin before execution and resulting files are
-        # transfered back to the central Qiita master/worker. In this case, files are
-        # pulled / pushed through functions qiita_client.fetch_file_from_central and
+        # A second scenario is that your plugins execute as independent jobs on
+        # another machine, e.g. as docker containers or other cloud techniques.
+        # Intentionally, you don't want to use a shared filesystem, but you
+        # have to make sure necessary input files are provided to the
+        # containerized plugin before execution and resulting files are
+        # transfered back to the central Qiita master/worker. In this case,
+        # files are pulled / pushed through functions
+        # qiita_client.fetch_file_from_central and
         # qiita_client.push_file_to_central, respectivey.
-        # Actually, all files need to be decorated with this function. The decision how
-        # data are transferred is then made within these two functions according to the
-        # "plugincoupling" setting.
+        # Actually, all files need to be decorated with this function.
+        # The decision how data are transferred is then made within these two
+        # functions according to the "plugincoupling" setting.
         if plugincoupling not in self._ALLOWED_PLUGIN_COUPLINGS:
-            raise ValueError("valid plugincoupling values are ['%s'], but you provided %s" % ("', '".join(self._ALLOWED_PLUGIN_COUPLINGS), plugincoupling))
+            raise ValueError(
+                ("valid plugincoupling values are ['%s'], but you "
+                 "provided %s") % (
+                     "', '".join(self._ALLOWED_PLUGIN_COUPLINGS),
+                     plugincoupling))
         self.plugincoupling = plugincoupling
 
         # Will hold the different commands
@@ -173,7 +184,8 @@ def __init__(self, name, version, description, publications=None, plugincoupling
             'QIITA_PLUGINS_DIR', join(expanduser('~'), '.qiita_plugins'))
         self.conf_fp = join(conf_dir, "%s_%s.conf" % (self.name, self.version))
 
-    def generate_config(self, env_script, start_script, server_cert=None, plugin_couling=_ALLOWED_PLUGIN_COUPLINGS[0]):
+    def generate_config(self, env_script, start_script, server_cert=None,
+                        plugin_couling=_ALLOWED_PLUGIN_COUPLINGS[0]):
         """Generates the plugin configuration file
 
         Parameters
@@ -188,7 +200,7 @@ def generate_config(self, env_script, start_script, server_cert=None, plugin_cou
             path to the Qiita certificate so the plugin can connect over
             HTTPS to it
         plugin_coupling : str
-            Type of coupling of plugin to central for file exchange. 
+            Type of coupling of plugin to central for file exchange.
             Valid values are 'filesystem' and 'https'.
         """
         logger.debug('Entered BaseQiitaPlugin.generate_config()')
@@ -214,7 +226,8 @@ def _register_command(self, command):
         command: QiitaCommand
             The command to be added to the plugin
         """
-        logger.debug('Entered BaseQiitaPlugin._register_command(%s)' % command.name)
+        logger.debug('Entered BaseQiitaPlugin._register_command(%s)' %
+                     command.name)
         self.task_dict[command.name] = command
 
     def _register(self, qclient):
@@ -277,7 +290,8 @@ def __call__(self, server_url, job_id, output_dir):
                               # from validating the server's cert using
                               # certifi's pem cache.
                               ca_cert=config.get('oauth2', 'SERVER_CERT'),
-                              plugincoupling=config.get('network', 'PLUGINCOUPLING'))
+                              plugincoupling=config.get('network',
+                                                        'PLUGINCOUPLING'))
 
         if job_id == 'register':
             self._register(qclient)
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 97a5069..6e079b1 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -183,7 +183,8 @@ class QiitaClient(object):
     get
     post
     """
-    def __init__(self, server_url, client_id, client_secret, ca_cert=None, plugincoupling='filesystem'):
+    def __init__(self, server_url, client_id, client_secret, ca_cert=None,
+                 plugincoupling='filesystem'):
         self._server_url = server_url
         self._session = requests.Session()
 
@@ -367,7 +368,8 @@ def _request_retry(self, req, url, rettype='json', **kwargs):
         retries = MAX_RETRIES
         while retries > 0:
             retries -= 1
-            r = self._request_oauth2(req, rettype, url, verify=self._verify, **kwargs)
+            r = self._request_oauth2(
+                req, rettype, url, verify=self._verify, **kwargs)
             r.close()
             # There are some error codes that the specification says that they
             # shouldn't be retried
@@ -389,7 +391,10 @@ def _request_retry(self, req, url, rettype='json', **kwargs):
                         if rettype == 'content':
                             return r.content
                         else:
-                            raise ValueError("return type rettype='%s' cannot be understand. Choose from 'json' (default) or 'content!" % rettype)
+                            raise ValueError(
+                                ("return type rettype='%s' cannot be "
+                                 "understand. Choose from 'json' (default) "
+                                 "or 'content!") % rettype)
                 except ValueError:
                     return None
             stime = randint(MIN_TIME_SLEEP, MAX_TIME_SLEEP)
@@ -420,7 +425,8 @@ def get(self, url, rettype='json', **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.get()')
-        return self._request_retry(self._session.get, url, rettype=rettype, **kwargs)
+        return self._request_retry(
+            self._session.get, url, rettype=rettype, **kwargs)
 
     def post(self, url, **kwargs):
         """Execute a post request against the Qiita server
@@ -438,7 +444,8 @@ def post(self, url, **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.post(%s)' % url)
-        return self._request_retry(self._session.post, url, rettype='json', **kwargs)
+        return self._request_retry(
+            self._session.post, url, rettype='json', **kwargs)
 
     def patch(self, url, op, path, value=None, from_p=None, **kwargs):
         """Executes a JSON patch request against the Qiita server
@@ -497,7 +504,8 @@ def patch(self, url, op, path, value=None, from_p=None, **kwargs):
         # we made sure that data is correctly formatted here
         kwargs['data'] = data
 
-        return self._request_retry(self._session.patch, url, rettype='json', **kwargs)
+        return self._request_retry(
+            self._session.patch, url, rettype='json', **kwargs)
 
     # The functions are shortcuts for common functionality that all plugins
     # need to implement.
@@ -520,7 +528,8 @@ def http_patch(self, url, **kwargs):
             The JSON response from the server
         """
         logger.debug('Entered QiitaClient.http_patch()')
-        return self._request_retry(self._session.patch, url, rettype='json', **kwargs)
+        return self._request_retry(
+            self._session.patch, url, rettype='json', **kwargs)
 
     def start_heartbeat(self, job_id):
         """Create and start a thread that would send heartbeats to the server
@@ -741,7 +750,9 @@ def fetch_file_from_central(self, filepath):
             logger.debug('Requesting file %s from qiita server.' % filepath)
 
