geoseeq 0.5.6a5__py3-none-any.whl → 0.5.6a7__py3-none-any.whl

geoseeq/cli/main.py

@@ -53,7 +53,7 @@ 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('0.5.6a5')  # remember to update setup
+    click.echo('0.5.6a7')  # remember to update setup
 
 
 @main.group('advanced')

geoseeq/remote_object.py

@@ -1,4 +1,5 @@
 import logging
+from pandas import to_datetime
 
 from requests.exceptions import HTTPError
 
@@ -57,6 +58,14 @@ class RemoteObject:
 
     def cache_blob(self, blob):
         return self.cache.cache_blob(self, blob)
+    
+    @property
+    def updated_at_timestamp(self):
+        """Return the updated_at field as a unix timestamp (in seconds).
+        
+        timestamp from servercomes as a string: '2024-03-13T09:06:56.582551Z' 
+        """
+        return to_datetime(self.updated_at).timestamp()
 
     def load_blob(self, blob, allow_overwrite=False):
         logger.debug(f"Loading blob. {blob}")

geoseeq/result/file_download.py

@@ -2,7 +2,7 @@
 import urllib.request
 import logging
 import requests
-from os.path import basename, getsize, join, isfile
+from os.path import basename, getsize, join, isfile, getmtime
 from pathlib import Path
 from tempfile import NamedTemporaryFile
 
@@ -82,12 +82,30 @@ class ResultFileDownload:
             return url
         else:
             return self.stored_data[key]
+        
+    
+    def _download_flag_path(self, filename, flag_suffix='.gs_downloaded'):
+        return filename + flag_suffix
+        
+    def download_needs_update(self, filename, flag_suffix='.gs_downloaded', slack=5):
+        """Return True if the file needs to be downloaded, False otherwise.
+        
+        If either the file or the flag file does not exist, return True.
+        If the flag file is older than `updated_at` in the result, return True.
+        Otherwise, return False.
+        """
+        if isfile(filename) and isfile(self._download_flag_path(filename, flag_suffix)):
+            if self.updated_at_timestamp - getmtime(self._download_flag_path(filename, flag_suffix)) > slack:
+                return True
+            return False
+        return True
 
     def download(self, filename=None, flag_suffix='.gs_downloaded', cache=True, head=None, progress_tracker=None):
         """Return a local filepath to the file in this result. Download the file if necessary.
         
         When the file is downloaded, it is cached in the result object. Subsequent calls to download
-        on this object will return the cached file unless cache=False is specified.
+        on this object will return the cached file unless cache=False is specified or the file is updated
+        on the server.
 
         A flag file is created when the file download is complete. Subsequent calls to download
         will return the cached file if the flag file exists unless cache=False is specified.
@@ -101,13 +119,14 @@ class ResultFileDownload:
             filename = self._cached_filename
 
         blob_type = self.stored_data.get("__type__", "").lower()
-        if cache and self._cached_filename:
-            return self._cached_filename
-        flag_filename = filename + flag_suffix
-        if cache and flag_suffix:
-            # check if file and flag file exist, if so, return filename
-            if isfile(filename) and isfile(flag_filename):
-                return filename
+        needs_update = self.download_needs_update(filename, flag_suffix)
+        if not needs_update:
+            if cache and self._cached_filename:
+                return self._cached_filename
+            if cache and flag_suffix:
+                # check if file and flag file exist, if so, return filename
+                if isfile(filename) and isfile(self._download_flag_path(filename, flag_suffix)):
+                    return filename
 
         url = self.get_download_url()
         filepath = download_url(
@@ -116,7 +135,7 @@ class ResultFileDownload:
         )
         if cache and flag_suffix:
             # create flag file
-            open(flag_filename, 'a').close()
+            open(self._download_flag_path(filename, flag_suffix), 'a').close()
         if cache:
             self._cached_filename = filepath
         return filepath

{geoseeq-0.5.6a5.dist-info → geoseeq-0.5.6a7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a5
+Version: 0.5.6a7
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a5.dist-info → geoseeq-0.5.6a7.dist-info}/RECORD

