geoseeq 0.6.10__py3-none-any.whl → 0.6.12.dev0__py3-none-any.whl

geoseeq/cli/main.py

@@ -54,7 +54,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.6.10')  # remember to update pyproject.toml
+    click.echo('0.6.12dev0')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

geoseeq/sample.py

@@ -200,6 +200,7 @@ class Sample(RemoteObject):
         """
         url = f"data/samples/{self.uuid}/all-fastqs"
         blob = self.knex.get(url)
+        print(blob)
         files = {}
         for read_type, folders in blob.items():
             files[read_type] = {}
@@ -208,8 +209,8 @@ class Sample(RemoteObject):
                 if read_type in ["short_read::paired_end"]:
                     files[read_type][folder_name].append(
                         [
-                            self._grn_to_file(file_grns[0]),
-                            self._grn_to_file(file_grns[1]),
+                            self._grn_to_file(file_grns[0][0]),
+                            self._grn_to_file(file_grns[0][1]),
                         ]
                     )
                 else:

geoseeq/upload_download_manager.py

@@ -127,15 +127,22 @@ class GeoSeeqUploadManager:
 
 
 def _download_one_file(args):
-    url, file_path, pbar, ignore_errors, head, log_level, parallel_downloads = args
+    original_url, file_path, callback, pbar, ignore_errors, head, log_level, parallel_downloads = args
     if parallel_downloads:
         _make_in_process_logger(log_level)
-    if isinstance(url, ResultFile):
-        url = url.get_download_url()
+    if isinstance(original_url, ResultFile):
+        url = original_url.get_download_url()
+    else:
+        url = original_url
     try:
         if dirname(file_path):
             makedirs(dirname(file_path), exist_ok=True)
-        return download_url(url, filename=file_path, progress_tracker=pbar, head=head)
+        local_path = download_url(url, filename=file_path, progress_tracker=pbar, head=head)
+        if callback is not None:
+            callback_result = callback(local_path)
+        else:
+            callback_result = None
+        return local_path, original_url, callback_result
     except Exception as e:
         if ignore_errors:
             logger.error(f"Error downloading {url}: {e}")
@@ -153,13 +160,14 @@ class GeoSeeqDownloadManager:
         self.log_level = log_level
         self._result_files = []
 
-    def add_download(self, url, file_path=None, progress_tracker=None):
+
+    def add_download(self, url, file_path=None, progress_tracker=None, callback=None):
         if not file_path:
             if isinstance(url, ResultFile):
                 file_path = url.get_local_filename()
             else:
                 raise ValueError("file_path must be provided if url is not a ResultFile object.")
-        self._result_files.append((url, file_path))
+        self._result_files.append((url, file_path, callback))
 
 
     def add_result_folder_download(self, result_folder, local_folder_path, hidden_files=True):
@@ -170,14 +178,14 @@ class GeoSeeqDownloadManager:
 
     def get_preview_string(self):
         out = ["Download Preview:"]
-        for url, file_path in self._result_files:
+        for url, file_path, _ in self._result_files:
             out.append(f"{url} -> {file_path}")
         return "\n".join(out)
     
     def get_url_string(self):
         self._convert_result_files_to_urls()
         out = []
-        for url, _ in self._result_files:
+        for url, _, _ in self._result_files:
             out.append(url)
         return "\n".join(out)
     
@@ -187,17 +195,21 @@ class GeoSeeqDownloadManager:
     def _convert_result_files_to_urls(self):
         self._result_files = [(
             url.get_download_url() if isinstance(url, ResultFile) else url,
-            file_path,
-        ) for url, file_path in self._result_files]
+            file_path, callback
+        ) for url, file_path, callback in self._result_files]
 
     def download_files(self):
+        """Return a list of 3-ples (local_path, remote url, callback_result).
+        
+        If no callback was provided with the file callback result is None
+        """
         self._convert_result_files_to_urls()
         download_args = [(
-            url, file_path,
+            url, file_path, callback,
             self.progress_tracker_factory(file_path),
             self.ignore_errors, self.head, self.log_level,
             self.n_parallel_downloads > 1
-        ) for url, file_path in self._result_files]
+        ) for url, file_path, callback in self._result_files]
         out = []
         if self.n_parallel_downloads == 1:
             logger.info(f"Downloading files in series.")