             # actual call to Qiita central to obtain file content
-            content = self.get('/cloud/fetch_file_from_central/' + filepath, rettype='content')
+            content = self.get(
+                '/cloud/fetch_file_from_central/' + filepath,
+                rettype='content')
 
             # create necessary directory locally
             os.makedirs(os.path.dirname(filepath), exist_ok=True)
@@ -752,7 +763,9 @@ def fetch_file_from_central(self, filepath):
 
             return filepath
 
-        raise ValueError("File communication protocol '%s' as defined in plugins configuration is NOT defined." % self._plugincoupling)
+        raise ValueError(
+            ("File communication protocol '%s' as defined in plugins "
+             "configuration is NOT defined.") % self._plugincoupling)
 
     def push_file_to_central(self, filepath):
         if self._plugincoupling == 'filesystem':
@@ -761,9 +774,12 @@ def push_file_to_central(self, filepath):
         if self._plugincoupling == 'https':
             logger.debug('Submitting file %s to qiita server.' % filepath)
 
-            self.post('/cloud/push_file_to_central/',
+            self.post(
+                '/cloud/push_file_to_central/',
                 files={os.path.dirname(filepath): open(filepath, 'rb')})
 
             return filepath
 
-        raise ValueError("File communication protocol '%s' as defined in plugins configuration is NOT defined." % self._plugincoupling)
+        raise ValueError(
+            ("File communication protocol '%s' as defined in plugins "
+             "configuration is NOT defined.") % self._plugincoupling)

From 8d0844dc05868bbeac370d62aa235699c0ec9610 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 16:41:51 +0200
Subject: [PATCH 05/30] adapting test to new configuration option

---
 qiita_client/tests/test_plugin.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/qiita_client/tests/test_plugin.py b/qiita_client/tests/test_plugin.py
index ab87f6b..fcf8920 100644
--- a/qiita_client/tests/test_plugin.py
+++ b/qiita_client/tests/test_plugin.py
@@ -147,7 +147,10 @@ def html_generator_func(a, b, c, d):
                      'PUBLICATIONS = \n',
                      '\n',
                      '[oauth2]\n',
-                     'SERVER_CERT = \n']
+                     'SERVER_CERT = \n',
+                     '\n',
+                     '[network]\n',
+                     'plugincoupling = \n']
         # We will test the last 2 lines independently since they're variable
         # in each test run
         self.assertEqual(conf[:-2], exp_lines)

From 47a4551af0805e0ff5d17e7572d7e743f83b6a17 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 16:54:55 +0200
Subject: [PATCH 06/30] start working on tests

---
 qiita_client/tests/test_qiita_client.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 12689e8..02e7b1f 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -385,6 +385,17 @@ def test_artifact_and_preparation_files(self):
         self.assertEqual(fobs, fexp)
         self.assertEqual(piobs.shape, (2, 1))
 
+    def test_fetch_file_from_central(self):
+        self.tester._plugincoupling = 'filesystem'
+
+        ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
+        print("STEFAN", ainfo)
+
+        # fp_query = '/home/runner/work/qiita/qiita/qiita_db/support_files/
+        # test_data/templates/FASTA_QUAL_preprocessing_sample_template.txt'
+        # fp_res = fetch_file_from_central('')
+        pass
+
 
 if __name__ == '__main__':
     main()

From 8d220216339cf69b583c26a26d85e5215ecc0a1a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 17:04:01 +0200
Subject: [PATCH 07/30] check spelling

---
 qiita_client/tests/test_plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qiita_client/tests/test_plugin.py b/qiita_client/tests/test_plugin.py
index fcf8920..8057139 100644
--- a/qiita_client/tests/test_plugin.py
+++ b/qiita_client/tests/test_plugin.py
@@ -150,7 +150,7 @@ def html_generator_func(a, b, c, d):
                      'SERVER_CERT = \n',
                      '\n',
                      '[network]\n',
-                     'plugincoupling = \n']
+                     'PLUGINCOUPLING = \n']
         # We will test the last 2 lines independently since they're variable
         # in each test run
         self.assertEqual(conf[:-2], exp_lines)

From e032053f4532bcd1d692018a5ec7f7ce4aa1239b Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 17:09:31 +0200
Subject: [PATCH 08/30] fixing existing test

---
 qiita_client/tests/test_plugin.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/qiita_client/tests/test_plugin.py b/qiita_client/tests/test_plugin.py
index 8057139..ba4f80a 100644
--- a/qiita_client/tests/test_plugin.py
+++ b/qiita_client/tests/test_plugin.py
@@ -147,15 +147,14 @@ def html_generator_func(a, b, c, d):
                      'PUBLICATIONS = \n',
                      '\n',
                      '[oauth2]\n',
-                     'SERVER_CERT = \n',
-                     '\n',
-                     '[network]\n',
-                     'PLUGINCOUPLING = \n']
+                     'SERVER_CERT = \n']
         # We will test the last 2 lines independently since they're variable
         # in each test run
-        self.assertEqual(conf[:-2], exp_lines)
-        self.assertTrue(conf[-2].startswith('CLIENT_ID = '))
-        self.assertTrue(conf[-1].startswith('CLIENT_SECRET = '))
+        self.assertEqual(conf[:-5], exp_lines)
+        self.assertTrue(conf[-5].startswith('CLIENT_ID = '))
+        self.assertTrue(conf[-4].startswith('CLIENT_SECRET = '))
+        self.assertTrue(conf[-2].startswith('[network]'))
+        self.assertTrue(conf[-2].startswith('PLUGINCOUPLING = '))
 
     def test_call(self):
         def validate_func(a, b, c, d):

From 7d5b09846ee9ed9b20cd6db13e6d0a0493b62311 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 15 Aug 2025 17:14:28 +0200
Subject: [PATCH 09/30] wrong list index

---
 qiita_client/tests/test_plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qiita_client/tests/test_plugin.py b/qiita_client/tests/test_plugin.py
index ba4f80a..43a8eca 100644
--- a/qiita_client/tests/test_plugin.py
+++ b/qiita_client/tests/test_plugin.py
@@ -154,7 +154,7 @@ def html_generator_func(a, b, c, d):
         self.assertTrue(conf[-5].startswith('CLIENT_ID = '))
         self.assertTrue(conf[-4].startswith('CLIENT_SECRET = '))
         self.assertTrue(conf[-2].startswith('[network]'))
-        self.assertTrue(conf[-2].startswith('PLUGINCOUPLING = '))
+        self.assertTrue(conf[-1].startswith('PLUGINCOUPLING = '))
 
     def test_call(self):
         def validate_func(a, b, c, d):

