a more versatile function

Author: sjanssen2

qiita_client/testing.py

@@ -8,7 +8,7 @@
 
 from unittest import TestCase
 from os import environ, sep
-from os.path import isabs, join, exists
+from os.path import join, relpath
 from time import sleep
 
 from qiita_client import QiitaClient
@@ -84,29 +84,46 @@ def _wait_for_running_job(self, job_id):
 
         return status
 
-    def _fix_plugincoupling_filepath(self, fp, BASE_DATA_DIR="/qiita_data/"):
-        # In some plugin tests, example files are generated temporarily on
-        # local tmp directories. This is fine for plugincoupling == filesystem
-        # but will cause "File not found errors" when communication through
-        # other protocols as the file actually has never been pushed to Qiita
-        # main. This helper function shall fix this by copying the according
-        # files over to Qiita main WHEN not using "filesystem" and fix the
-        # according file paths, i.e. we need to prepend the BASE_DATA_DIR to
-        # the filename, which should be '/qiita_data/' e.g. here
-        # https://github.com/jlab/qiita-keycloak
-        if not exists(fp):
-            raise ValueError("Filepath does not exist!")
+    def deposite_in_qiita_basedir(self, fps, update_fp_only=False):
+        """Pushs a file to qiita main AND adapts given filepath accordingly.
 
+        A helper function to fix file paths in tests such that they point to the
+        expected BASE_DATA_DIR. This becomes necessary when uncoupling the
+        plugin filesystem as some methods now actually fetches expected files
+        from BASE_DATA_DIR. This will fail for protocols other than filesystem
+        IF files are created locally by the plugin test.
+
+        Parameters
+        ----------
+        fps : str or [str]
+            Filepath or list of filepaths to file(s) that shall be part of
+            BASE_DATA_DIR, but currently points to some tmp file for testing.
+        update_fp_only : bool
+            Some tests operate on filepaths only - files do not actually need to
+            exist. Thus, we don't need to tranfer a file.
+        """
         if self.qclient._plugincoupling == 'filesystem':
-            return fp
+            return fps
+
+        # use artifact 1 info to determine BASA_DATA_DIR, as we know that the
+        # filepath ends with ....raw_data/1_s_G1_L001_sequences.fastq.gz, thus
+        # BASE_DATA_DIR must be the prefix, e.g. /qiita_data/
+        # This might break IF file
+        #    qiita-spots/qiita/qiita_db/support_files/populate_test_db.sql
+        # changes.
+        ainfo = self.qclient.get('/qiita_db/artifacts/1/')
+        base_data_dir = ainfo['files']['raw_forward_seqs'][0]['filepath'][
+            :(-1 * len('raw_data/1_s_G1_L001_sequences.fastq.gz'))]
+        if isinstance(fps, str):
+            if not update_fp_only:
+                self.qclient.push_file_to_central(fps)
+            return join(base_data_dir, relpath(fps, sep))
+        elif isinstance(fps, list):
+            for fp in fps:
+                if not update_fp_only:
+                    self.qclient.push_file_to_central(fp)
+            return [join(base_data_dir, relpath(fp, sep)) for fp in fps]
         else:
-            processed_fp = fp
-            # chop off leading / for join to work properly when prepending
-            # the BASE_DATA_DIR
-            if isabs(processed_fp):
-                processed_fp = processed_fp[len(sep):]
-            processed_fp = join(BASE_DATA_DIR, processed_fp)
-            # ensure file is transferred to qiita main
-            self.qclient.push_file_to_central(fp)
-            # return the filepath prepended with qiita main base_data_dir
-            return processed_fp
+            raise ValueError(
+                "_deposite_in_qiita_basedir is not implemented for type %s"
+                % type(fps))