{geoseeq-0.6.10.dist-info → geoseeq-0.6.12.dev0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.10
+Version: 0.6.12.dev0
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>
@@ -17,6 +17,7 @@ Requires-Dist: click
 Requires-Dist: pandas
 Requires-Dist: biopython
 Requires-Dist: tqdm
+Dynamic: author
 
 # Geoseeq API Client
 

{geoseeq-0.6.10.dist-info → geoseeq-0.6.12.dev0.dist-info}/RECORD

@@ -9,9 +9,9 @@ geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
 geoseeq/project.py,sha256=kN6m1N4Tlud7saU03Sbir-oIBnXet_Cwi2OVVdaeag0,13929
 geoseeq/remote_object.py,sha256=GYN6PKU7Zz3htIdpFjfZiFejzGqqJHbJyKlefM1Eixk,7151
-geoseeq/sample.py,sha256=OU4H-U8XxsFosfa9wcWWrHq9NVT3nDKZcvPtPGGlLlk,8310
+geoseeq/sample.py,sha256=nlvmSy2WmiOMamkulNRloFPX7E9jVs34m1vO1PSOrHU,8336
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
-geoseeq/upload_download_manager.py,sha256=FMRqLLg77o1qFbWZc5Yc86a2pjeZrrn1rHJr1iaxKCU,8757
+geoseeq/upload_download_manager.py,sha256=jVGZn9xXa4HZUFRFZawRRhfzFc8f2U8x06P-WTDDSNw,9271
 geoseeq/user.py,sha256=tol8i1UGLRrbMw5jeJDnna1ikRgrCDd50Jxz0a1lSgg,690
 geoseeq/utils.py,sha256=ZXpWb2MetUIeLrExiXb7IaOXYrW1pvrdP3o0KWzbwCs,4035
 geoseeq/work_orders.py,sha256=5uLVVfdKE8qh4gGaHkdBpXJGRTujuSg59knWCqEET4A,8071
@@ -22,7 +22,7 @@ geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
 geoseeq/cli/download.py,sha256=W3OswqpHg1thzW6CJ7IcSS0Te2LA2WfgYISQMSl4GQg,18921
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=NPW0EHw2JSdyQ5_nCSPiCsEsy0ZKJ1u7WJa9RQfMmqI,3918
+geoseeq/cli/main.py,sha256=wiZwbHB21qaqERjOk1tvkgX7pyhJv2_vSfe9tp1NItI,3922
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/project.py,sha256=V5SdXm2Hwo2lxrkpwRDedw-mAE4XnM2uwT-Gj1D90VQ,3030
@@ -85,9 +85,9 @@ geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_api_client.py,sha256=TS5njc5pcPP_Ycy-ljcfPVT1hQRBsFVdQ0lCqBmoesU,12810
 tests/test_plotting.py,sha256=TcTu-2ARr8sxZJ7wPQxmbs3-gHw7uRvsgrhhhg0qKik,784
-geoseeq-0.6.10.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.6.10.dist-info/METADATA,sha256=moKunTjFSy4nQVg0X-Es5JmhsyPwtU9DZr-LIR6bCUE,4916
-geoseeq-0.6.10.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
-geoseeq-0.6.10.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.6.10.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.6.10.dist-info/RECORD,,
+geoseeq-0.6.12.dev0.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.6.12.dev0.dist-info/METADATA,sha256=PC7pMgWpLQfZMsADepB4xj7y4zBpNjGJdP0DkcB7ccY,4937
+geoseeq-0.6.12.dev0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+geoseeq-0.6.12.dev0.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.6.12.dev0.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.6.12.dev0.dist-info/RECORD,,

{geoseeq-0.6.10.dist-info → geoseeq-0.6.12.dev0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.7.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any