From 349ab443624346ad65e44c207b40f9efc88b8568 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 18 Aug 2025 12:19:46 +0200
Subject: [PATCH 10/30] initial tests + docstrings

---
 qiita_client/qiita_client.py            | 64 +++++++++++++++++++++----
 qiita_client/tests/test_qiita_client.py | 36 ++++++++++++--
 2 files changed, 85 insertions(+), 15 deletions(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 6e079b1..4985fc5 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 import os
+import shutil
 import time
 import requests
 import threading
@@ -742,11 +743,53 @@ def _process_files_per_sample_fastq(self, files, prep_info,
 
         return sample_names, prep_info
 
-    def fetch_file_from_central(self, filepath):
+    def fetch_file_from_central(self, filepath, prefix=''):
+        """Moves content of a file from Qiita's central base_data_dir to a
+           local plugin file-system.
+
+           By default, this is exactly the same location, i.e. the return
+           filepath is identical to the requested one and nothing is moved /
+           copied.
+           However, for less tight plugin couplings, file content can be
+           transferred via https for situations where the plugin does not have
+           native access to Qiita's overall base_data_dir.
+
+        Parameters
+        ----------
+        filepath : str
+            The filepath in Qiita's central base_data_dir to the requested
+            file content
+        prefix : str
+            Primarily for testing: prefix the target filepath with this
+            filepath prefix to
+            a) in 'filesystem' mode: create an actual file copy (for testing)
+               If prefix='', nothing will be copied/moved
+            b) in 'https' mode: flexibility to locate files differently in
+               plugin local file system.
+
+        Returns
+        -------
+        str : the filepath of the requested file within the local file system
+        """
+        target_filepath = filepath
+        if prefix != '':
+            # strip off root
+            if filepath.startswith(os.path.abspath(os.sep)):
+                target_filepath = target_filepath[
+                    len(os.path.abspath(os.sep)):]
+            # prefix filepath with given prefix
+            target_filepath = os.path.join(prefix, target_filepath)
+
         if self._plugincoupling == 'filesystem':
-            return filepath
+            if prefix != '':
+                # create necessary directory locally
+                os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
+
+                shutil.copyfile(filepath, target_filepath)
+
+            return target_filepath
 
-        if self._plugincoupling == 'https':
+        elif self._plugincoupling == 'https':
             logger.debug('Requesting file %s from qiita server.' % filepath)
 
             # actual call to Qiita central to obtain file content
@@ -755,23 +798,24 @@ def fetch_file_from_central(self, filepath):
                 rettype='content')
 
             # create necessary directory locally
-            os.makedirs(os.path.dirname(filepath), exist_ok=True)
+            os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
 
             # write retrieved file content
-            with open(filepath, 'wb') as f:
+            with open(target_filepath, 'wb') as f:
                 f.write(content)
 
-            return filepath
+            return target_filepath
 
-        raise ValueError(
-            ("File communication protocol '%s' as defined in plugins "
-             "configuration is NOT defined.") % self._plugincoupling)
+        else:
+            raise ValueError(
+                ("File communication protocol '%s' as defined in plugins "
+                 "configuration is NOT defined.") % self._plugincoupling)
 
     def push_file_to_central(self, filepath):
         if self._plugincoupling == 'filesystem':
             return filepath
 
-        if self._plugincoupling == 'https':
+        elif self._plugincoupling == 'https':
             logger.debug('Submitting file %s to qiita server.' % filepath)
 
             self.post(
diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 02e7b1f..a59bdd8 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from unittest import TestCase, main
+import filecmp
 from os import remove, close
 from os.path import basename, exists
 from tempfile import mkstemp
@@ -389,12 +390,37 @@ def test_fetch_file_from_central(self):
         self.tester._plugincoupling = 'filesystem'
 
         ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
-        print("STEFAN", ainfo)
+        fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
 
-        # fp_query = '/home/runner/work/qiita/qiita/qiita_db/support_files/
-        # test_data/templates/FASTA_QUAL_preprocessing_sample_template.txt'
-        # fp_res = fetch_file_from_central('')
-        pass
+        # mode: filesystem, prefix='': no copy, directly return given fp
+        fp_obs = self.tester.fetch_file_from_central(fp)
+        self.assertEqual(fp, fp_obs)
+
+        # mode: filesystem, prefix='/karl': make file copy
+        self.clean_up_files.append('/karl' + fp)
+        fp_obs = self.tester.fetch_file_from_central(fp, prefix='/karl')
+        self.assertEqual('/karl' + fp, fp_obs)
+        self.assertTrue(filecmp.cmp(fp, fp_obs, shallow=False))
+
+        # non existing mode
+        with self.assertRaises(ValueError):
+            self.tester._plugincoupling = 'foo'
+            self.tester.fetch_file_from_central(fp)
+
+    def test_push_file_to_central(self):
+        self.tester._plugincoupling = 'filesystem'
+
+        ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
+        fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
+
+        # mode: filesystem
+        fp_obs = self.tester.push_file_to_central(fp)
+        self.assertEqual(fp, fp_obs)
+
+        # non existing mode
+        with self.assertRaises(ValueError):
+            self.tester._plugincoupling = 'foo'
+            self.tester.push_file_to_central(fp)
 
 
 if __name__ == '__main__':

From 1fdf1e5a16bdd5271f1d260c80c8b8cfa3197cf7 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 18 Aug 2025 12:27:19 +0200
Subject: [PATCH 11/30] use a prefix user has access to

---
 qiita_client/qiita_client.py            | 19 +++++++++++++++++++
 qiita_client/tests/test_qiita_client.py |  9 +++++----
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 4985fc5..0c3b277 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -812,6 +812,25 @@ def fetch_file_from_central(self, filepath, prefix=''):
                  "configuration is NOT defined.") % self._plugincoupling)
 
     def push_file_to_central(self, filepath):
+        """Pushs filecontent to Qiita's central base_data_dir directory.
+
+        By default, plugin and Qiita's central base_data_dir filesystems are
+        identical. In this case, no files are touched and the filepath is
+        directly returned.
+        If however, plugincoupling is set to 'https', the content of the file
+        is sent via https POST to Qiita's master/worker, which has to receive
+        and store in an appropriate location.
+
+        Parameters
+        ----------
+        filepath : str
+            The filepath of the files whos content shall be send to Qiita's
+            central base_data_dir
+
+        Returns
+        -------
+        The given filepath - to be transparent in plugin code.
+        """
         if self._plugincoupling == 'filesystem':
             return filepath
 
diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index a59bdd8..580250c 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -9,7 +9,7 @@
 from unittest import TestCase, main
 import filecmp
 from os import remove, close
-from os.path import basename, exists
+from os.path import basename, exists, expanduser, join
 from tempfile import mkstemp
 from json import dumps
 import pandas as pd
@@ -397,9 +397,10 @@ def test_fetch_file_from_central(self):
         self.assertEqual(fp, fp_obs)
 