@@ -8,7 +8,7 @@ geoseeq/knex.py,sha256=6fPO8F8yxgBgBXZiliMJvYYjgf_16chfJPyWLe-kpPk,7898
 geoseeq/organization.py,sha256=a9xmGDE0tQsjPJfyFkYnWagxZ8xpdeckkwvkhH6LNIk,2462
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
 geoseeq/project.py,sha256=-9Y2ik0-BpT3iqh89v8VQBbdadhI58oaUP9oZK8oetc,13741
-geoseeq/remote_object.py,sha256=e0mIVNhslu1bjR7zP1Pr5HzD4ZX6S4ezhVdeJyCjf8o,6816
+geoseeq/remote_object.py,sha256=Es-JlAz8iLRmCpAzh1MOwUh2MqtbuQM-p8wHIBAqNlQ,7131
 geoseeq/sample.py,sha256=whgEVk6GnDJJLjn5uTOqFqRtVxZD3BgjTo7brAC5noU,7981
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
 geoseeq/upload_download_manager.py,sha256=Xk5VB5qkDRZGQj6DqXOEzUmphXltF66FAVjxKWaweUE,7090
@@ -22,7 +22,7 @@ geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
 geoseeq/cli/download.py,sha256=ldpqpnRe00utb1EL1T_5CyPbFrZbtauIvOSOHtxz9qc,17656
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=Wm6SuP5uooFPwWhCeN1LjLazB-fOszuqGd6C0Z6E1Vk,3259
+geoseeq/cli/main.py,sha256=ONd6tMTFSLtEQ8MiL53Ig2Gncindxmpcgm8MXBWWCE8,3259
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/run.py,sha256=bx2AV6VIqOSTlxUda78xl0XxcZ8TXlQx02-e7iLQPwI,3838
@@ -63,7 +63,7 @@ geoseeq/plotting/map/map.py,sha256=h2QPLGqe-SamhfaTij53S9cQIiO8orCJUAUh0hRicSM,3
 geoseeq/plotting/map/overlay.py,sha256=4VmxqOESTQra9tPr8b8OLEUhJSit9lNipabeSznEYwE,1795
 geoseeq/result/__init__.py,sha256=IFHIyRV8ZzuKIfwfze1SXgcKwNMcSgMAknLHMkwjXIU,356
 geoseeq/result/bioinfo.py,sha256=QQtbyogrdro9avJSN0713sxLVnVeA24mFw3hWtKDKyw,1782
-geoseeq/result/file_download.py,sha256=n2dE78n5UTxlxtQ6gSnerW7TQEGaiETsb3U9ev0HkT4,4589
+geoseeq/result/file_download.py,sha256=XQA5bdQJJSZIgbFcN09OvVdLq12fnA98kPCIONAkLk0,5568
 geoseeq/result/file_upload.py,sha256=dl5T3bUNfb4JdotldAQxZV0wwYcA_XUTlHOApFl8Bgw,7390
 geoseeq/result/result_file.py,sha256=HG1gKpgIcWImWuf6LduVLEOyW_auuQ-dWld8MNOXGLE,8433
 geoseeq/result/result_folder.py,sha256=6porOXPh7Tpxw3oX5yMRPYQzNCGYqszqmFJd3SwQmTc,11122
@@ -80,9 +80,9 @@ 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-0.5.6a5.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.5.6a5.dist-info/METADATA,sha256=kDZulOXqCBH3DrrT6xqFzoI38W3EXsayd1Gdox8hO-U,4805
-geoseeq-0.5.6a5.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-geoseeq-0.5.6a5.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.5.6a5.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.5.6a5.dist-info/RECORD,,
+geoseeq-0.5.6a7.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.5.6a7.dist-info/METADATA,sha256=2FR5sXg1kzhWv9LZHlcaKxgLUmGSeLpRdxqVZJN861A,4805
+geoseeq-0.5.6a7.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+geoseeq-0.5.6a7.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.5.6a7.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.5.6a7.dist-info/RECORD,,