geoseeq 0.6.6a1__py3-none-any.whl → 0.6.8a1__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('0.6.6')  # remember to update setup
+    click.echo('0.6.8')  # remember to update setup
 
 
 @main.group('advanced')

geoseeq/cli/shared_params/opts_and_args.py

@@ -14,7 +14,7 @@ private_option = click.option('--private/--public', default=True, help='Make obj
 link_option = click.option(
     '--link-type',
     default='upload',
-    type=click.Choice(['upload', 's3', 'ftp', 'azure', 'sra']),
+    type=click.Choice(['upload', 's3', 'ftp', 'azure', 'sra', 'http']),
     help='Link the files from a cloud storage service instead of copying them'
 )
 yes_option = click.option('--yes/--confirm', default=False, help='Skip confirmation prompts')

geoseeq/result/file_download.py

@@ -15,6 +15,7 @@ from .resumable_download_tracker import ResumableDownloadTracker
 
 logger = logging.getLogger("geoseeq_api")  # Same name as calling module
 
+
 def url_to_id(url):
     url = url.split("?")[0]
     return md5(url.encode()).hexdigest()[:16]
@@ -80,6 +81,8 @@ def guess_download_kind(url):
         return 's3'
     elif 'ftp' in url:
         return 'ftp'
+    elif 'http' in url:  # note works for https too
+        return 'http'
     else:
         return 'generic'
 
@@ -103,6 +106,9 @@ def download_url(url, kind='guess', filename=None, head=None, progress_tracker=N
         return _download_head(url, filename, head=head)
     elif kind == 'ftp':
         return download_ftp(url, filename, head=head)
+    elif kind == 'http':
+        # for http[s] files we care about head is often respected in practice (e.g. by the ENA) 
+        return _download_head(url, filename, head=head, progress_tracker=progress_tracker)
     else:
         raise ValueError(f"Unknown download kind: {kind}")
 
@@ -113,7 +119,7 @@ class ResultFileDownload:
     def get_download_url(self):
         """Return a URL that can be used to download the file for this result."""
         blob_type = self.stored_data.get("__type__", "").lower()
-        if blob_type not in ["s3", "sra", "ftp", "azure"]:
+        if blob_type not in ["s3", "sra", "ftp", "azure", "http"]:
             raise ValueError(f'Unknown URL type: "{blob_type}"')
         key = 'url' if 'url' in self.stored_data else 'uri'
         if blob_type in ["s3", "azure"]:
@@ -127,7 +133,6 @@ class ResultFileDownload:
         else:
             return self.stored_data[key]
         
-    
     def _download_flag_path(self, filename, flag_suffix='.gs_downloaded'):
         return filename + flag_suffix
         

geoseeq/result/result_file.py

@@ -149,6 +149,9 @@ class ResultFile(RemoteObject, ResultFileUpload, ResultFileDownload):
             return self.link_sra(*args, **kwargs)
         elif link_type == "azure":
             return self.link_azure(*args, **kwargs)
+        elif link_type == "http":
+            return self.link_http(*args, **kwargs)
+        assert False, f"Unknown link type: {link_type}"
 
     def link_s3(self, url, endpoint_url=None):
         """Link this field to an S3 object.
@@ -207,6 +210,18 @@ class ResultFile(RemoteObject, ResultFileUpload, ResultFileDownload):
         }
         return self.save()
     
+    def link_http(self, url):
+        """Link this field to an HTTP object.
+
+        Args:
+            url (str): The URL of the HTTP object.
+        """
+        self.stored_data = {
+            "__type__": "http",
+            "url": url,
+        }
+        return self.save()
+    
     def idem(self):
         try:
             return super().idem()

geoseeq/sample.py

@@ -215,7 +215,7 @@ class Sample(RemoteObject):
                         )
                     else:
                         files[read_type][folder_name].append(
-                            self._grn_to_file(file_grn)
+                            self._grn_to_file(file_grn[0])
                         )
         return files
     

{geoseeq-0.6.6a1.dist-info → geoseeq-0.6.8a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.6.6a1
+Version: 0.6.8a1
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.6a1.dist-info → geoseeq-0.6.8a1.dist-info}/RECORD