         # mode: filesystem, prefix='/karl': make file copy
-        self.clean_up_files.append('/karl' + fp)
-        fp_obs = self.tester.fetch_file_from_central(fp, prefix='/karl')
-        self.assertEqual('/karl' + fp, fp_obs)
+        prefix = join(expanduser("~"), '/karl')
+        self.clean_up_files.append(prefix + fp)
+        fp_obs = self.tester.fetch_file_from_central(fp, prefix=prefix)
+        self.assertEqual(prefix + fp, fp_obs)
         self.assertTrue(filecmp.cmp(fp, fp_obs, shallow=False))
 
         # non existing mode

From 748f72729c120d1241e539fe742db49805126de6 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 18 Aug 2025 12:32:19 +0200
Subject: [PATCH 12/30] remove /

---
 qiita_client/tests/test_qiita_client.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 580250c..587c4fb 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -397,7 +397,7 @@ def test_fetch_file_from_central(self):
         self.assertEqual(fp, fp_obs)
 
         # mode: filesystem, prefix='/karl': make file copy
-        prefix = join(expanduser("~"), '/karl')
+        prefix = join(expanduser("~"), 'karl')
         self.clean_up_files.append(prefix + fp)
         fp_obs = self.tester.fetch_file_from_central(fp, prefix=prefix)
         self.assertEqual(prefix + fp, fp_obs)

From 8f2680496dae8a7787484fa2b5256c95e381641a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 12:50:01 +0200
Subject: [PATCH 13/30] capitalize comments

---
 qiita_client/qiita_client.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 0c3b277..12ec361 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -744,7 +744,7 @@ def _process_files_per_sample_fastq(self, files, prep_info,
         return sample_names, prep_info
 
     def fetch_file_from_central(self, filepath, prefix=''):
-        """Moves content of a file from Qiita's central base_data_dir to a
+        """Moves content of a file from Qiita's central BASE_DATA_DIR to a
            local plugin file-system.
 
            By default, this is exactly the same location, i.e. the return
@@ -752,12 +752,12 @@ def fetch_file_from_central(self, filepath, prefix=''):
            copied.
            However, for less tight plugin couplings, file content can be
            transferred via https for situations where the plugin does not have
-           native access to Qiita's overall base_data_dir.
+           native access to Qiita's overall BASE_DATA_DIR.
 
         Parameters
         ----------
         filepath : str
-            The filepath in Qiita's central base_data_dir to the requested
+            The filepath in Qiita's central BASE_DATA_DIR to the requested
             file content
         prefix : str
             Primarily for testing: prefix the target filepath with this
@@ -812,9 +812,9 @@ def fetch_file_from_central(self, filepath, prefix=''):
                  "configuration is NOT defined.") % self._plugincoupling)
 
     def push_file_to_central(self, filepath):
-        """Pushs filecontent to Qiita's central base_data_dir directory.
+        """Pushs filecontent to Qiita's central BASE_DATA_DIR directory.
 
-        By default, plugin and Qiita's central base_data_dir filesystems are
+        By default, plugin and Qiita's central BASE_DATA_DIR filesystems are
         identical. In this case, no files are touched and the filepath is
         directly returned.
         If however, plugincoupling is set to 'https', the content of the file
@@ -825,7 +825,7 @@ def push_file_to_central(self, filepath):
         ----------
         filepath : str
             The filepath of the files whos content shall be send to Qiita's
-            central base_data_dir
+            central BASE_DATA_DIR
 
         Returns
         -------

From 509b3d5763aeaa616c95304e2caeb0a4c7d5d71d Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 12:50:25 +0200
Subject: [PATCH 14/30] use qiita branch

---
 .github/workflows/qiita-ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index d09ac5e..1559611 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -52,8 +52,9 @@ jobs:
 
           # we need to download qiita directly so we have "easy" access to
           # all config files
-          wget https://github.com/biocore/qiita/archive/dev.zip
-          unzip dev.zip
+          # wget https://github.com/biocore/qiita/archive/dev.zip
+          # unzip dev.zip
+          git clone -b uncouplePlugins https://github.com/jlab/qiita.git
 
           # pull out the port so we can modify the configuration file easily
           pgport=${{ job.services.postgres.ports[5432] }}

From 0cc6a50ebef4eb7163301bbbe146dd755236a3be Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 12:53:03 +0200
Subject: [PATCH 15/30] specify directory name

---
 .github/workflows/qiita-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 1559611..aefc5dd 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -54,7 +54,7 @@ jobs:
           # all config files
           # wget https://github.com/biocore/qiita/archive/dev.zip
           # unzip dev.zip
-          git clone -b uncouplePlugins https://github.com/jlab/qiita.git
+          git clone -b uncouplePlugins https://github.com/jlab/qiita.git qiita-dev
 
           # pull out the port so we can modify the configuration file easily
           pgport=${{ job.services.postgres.ports[5432] }}

From 738ab79a6b84417a5d4e4ad70abf0bfb3d012629 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 12:59:41 +0200
Subject: [PATCH 16/30] add testing https protocol

---
 qiita_client/tests/test_qiita_client.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 587c4fb..15e4f77 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -408,6 +408,14 @@ def test_fetch_file_from_central(self):
             self.tester._plugincoupling = 'foo'
             self.tester.fetch_file_from_central(fp)
 
+        # change transfer mode to https
+        self.tester._plugincoupling = 'https'
+        prefix = join(expanduser("~"), 'kurt')
+        self.clean_up_files.append(prefix + fp)
+        fp_obs = self.tester.fetch_file_from_central(fp, prefix=prefix)
+        self.assertEqual(prefix + fp, fp_obs)
+        self.assertTrue(filecmp.cmp(fp, fp_obs, shallow=False))
+
     def test_push_file_to_central(self):
         self.tester._plugincoupling = 'filesystem'
 
@@ -423,6 +431,15 @@ def test_push_file_to_central(self):
             self.tester._plugincoupling = 'foo'
             self.tester.push_file_to_central(fp)
 
+        # change transfer mode to https
+        self.tester._plugincoupling = 'https'
+        fp_source = 'foo.bar'
+        with open(fp_source, 'w') as f:
+            f.write("this is a test\n")
+        self.clean_up_files.append(fp_source)
+        fp_obs = self.tester.push_file_to_central(fp_source)
+        self.assertEqual(fp_source, fp_obs)
+
 
 if __name__ == '__main__':
     main()

