geoseeq 0.6.14.dev4__py3-none-any.whl → 0.6.14.dev6__py3-none-any.whl

geoseeq/cli/download.py

@@ -379,10 +379,10 @@ def cli_download_ids(state, cores, target_dir, file_name, yes, download, head, i
 
 
 def _get_sample_result_files_with_names(sample, module_name=None, first=False):
+    result_files_with_names = []
     for read_type, folder in sample.get_all_fastqs().items():
         if module_name and module_name != read_type:
             continue
-        result_files_with_names = []
         for folder_name, result_files in folder.items():
             for lane_num, result_file in enumerate(result_files):
                 lane_num = lane_num + 1  # 1 indexed

geoseeq/cli/main.py

@@ -55,7 +55,7 @@ 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('0.6.14dev4')  # remember to update pyproject.toml
+    click.echo('0.6.14dev6')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

geoseeq/cli/upload/upload_reads.py

@@ -118,11 +118,19 @@ def _is_fastq(path, fq_exts=['.fastq', '.fq'], compression_exts=['.gz', '.bz2',
     return False
 
 
-def flatten_list_of_fastqs(filepaths):
+def _is_fasta(path, fa_exts=['.fasta', '.fa'], compression_exts=['.gz', '.bz2', '']):
+    for fa_ext in fa_exts:
+        for compression_ext in compression_exts:
+            if path.endswith(fa_ext + compression_ext):
+                return True
+    return False
+
+
+def flatten_list_of_fastxs(filepaths):
     """Turn a list of fastq filepaths and txt files containing fastq filepaths into a single list of fastq filepaths."""
     flattened = []
     for path in filepaths:
-        if _is_fastq(path):
+        if _is_fastq(path) or _is_fasta(path):
             flattened.append(path)
         else:
             with open(path) as f:
@@ -218,7 +226,7 @@ def cli_upload_reads_wizard(state, cores, overwrite, yes, regex, private, link_t
     """
     knex = state.get_knex()
     proj = handle_project_id(knex, project_id, yes, private)
-    filepaths = {basename(line): line for line in flatten_list_of_fastqs(fastq_files)}
+    filepaths = {basename(line): line for line in flatten_list_of_fastxs(fastq_files)}
     click.echo(f'Found {len(filepaths)} files to upload.', err=True)
     regex = _get_regex(knex, filepaths, module_name, proj, regex)
     groups = _group_files(knex, filepaths, module_name, regex, yes)

geoseeq/project.py

@@ -170,20 +170,19 @@ class Project(RemoteObject):
         Alias for result_folder."""
         return self.result_folder(*args, **kwargs)
 
-    def get_samples(self, cache=True, error_handler=None):
+    def get_samples(self, cache=True, error_handler=None, fetch=True):
         """Yield samples fetched from the server."""
         if cache and self._get_sample_cache:
             for sample in self._get_sample_cache:
                 yield sample
             return
-        url = f"sample_groups/{self.uuid}/samples"
+        url = f"sample_groups/{self.uuid}/samples-list?page=1&page_size=100"
         for sample_blob in paginated_iterator(self.knex, url, error_handler=error_handler):
             sample = self.sample(sample_blob["name"])
-            sample.load_blob(sample_blob)
-            sample.cache_blob(sample_blob)
-            # We just fetched from the server so we change the RemoteObject
-            # meta properties to reflect that
-            sample._already_fetched = True
+            sample.uuid = sample_blob["uuid"]
+            sample.metadata = sample_blob["metadata"]
+            if fetch:
+                sample.get()
             sample._modified = False
             if cache:
                 self._get_sample_cache.append(sample)
@@ -199,7 +198,7 @@ class Project(RemoteObject):
             for sample in self._get_sample_cache:
                 yield sample.uuid
             return
-        url = f"sample_groups/{self.uuid}/samples"
+        url = f"sample_groups/{self.uuid}/samples-list?page=1"
         for sample_blob in paginated_iterator(self.knex, url, error_handler=error_handler):
             yield sample_blob['uuid']
 

geoseeq/result/file_download.py

@@ -107,7 +107,9 @@ def download_url(url, kind='guess', filename=None, head=None, progress_tracker=N
     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) 
+        # for http[s] files we care about head is often respected in practice (e.g. by the ENA)
+        if not url.startswith("http"):
+            url = "https://" + url
         return _download_head(url, filename, head=head, progress_tracker=progress_tracker)
     else:
         raise ValueError(f"Unknown download kind: {kind}")
@@ -179,7 +181,7 @@ class ResultFileDownload:
 
         url = self.get_download_url()
         filepath = download_url(
-            url, blob_type, filename,
+            url, kind=blob_type, filename=filename,
             head=head, progress_tracker=progress_tracker,
         )
         if cache and flag_suffix:

{geoseeq-0.6.14.dev4.dist-info → geoseeq-0.6.14.dev6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev4
+Version: 0.6.14.dev6
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.14.dev4.dist-info → geoseeq-0.6.14.dev6.dist-info}/RECORD

@@ -7,7 +7,7 @@ geoseeq/file_system_cache.py,sha256=HzVZWtwLD2fjWWSo_UfWmGeBltm9He4lP_OqzKwNGWg,
 geoseeq/knex.py,sha256=zcjafsmUn9SC3LlRnvvaXpr-pHYZ0IXk7LpzuUoE3MI,8312
 geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
-geoseeq/project.py,sha256=kN6m1N4Tlud7saU03Sbir-oIBnXet_Cwi2OVVdaeag0,13929
+geoseeq/project.py,sha256=Ba3yvrSyPVnEM5_VGSQu6YPH3CTwE3fHs4JjAepEK7g,13880
 geoseeq/remote_object.py,sha256=GYN6PKU7Zz3htIdpFjfZiFejzGqqJHbJyKlefM1Eixk,7151
 geoseeq/sample.py,sha256=HAfMiDPHp1UJgIA2lI6oGnNit4YKyj7nx9X07CCN98U,8316
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
@@ -20,11 +20,11 @@ geoseeq/cli/__init__.py,sha256=4WnK87K5seRK3SGJAxNWnQTqyg5uBhdhrOrzB1D4b3M,24
 geoseeq/cli/constants.py,sha256=Do5AUf9lMO9_P8KpFJ3XwwFBAWsxSjZ6sx9_QEGyC_c,176
 geoseeq/cli/copy.py,sha256=02U9kdrAIbbM8MlRMLL6p-LMYFSuRObE3h5jyvcL__M,2275
 geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
-geoseeq/cli/download.py,sha256=Aul4Gk49e0Y0R4kH7sD1iJ9SgJDJsrRfXjfRo88-SJE,21309
+geoseeq/cli/download.py,sha256=cOLIVzAfxpOJnSd4WKWR-HCkOrKjPMbgYaNXDSd9i90,21305
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/find_grn.py,sha256=oMDxkzGQBQb2_cCuvmwoeHOsFHqyO9RLeJzrB6bAe5M,439
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=olfB8IkiY7bO2XbppkWrTdm-PMG0u_jccZk-2Aj0GMM,3987
+geoseeq/cli/main.py,sha256=ufRoSCJh1D5jas9rZO6ypKRHTRh0jL2ET7fXAV5oD2E,3987
 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
@@ -43,7 +43,7 @@ geoseeq/cli/shared_params/opts_and_args.py,sha256=_DcJ-TqgrbBaeDd-kuHEx2gLZPQN6E
 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
-geoseeq/cli/upload/upload_reads.py,sha256=dvmOVq0lJSbpQDyWkNEnZmhkMvfEByV-i8xD75Ai4dA,10706
+geoseeq/cli/upload/upload_reads.py,sha256=Q5gihBmQM9jQx0QSj5qPH8sc8CkVNE1_DD5JradXBdg,10990
 geoseeq/contrib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geoseeq/contrib/ncbi/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geoseeq/contrib/ncbi/api.py,sha256=WQeLoGA_-Zha-QeSO8_i7HpvXyD8UkV0qc5okm11KiA,1056
@@ -68,7 +68,7 @@ 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=F0qSlZyrzh7G2R-qxmGwRicTJiojBUbcBN_SWF1sZac,8123
+geoseeq/result/file_download.py,sha256=5IXg_dIWlrRHBJQssO42da5_bIJOyH0_b8K2KWVAFBE,8210
 geoseeq/result/file_upload.py,sha256=xs1DrI-h4ZP7xN8HPBc3SFpcPAxR5HAolraP1Zu7tvE,10648
 geoseeq/result/result_file.py,sha256=A2PIdkuNY0czXLXPenSRdUPdCFdjJGGqs3nBOflNwnA,9099
 geoseeq/result/result_folder.py,sha256=-m1lDVLpNHKy-JUGihboVzvdMJEnHossyRnxmBe1XLo,11140
@@ -87,9 +87,9 @@ 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-0.6.14.dev4.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.6.14.dev4.dist-info/METADATA,sha256=5d01roEOeHuNDH3Jgh2ScJyhc7mdn3JbB2rq32vV90k,4937
-geoseeq-0.6.14.dev4.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-geoseeq-0.6.14.dev4.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.6.14.dev4.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.6.14.dev4.dist-info/RECORD,,
+geoseeq-0.6.14.dev6.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.6.14.dev6.dist-info/METADATA,sha256=Yg0PM7m43T1S2-aC-vXwJsQ4SDh1JqkUqAbL2qePFBk,4937
+geoseeq-0.6.14.dev6.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+geoseeq-0.6.14.dev6.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.6.14.dev6.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.6.14.dev6.dist-info/RECORD,,