geoseeq 0.6.6a1__tar.gz → 0.6.8__tar.gz

{geoseeq-0.6.6a1 → geoseeq-0.6.8}/PKG-INFO

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

{geoseeq-0.6.6a1 → geoseeq-0.6.8}/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-0.6.6a1 → geoseeq-0.6.8}/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-0.6.6a1 → geoseeq-0.6.8}/geoseeq/remote_object.py

@@ -165,6 +165,7 @@ class RemoteObject:
             self._modified = False
         else:
             logger.debug(f"RemoteBlob has not been modified. Nothing to save. {self}")
+        return self
 
     def idem(self):
         """Make the state of this object match the server."""

{geoseeq-0.6.6a1 → geoseeq-0.6.8}/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-0.6.6a1 → geoseeq-0.6.8}/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-0.6.6a1 → geoseeq-0.6.8}/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 → geoseeq-0.6.8}/geoseeq.egg-info/PKG-INFO

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

{geoseeq-0.6.6a1 → geoseeq-0.6.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.6.6a1"
+version = "0.6.8"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]