From 0849ca7f4a72ee0d8aaea66164b06b9046631770 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 15:56:29 +0200
Subject: [PATCH 17/30] fix protected

---
 .github/workflows/qiita-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index aefc5dd..646bd18 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -106,6 +106,7 @@ jobs:
           export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf
           export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
+          sed "s#/Users/username/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
           nginx -c ${NGINX_FILE_NEW}
 
           echo "3. Setting up qiita"

From e1cb5b6836def496bfa49a9e314fa0dcf3b5e2d5 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 17:32:32 +0200
Subject: [PATCH 18/30] operate on file copy

---
 .github/workflows/qiita-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 646bd18..d7dbfa9 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -105,8 +105,8 @@ jobs:
           mkdir -p ${CONDA_PREFIX}/var/run/nginx/
           export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf
           export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf
-          sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
-          sed "s#/Users/username/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
+          sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
+          sed -i "s#/Users/username/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE_NEW}
           nginx -c ${NGINX_FILE_NEW}
 
           echo "3. Setting up qiita"

From ba929a2201a7fa8d3ef47283446a6d3d652b14bc Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 17:40:37 +0200
Subject: [PATCH 19/30] debug

---
 qiita_client/tests/test_qiita_client.py | 48 +++++++++++++------------
 1 file changed, 25 insertions(+), 23 deletions(-)

diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 15e4f77..48ba7bf 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -412,33 +412,35 @@ def test_fetch_file_from_central(self):
         self.tester._plugincoupling = 'https'
         prefix = join(expanduser("~"), 'kurt')
         self.clean_up_files.append(prefix + fp)
+        print("STEFAN", fp, prefix)
         fp_obs = self.tester.fetch_file_from_central(fp, prefix=prefix)
+        print("STEFAN2", fp_obs)
         self.assertEqual(prefix + fp, fp_obs)
         self.assertTrue(filecmp.cmp(fp, fp_obs, shallow=False))
 
-    def test_push_file_to_central(self):
-        self.tester._plugincoupling = 'filesystem'
-
-        ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
-        fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
-
-        # mode: filesystem
-        fp_obs = self.tester.push_file_to_central(fp)
-        self.assertEqual(fp, fp_obs)
-
-        # non existing mode
-        with self.assertRaises(ValueError):
-            self.tester._plugincoupling = 'foo'
-            self.tester.push_file_to_central(fp)
-
-        # change transfer mode to https
-        self.tester._plugincoupling = 'https'
-        fp_source = 'foo.bar'
-        with open(fp_source, 'w') as f:
-            f.write("this is a test\n")
-        self.clean_up_files.append(fp_source)
-        fp_obs = self.tester.push_file_to_central(fp_source)
-        self.assertEqual(fp_source, fp_obs)
+    # def test_push_file_to_central(self):
+    #     self.tester._plugincoupling = 'filesystem'
+
+    #     ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
+    #     fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
+
+    #     # mode: filesystem
+    #     fp_obs = self.tester.push_file_to_central(fp)
+    #     self.assertEqual(fp, fp_obs)
+
+    #     # non existing mode
+    #     with self.assertRaises(ValueError):
+    #         self.tester._plugincoupling = 'foo'
+    #         self.tester.push_file_to_central(fp)
+
+    #     # change transfer mode to https
+    #     self.tester._plugincoupling = 'https'
+    #     fp_source = 'foo.bar'
+    #     with open(fp_source, 'w') as f:
+    #         f.write("this is a test\n")
+    #     self.clean_up_files.append(fp_source)
+    #     fp_obs = self.tester.push_file_to_central(fp_source)
+    #     self.assertEqual(fp_source, fp_obs)
 
 
 if __name__ == '__main__':

From 1d26830e7e19fca7071203a1b505e1af2baea9ed Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 17:50:51 +0200
Subject: [PATCH 20/30] avoid //

---
 .github/workflows/qiita-ci.yml | 2 +-
 qiita_client/qiita_client.py   | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index d7dbfa9..8615d3e 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -106,7 +106,7 @@ jobs:
           export NGINX_FILE=`pwd`/qiita-dev/qiita_pet/nginx_example.conf
           export NGINX_FILE_NEW=`pwd`/qiita-dev/qiita_pet/nginx_example_local.conf
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev#g" ${NGINX_FILE} > ${NGINX_FILE_NEW}
-          sed -i "s#/Users/username/qiita#${PWD}/qiita-dev/#g" ${NGINX_FILE_NEW}
+          sed -i "s#/Users/username/qiita#${PWD}/qiita-dev#g" ${NGINX_FILE_NEW}
           nginx -c ${NGINX_FILE_NEW}
 
           echo "3. Setting up qiita"
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 12ec361..03d58e3 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -790,6 +790,10 @@ def fetch_file_from_central(self, filepath, prefix=''):
             return target_filepath
 
         elif self._plugincoupling == 'https':
+            # strip off root
+            if filepath.startswith(os.path.abspath(os.sep)):
+                filepath = filepath[len(os.path.abspath(os.sep)):]
+
             logger.debug('Requesting file %s from qiita server.' % filepath)
 
             # actual call to Qiita central to obtain file content

From 85c40f2217b534426952521899f8a3548e5f6859 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 17:59:26 +0200
Subject: [PATCH 21/30] remove trailing /

---
 .github/workflows/qiita-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 8615d3e..7c52dfb 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -94,7 +94,7 @@ jobs:
           conda activate qiita
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
-          sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
+          sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
 
           export REDBIOM_HOST="http://localhost:7379"
 

From 7c46442bfc049e828cfd3b204789869ce39c1f47 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 18:03:41 +0200
Subject: [PATCH 22/30] remove debug, activate endpoint, reactivate all tests

---
 .github/workflows/qiita-ci.yml          |  1 +
 qiita_client/tests/test_qiita_client.py | 48 ++++++++++++-------------
 2 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 7c52dfb..446d2b9 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -95,6 +95,7 @@ jobs:
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
+          sed -i "s/ENABLE_HTTPS_PLUGIN_FILETRANSFER = False/ENABLE_HTTPS_PLUGIN_FILETRANSFER = True/" ${QIITA_CONFIG_FP}
 
           export REDBIOM_HOST="http://localhost:7379"
 
diff --git a/qiita_client/tests/test_qiita_client.py b/qiita_client/tests/test_qiita_client.py
index 48ba7bf..15e4f77 100644
--- a/qiita_client/tests/test_qiita_client.py
+++ b/qiita_client/tests/test_qiita_client.py
@@ -412,35 +412,33 @@ def test_fetch_file_from_central(self):
         self.tester._plugincoupling = 'https'
         prefix = join(expanduser("~"), 'kurt')
         self.clean_up_files.append(prefix + fp)
-        print("STEFAN", fp, prefix)
         fp_obs = self.tester.fetch_file_from_central(fp, prefix=prefix)
-        print("STEFAN2", fp_obs)
         self.assertEqual(prefix + fp, fp_obs)
         self.assertTrue(filecmp.cmp(fp, fp_obs, shallow=False))
 