@@ -9,7 +9,7 @@ geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
 geoseeq/project.py,sha256=pVx4etzkYmYAYwcPJsjN9PrI-7GZEkAaz2Q5GFdng1s,13810
 geoseeq/remote_object.py,sha256=Es-JlAz8iLRmCpAzh1MOwUh2MqtbuQM-p8wHIBAqNlQ,7131
-geoseeq/sample.py,sha256=KkN9fUTkjTIvozR5y2pS9c6rt4jwHN2Bap38dU_Lrck,8391
+geoseeq/sample.py,sha256=TNtYL8ph2pG0R5ukDC4J2AwdA0xDK9Bx7dVQmQKIMQs,8394
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
 geoseeq/upload_download_manager.py,sha256=FMRqLLg77o1qFbWZc5Yc86a2pjeZrrn1rHJr1iaxKCU,8757
 geoseeq/user.py,sha256=tol8i1UGLRrbMw5jeJDnna1ikRgrCDd50Jxz0a1lSgg,690
@@ -22,7 +22,7 @@ geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
 geoseeq/cli/download.py,sha256=QTNA7qFjCdRJg2vKbAm5yH8WGlcF5fb5bSjm5QiI4XE,17768
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=JDSr0egFAe6PdEO1CBVJBn23zwExgjQVdrU5aHRzVQc,3908
+geoseeq/cli/main.py,sha256=Xs4Os4wKljPYhXK0g01FkcUWL-kIZjH_Cc7U87FFKNM,3908
 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
@@ -37,7 +37,7 @@ geoseeq/cli/shared_params/common_state.py,sha256=jiHZtL3TATMjEoqhbO7HT8KkLJr1QPs
 geoseeq/cli/shared_params/config.py,sha256=HQ0xQh_jdt3EKI5VXYqQXzo-s8Rm6YlziMyVX-kg598,1072
 geoseeq/cli/shared_params/id_handlers.py,sha256=501K9sCVkI0YGDQ62vXk_DM5lMMDrdB5spIS3cw9x9U,9299
 geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr3eeD3HNqzac,2741
-geoseeq/cli/shared_params/opts_and_args.py,sha256=LrDkv9WtUryM4uUMXPRk04-EBcTQ7q5V6Yu-XRDUvvA,2083
+geoseeq/cli/shared_params/opts_and_args.py,sha256=_DcJ-TqgrbBaeDd-kuHEx2gLZPQN6EHZYWh8Ag-d8Vg,2091
 geoseeq/cli/upload/__init__.py,sha256=3C9_S9t7chmYU-2ot89NV03x-EtmsjibulErKaU9w1k,627
 geoseeq/cli/upload/upload.py,sha256=JZkhe1q3KOp7-tKyzwi860TQhZoNDnZs4yB2PJhOjl0,10081
 geoseeq/cli/upload/upload_advanced.py,sha256=Jq5eGe-wOdrzxGWVwaFPg0BAJcW0YSx_eHEmYjJeKuA,3434
@@ -66,9 +66,9 @@ geoseeq/plotting/map/overlay.py,sha256=4VmxqOESTQra9tPr8b8OLEUhJSit9lNipabeSznEY
 geoseeq/result/__init__.py,sha256=IFHIyRV8ZzuKIfwfze1SXgcKwNMcSgMAknLHMkwjXIU,356
 geoseeq/result/bioinfo.py,sha256=QQtbyogrdro9avJSN0713sxLVnVeA24mFw3hWtKDKyw,1782
 geoseeq/result/file_chunker.py,sha256=bXq1csuRtqMB5sbH-AfWo6gdPwrivv5DJPuHVj-h08w,1758
-geoseeq/result/file_download.py,sha256=KalIkwBbFI8xRpbhToixfd1KMAu_0FYwxdKq146NAHw,7832
+geoseeq/result/file_download.py,sha256=F0qSlZyrzh7G2R-qxmGwRicTJiojBUbcBN_SWF1sZac,8123
 geoseeq/result/file_upload.py,sha256=xs1DrI-h4ZP7xN8HPBc3SFpcPAxR5HAolraP1Zu7tvE,10648
-geoseeq/result/result_file.py,sha256=1Yj9fkZhds3J-tay6eNH2-EHi00MovHGV1M80_ckHD8,8677
+geoseeq/result/result_file.py,sha256=A2PIdkuNY0czXLXPenSRdUPdCFdjJGGqs3nBOflNwnA,9099
 geoseeq/result/result_folder.py,sha256=-m1lDVLpNHKy-JUGihboVzvdMJEnHossyRnxmBe1XLo,11140
 geoseeq/result/resumable_download_tracker.py,sha256=YEzqHBBnE7L3XokTvlTAhHZ8TcDTIE_pyTQ7YadOfbU,3667
 geoseeq/result/resumable_upload_tracker.py,sha256=2aI09gYz2yw63jEXqs8lmCRKQ79TIc3YuPETvP0Jeek,3811
@@ -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-0.6.6a1.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.6.6a1.dist-info/METADATA,sha256=x_h48P9AwhPkC3Tn-3ExOsm6v-3_exvPPsfeqfAPTqI,4917
-geoseeq-0.6.6a1.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-geoseeq-0.6.6a1.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.6.6a1.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.6.6a1.dist-info/RECORD,,
+geoseeq-0.6.8a1.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.6.8a1.dist-info/METADATA,sha256=VYP9ZUkWW0VlupB6D-V5esY4GJeCihiFFAPKukdYbm4,4917
+geoseeq-0.6.8a1.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+geoseeq-0.6.8a1.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.6.8a1.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.6.8a1.dist-info/RECORD,,

{geoseeq-0.6.6a1.dist-info → geoseeq-0.6.8a1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.1.2)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any