-    # def test_push_file_to_central(self):
-    #     self.tester._plugincoupling = 'filesystem'
-
-    #     ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
-    #     fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
-
-    #     # mode: filesystem
-    #     fp_obs = self.tester.push_file_to_central(fp)
-    #     self.assertEqual(fp, fp_obs)
-
-    #     # non existing mode
-    #     with self.assertRaises(ValueError):
-    #         self.tester._plugincoupling = 'foo'
-    #         self.tester.push_file_to_central(fp)
-
-    #     # change transfer mode to https
-    #     self.tester._plugincoupling = 'https'
-    #     fp_source = 'foo.bar'
-    #     with open(fp_source, 'w') as f:
-    #         f.write("this is a test\n")
-    #     self.clean_up_files.append(fp_source)
-    #     fp_obs = self.tester.push_file_to_central(fp_source)
-    #     self.assertEqual(fp_source, fp_obs)
+    def test_push_file_to_central(self):
+        self.tester._plugincoupling = 'filesystem'
+
+        ainfo = self.tester.get("/qiita_db/artifacts/%s/" % 1)
+        fp = ainfo['files']['raw_forward_seqs'][0]['filepath']
+
+        # mode: filesystem
+        fp_obs = self.tester.push_file_to_central(fp)
+        self.assertEqual(fp, fp_obs)
+
+        # non existing mode
+        with self.assertRaises(ValueError):
+            self.tester._plugincoupling = 'foo'
+            self.tester.push_file_to_central(fp)
+
+        # change transfer mode to https
+        self.tester._plugincoupling = 'https'
+        fp_source = 'foo.bar'
+        with open(fp_source, 'w') as f:
+            f.write("this is a test\n")
+        self.clean_up_files.append(fp_source)
+        fp_obs = self.tester.push_file_to_central(fp_source)
+        self.assertEqual(fp_source, fp_obs)
 
 
 if __name__ == '__main__':

From d9543c9575f0171620c17f4e87897ed5cf52a905 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 19 Aug 2025 23:10:29 +0200
Subject: [PATCH 23/30] set path to / of only filename is given

---
 qiita_client/qiita_client.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 03d58e3..16a7c5e 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -841,9 +841,14 @@ def push_file_to_central(self, filepath):
         elif self._plugincoupling == 'https':
             logger.debug('Submitting file %s to qiita server.' % filepath)
 
+            # target path, i.e. without filename
+            dirpath = os.path.dirname(filepath)
+            if dirpath == "":
+                dirpath = "/"
+
             self.post(
                 '/cloud/push_file_to_central/',
-                files={os.path.dirname(filepath): open(filepath, 'rb')})
+                files={dirpath: open(filepath, 'rb')})
 
             return filepath
 

From b9ade44b1d1a59425c95771e069ab1441549d8fa Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 20 Aug 2025 10:26:18 +0200
Subject: [PATCH 24/30] fix typo

---
 qiita_client/plugin.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index b0cc4c6..71ff9b0 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -185,7 +185,7 @@ def __init__(self, name, version, description, publications=None,
         self.conf_fp = join(conf_dir, "%s_%s.conf" % (self.name, self.version))
 
     def generate_config(self, env_script, start_script, server_cert=None,
-                        plugin_couling=_ALLOWED_PLUGIN_COUPLINGS[0]):
+                        plugin_coupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
         """Generates the plugin configuration file
 
         Parameters
@@ -216,7 +216,7 @@ def generate_config(self, env_script, start_script, server_cert=None,
                                      env_script, start_script,
                                      self._plugin_type, self.publications,
                                      server_cert, client_id, client_secret,
-                                     plugin_couling))
+                                     plugin_coupling))
 
     def _register_command(self, command):
         """Registers a command in the plugin

From e336fbc60d2beee74b04f24574d4bb2636ed4f12 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 27 Aug 2025 10:54:55 +0200
Subject: [PATCH 25/30] enable environment variable, configuration file and
 default for "plugincoupling"

---
 qiita_client/plugin.py       | 21 +++++++++++++++++++--
 qiita_client/qiita_client.py |  1 +
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index 71ff9b0..f57ee78 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -282,6 +282,24 @@ def __call__(self, server_url, job_id, output_dir):
         with open(self.conf_fp, 'U') as conf_file:
             config.readfp(conf_file)
 
+        # the plugin coupling protocoll can be set in three ways
+        # 1. default is always "filesystem", i.e. first value in
+        #    _ALLOWED_PLUGIN_COUPLINGS. This is to be downward compatible.
+        # 2. the plugin configuration can hold a section 'network' with an
+        #    option 'PLUGINCOUPLING'. For old config files, this might not
+        #    (yet) be the case. Therefore, we are double checking existance
+        #    of this section and parameter here.
+        # 3. you can set the environment variable QIITA_PLUGINCOUPLING
+        # Precedence is 3, 2, 1, i.e. the environment variable overrides the
+        # other two ways.
+        plugincoupling = self._ALLOWED_PLUGIN_COUPLINGS[0]
+        if config.has_section('network') and \
+           config.has_option('network', 'PLUGINCOUPLING'):
+            plugincoupling = config.get('network', 'PLUGINCOUPLING')
+        if 'QIITA_PLUGINCOUPLING' in environ.keys() and \
+           environ['QIITA_PLUGINCOUPLING'] is not None:
+            plugincoupling = environ['QIITA_PLUGINCOUPLING']
+
         qclient = QiitaClient(server_url, config.get('oauth2', 'CLIENT_ID'),
                               config.get('oauth2', 'CLIENT_SECRET'),
                               # for this group of tests, confirm optional
@@ -290,8 +308,7 @@ def __call__(self, server_url, job_id, output_dir):
                               # from validating the server's cert using
                               # certifi's pem cache.
                               ca_cert=config.get('oauth2', 'SERVER_CERT'),
-                              plugincoupling=config.get('network',
-                                                        'PLUGINCOUPLING'))
+                              plugincoupling=plugincoupling)
 
         if job_id == 'register':
             self._register(qclient)
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 16a7c5e..7246eb9 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -221,6 +221,7 @@ def __init__(self, server_url, client_id, client_secret, ca_cert=None,
         self._token = None
         self._fetch_token()
 
+        # store protocol for plugin coupling
         self._plugincoupling = plugincoupling
 
     def _fetch_token(self):

From c2d597647b3a22792a7dcd88408895e81d33ceb6 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 27 Aug 2025 21:10:39 +0200
Subject: [PATCH 26/30] revert to qiita dev and remove
 ENABLE_HTTPS_PLUGIN_FILETRANSFER

---
 .github/workflows/qiita-ci.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 446d2b9..d3c6558 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -52,9 +52,8 @@ jobs:
 
           # we need to download qiita directly so we have "easy" access to
           # all config files
-          # wget https://github.com/biocore/qiita/archive/dev.zip
-          # unzip dev.zip
-          git clone -b uncouplePlugins https://github.com/jlab/qiita.git qiita-dev
+          wget https://github.com/biocore/qiita/archive/dev.zip
+          unzip dev.zip
 
           # pull out the port so we can modify the configuration file easily
           pgport=${{ job.services.postgres.ports[5432] }}
@@ -95,7 +94,6 @@ jobs:
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}
-          sed -i "s/ENABLE_HTTPS_PLUGIN_FILETRANSFER = False/ENABLE_HTTPS_PLUGIN_FILETRANSFER = True/" ${QIITA_CONFIG_FP}
 
           export REDBIOM_HOST="http://localhost:7379"
 

From 65e6f4805b4362f7d37f23efb1028e67a5302d02 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 29 Aug 2025 08:23:01 +0200
Subject: [PATCH 27/30] address Antonio's great suggestions

---
 qiita_client/plugin.py       | 18 +++++++++---------
 qiita_client/qiita_client.py |  6 +++---
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index f57ee78..6f47b2f 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -136,11 +136,11 @@ def __init__(self, name, description, can_be_submitted_to_ebi,
 
 
 class BaseQiitaPlugin(object):
-    # default must be first element
-    _ALLOWED_PLUGIN_COUPLINGS = ['filesystem', 'https']
+    _DEFAULT_PLUGIN_COUPLINGS = 'filesystem'
+    _ALLOWED_PLUGIN_COUPLINGS = [_DEFAULT_PLUGIN_COUPLINGS, 'https']
 
     def __init__(self, name, version, description, publications=None,
-                 plugincoupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
+                 plugincoupling=_DEFAULT_PLUGIN_COUPLINGS):
         logger.debug('Entered BaseQiitaPlugin.__init__()')
         self.name = name
         self.version = version
@@ -185,7 +185,7 @@ def __init__(self, name, version, description, publications=None,
         self.conf_fp = join(conf_dir, "%s_%s.conf" % (self.name, self.version))
 
     def generate_config(self, env_script, start_script, server_cert=None,
-                        plugin_coupling=_ALLOWED_PLUGIN_COUPLINGS[0]):
+                        plugin_coupling=_DEFAULT_PLUGIN_COUPLINGS):
         """Generates the plugin configuration file
 
         Parameters
@@ -201,7 +201,7 @@ def generate_config(self, env_script, start_script, server_cert=None,
             HTTPS to it
         plugin_coupling : str
             Type of coupling of plugin to central for file exchange.
-            Valid values are 'filesystem' and 'https'.
+            Valid values: see _ALLOWED_PLUGIN_COUPLINGS.
         """
         logger.debug('Entered BaseQiitaPlugin.generate_config()')
         sr = SystemRandom()
@@ -283,8 +283,8 @@ def __call__(self, server_url, job_id, output_dir):
             config.readfp(conf_file)
 
         # the plugin coupling protocoll can be set in three ways
-        # 1. default is always "filesystem", i.e. first value in
-        #    _ALLOWED_PLUGIN_COUPLINGS. This is to be downward compatible.
+        # 1. default is always "filesystem", i.e. _DEFAULT_PLUGIN_COUPLINGS
+        #    This is to be downward compatible.
         # 2. the plugin configuration can hold a section 'network' with an
         #    option 'PLUGINCOUPLING'. For old config files, this might not
         #    (yet) be the case. Therefore, we are double checking existance
@@ -292,7 +292,7 @@ def __call__(self, server_url, job_id, output_dir):
         # 3. you can set the environment variable QIITA_PLUGINCOUPLING
         # Precedence is 3, 2, 1, i.e. the environment variable overrides the
         # other two ways.
-        plugincoupling = self._ALLOWED_PLUGIN_COUPLINGS[0]
+        plugincoupling = self._DEFAULT_PLUGIN_COUPLINGS
         if config.has_section('network') and \
            config.has_option('network', 'PLUGINCOUPLING'):
             plugincoupling = config.get('network', 'PLUGINCOUPLING')
@@ -372,7 +372,7 @@ class QiitaTypePlugin(BaseQiitaPlugin):
 
     def __init__(self, name, version, description, validate_func,
                  html_generator_func, artifact_types, publications=None,
-                 plugincoupling=BaseQiitaPlugin._ALLOWED_PLUGIN_COUPLINGS[0]):
+                 plugincoupling=BaseQiitaPlugin._DEFAULT_PLUGIN_COUPLINGS):
         super(QiitaTypePlugin, self).__init__(name, version, description,
                                               publications=publications,
                                               plugincoupling=plugincoupling)
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 7246eb9..478945e 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -744,7 +744,7 @@ def _process_files_per_sample_fastq(self, files, prep_info,
 
         return sample_names, prep_info
 
-    def fetch_file_from_central(self, filepath, prefix=''):
+    def fetch_file_from_central(self, filepath, prefix=None):
         """Moves content of a file from Qiita's central BASE_DATA_DIR to a
            local plugin file-system.
 
@@ -764,7 +764,7 @@ def fetch_file_from_central(self, filepath, prefix=''):
             Primarily for testing: prefix the target filepath with this
             filepath prefix to
             a) in 'filesystem' mode: create an actual file copy (for testing)
-               If prefix='', nothing will be copied/moved
+               If prefix=None, nothing will be copied/moved
             b) in 'https' mode: flexibility to locate files differently in
                plugin local file system.
 
@@ -773,7 +773,7 @@ def fetch_file_from_central(self, filepath, prefix=''):
         str : the filepath of the requested file within the local file system
         """
         target_filepath = filepath
-        if prefix != '':
+        if (prefix is not None) and (prefix != ""):
             # strip off root
             if filepath.startswith(os.path.abspath(os.sep)):
                 target_filepath = target_filepath[

From 7b6ca636008b67858a2bf503d16c9a892de5a18e Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 29 Aug 2025 08:41:17 +0200
Subject: [PATCH 28/30] promoting comment to part of readme

---
 README.md                    | 29 +++++++++++++++++++++++++++++
 qiita_client/plugin.py       | 10 ----------
 qiita_client/qiita_client.py |  4 ++--
 3 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 2f7eb4d..21f7855 100644
--- a/README.md
+++ b/README.md
@@ -16,3 +16,32 @@ Also, if Qiita is running with the default server SSL certificate, you need to e
 
 export QIITA_ROOT_CA=<QIITA_INSTALL_PATH>/qiita_core/support_files/ci_rootca.crt
 ```
+
+Configure for cloud computing
+-----------------------------
+In the default scenario, Qiita main and Qiita plugins are executed on the same
+machines, maybe spread across a Slurm or other grid compute cluster, but main
+and plugins have direct access to all files in `BASE_DATA_DIR`.
+
+This can be different, if you set up Qiita within a cloud compute environment,
+where main and plugins do **not** share one file system. In this case, input-
+files must first be transferred from main to plugin, then plugin can do its
+processing and resulting files must be transferred back to main, once
+processing is finished. To achieve this, the qiita_client, as it is part of
+each plugin, provides the two functions for this file transfer
+`fetch_file_from_central` and `push_file_to_central`. According to
+`self._plugincoupling`, these functions operate on different "protocols";
+as of 2025-08-29, either "filesystem" or "https". Switch to **"https"** for
+cloud environments, default is **filesystem**.
+
+The plugin coupling protocoll can be set in three ways
+
+    1. default is always "filesystem", i.e. _DEFAULT_PLUGIN_COUPLINGS
+        This is to be downward compatible.
+    2. the plugin configuration can hold a section 'network' with an
+        option 'PLUGINCOUPLING'. For old config files, this might not
+        (yet) be the case. Therefore, we are double checking existance
+        of this section and parameter here.
+    3. you can set the environment variable QIITA_PLUGINCOUPLING
+        Precedence is 3, 2, 1, i.e. the environment variable overrides the
+        other two ways.
diff --git a/qiita_client/plugin.py b/qiita_client/plugin.py
index 6f47b2f..d455e48 100644
--- a/qiita_client/plugin.py
+++ b/qiita_client/plugin.py
@@ -282,16 +282,6 @@ def __call__(self, server_url, job_id, output_dir):
         with open(self.conf_fp, 'U') as conf_file:
             config.readfp(conf_file)
 
-        # the plugin coupling protocoll can be set in three ways
-        # 1. default is always "filesystem", i.e. _DEFAULT_PLUGIN_COUPLINGS
-        #    This is to be downward compatible.
-        # 2. the plugin configuration can hold a section 'network' with an
-        #    option 'PLUGINCOUPLING'. For old config files, this might not
-        #    (yet) be the case. Therefore, we are double checking existance
-        #    of this section and parameter here.
-        # 3. you can set the environment variable QIITA_PLUGINCOUPLING
-        # Precedence is 3, 2, 1, i.e. the environment variable overrides the
-        # other two ways.
         plugincoupling = self._DEFAULT_PLUGIN_COUPLINGS
         if config.has_section('network') and \
            config.has_option('network', 'PLUGINCOUPLING'):
diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 478945e..091733e 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -773,7 +773,7 @@ def fetch_file_from_central(self, filepath, prefix=None):
         str : the filepath of the requested file within the local file system
         """
         target_filepath = filepath
-        if (prefix is not None) and (prefix != ""):
+        if not prefix:
             # strip off root
             if filepath.startswith(os.path.abspath(os.sep)):
                 target_filepath = target_filepath[
@@ -782,7 +782,7 @@ def fetch_file_from_central(self, filepath, prefix=None):
             target_filepath = os.path.join(prefix, target_filepath)
 
         if self._plugincoupling == 'filesystem':
-            if prefix != '':
+            if not prefix:
                 # create necessary directory locally
                 os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
 

From 296e32c4910de8365e7085781223cf485c47faaf Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 29 Aug 2025 08:47:13 +0200
Subject: [PATCH 29/30] fix formatting

---
 README.md | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 21f7855..a921528 100644
--- a/README.md
+++ b/README.md
@@ -36,12 +36,12 @@ cloud environments, default is **filesystem**.
 
 The plugin coupling protocoll can be set in three ways
 
-    1. default is always "filesystem", i.e. _DEFAULT_PLUGIN_COUPLINGS
-        This is to be downward compatible.
-    2. the plugin configuration can hold a section 'network' with an
-        option 'PLUGINCOUPLING'. For old config files, this might not
-        (yet) be the case. Therefore, we are double checking existance
-        of this section and parameter here.
-    3. you can set the environment variable QIITA_PLUGINCOUPLING
-        Precedence is 3, 2, 1, i.e. the environment variable overrides the
-        other two ways.
+1. default is always `filesystem`, i.e. `_DEFAULT_PLUGIN_COUPLINGS`
+   This is to be downward compatible.
+2. the plugin configuration can hold a section `network` with an
+   option `PLUGINCOUPLING`. For old config files, this might not
+   (yet) be the case. Therefore, we are double checking existance
+   of this section and parameter here.
+3. you can set the environment variable `QIITA_PLUGINCOUPLING`
+   Precedence is 3, 2, 1, i.e. the environment variable overrides
+   the other two ways.
\ No newline at end of file

From 384e97de643653e75b20f42b9c1516bfb6ec5af6 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 29 Aug 2025 08:51:07 +0200
Subject: [PATCH 30/30] "not prefix" did not match properly

---
 qiita_client/qiita_client.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/qiita_client/qiita_client.py b/qiita_client/qiita_client.py
index 091733e..4b34613 100644
--- a/qiita_client/qiita_client.py
+++ b/qiita_client/qiita_client.py
@@ -773,7 +773,7 @@ def fetch_file_from_central(self, filepath, prefix=None):
         str : the filepath of the requested file within the local file system
         """
         target_filepath = filepath
-        if not prefix:
+        if (prefix is not None) and (prefix != ""):
             # strip off root
             if filepath.startswith(os.path.abspath(os.sep)):
                 target_filepath = target_filepath[
@@ -782,7 +782,7 @@ def fetch_file_from_central(self, filepath, prefix=None):
             target_filepath = os.path.join(prefix, target_filepath)
 
         if self._plugincoupling == 'filesystem':
-            if not prefix:
+            if (prefix is not None) and (prefix != ""):
                 # create necessary directory locally
                 os.makedirs(os.path.dirname(target_filepath), exist_ok=True)