geoseeq 0.7.10__py3-none-any.whl → 0.7.11__py3-none-any.whl

geoseeq/cli/download.py

@@ -428,7 +428,7 @@ def _get_sample_result_files_with_names(sample, module_name=None, which_fastqs_m
     return result_files_with_names
 
 
-def _make_read_configs(download_results, config_dir="."):
+def _make_read_configs(download_results, config_dir=".", name_mode="name"):
     """Make JSON config files that look like this.
     
     {
@@ -441,12 +441,14 @@ def _make_read_configs(download_results, config_dir="."):
         "geoseeq_uuid": "05bf22e9-9d25-42db-af25-31bc538a7006"
     }
     """
+    
     config_blobs = {}  # sample ids -> config_blobs
     download_results = sorted(download_results, key=lambda x: x[1][3])  # sort by lane number
     for local_path, (sample, read_type, read_num, lane_num), _ in download_results:
         if sample.name not in config_blobs:
-            config_blobs[sample.name] = {
-                "sample_name": sample.name,
+            sample_name = sample.name if name_mode == "name" else sample.uuid
+            config_blobs[sample_name] = {
+                "sample_name": sample_name,
                 "reads_1": [],
                 "reads_2": [],
                 "fastq_checksum": "",
@@ -455,9 +457,9 @@ def _make_read_configs(download_results, config_dir="."):
                 "geoseeq_uuid": sample.uuid,
             }
         if read_num == 1:
-            config_blobs[sample.name]["reads_1"].append(local_path)  # sorted by lane number
+            config_blobs[sample_name]["reads_1"].append(local_path)  # sorted by lane number
         else:
-            config_blobs[sample.name]["reads_2"].append(local_path)
+            config_blobs[sample_name]["reads_2"].append(local_path)
 
     # make config dir
     makedirs(config_dir, exist_ok=True)
@@ -635,4 +637,5 @@ def cli_download_fastqs(state,
         logger.info(f'Downloading {len(download_manager)} files to {target_dir}')
         download_results = download_manager.download_files()
         if config_dir:
-            _make_read_configs(download_results, config_dir)
+            name_mode = "name" if file_name_mode != "sample-uuid" else "uuid"
+            _make_read_configs(download_results, config_dir, name_mode=name_mode)

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("0.7.10")  # remember to update pyproject.toml
+    click.echo("0.7.11")  # remember to update pyproject.toml
 
 
 @main.group("advanced")

geoseeq/project.py

@@ -202,10 +202,6 @@ class Project(RemoteObject):
                 sample = self.sample(sample_blob["name"])
                 sample_blob["library"] = sample_blob["owner_project"]["uuid"]
                 sample.load_blob(sample_blob)
-                # sample.uuid = sample_blob["uuid"]
-                # sample.metadata = sample_blob["metadata"]
-                # if fetch:
-                #     sample.get()
                 sample._modified = False
                 sample._already_fetched = True
                 if cache:

{geoseeq-0.7.10.dist-info → geoseeq-0.7.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.10
+Version: 0.7.11
 Summary: GeoSeeq command line tools and python API
 Project-URL: Homepage, https://github.com/biotia/geoseeq_api_client
 Project-URL: Issues, https://github.com/biotia/geoseeq_api_client/issues

{geoseeq-0.7.10.dist-info → geoseeq-0.7.11.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=wtsakR0jZ07rTNtkkzsEug6aWB97eqLjqQ5EZ1XpHo0,17410
+geoseeq/project.py,sha256=oNC-x0fsfYL0F6v-N6QTaDht7T4NKlFJ4uPG9jRZSF4,17235
 geoseeq/remote_object.py,sha256=GYN6PKU7Zz3htIdpFjfZiFejzGqqJHbJyKlefM1Eixk,7151
 geoseeq/sample.py,sha256=oVUNnfqsRCCDUZdyI6fGylaMgLHd_7FLLJVGuOd5Jb8,10946
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
@@ -21,11 +21,11 @@ geoseeq/cli/__init__.py,sha256=4WnK87K5seRK3SGJAxNWnQTqyg5uBhdhrOrzB1D4b3M,24
 geoseeq/cli/constants.py,sha256=NtRSNBuna42605LE0sVywTPfmzYQnG-3yrT_M7Ml5B0,213
 geoseeq/cli/copy.py,sha256=02U9kdrAIbbM8MlRMLL6p-LMYFSuRObE3h5jyvcL__M,2275
 geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
-geoseeq/cli/download.py,sha256=j5y0VsqK5-FSHpkM4kYGJB1OERIB6dsVJuuUJjqub7E,25609
+geoseeq/cli/download.py,sha256=4ZqT63Tsh4QNTbWdYXLS6R-8fJVHagVFWCnrzNFdh1I,25808
 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=a47KNif6e1y7EqFJ3hF00j41pjPW8MHfu0XxyfKtBKY,4134
+geoseeq/cli/main.py,sha256=DJKc5NCjNiluXdEKt5biqqiGleUVrh75Trd30Sh8O18,4134
 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
@@ -92,8 +92,8 @@ geoseeq/vc/vc_cache.py,sha256=P4LXTbq2zOIv1OhP7Iw5MmypR2vXuy29Pq5K6gRvi-M,730
 geoseeq/vc/vc_dir.py,sha256=A9CLTh2wWCRzZjiLyqXD1vhtsWZGD3OjaMT5KqlfAXI,457
 geoseeq/vc/vc_sample.py,sha256=qZeioWydXvfu4rGMs20nICfNcp46y_XkND-bHdV6P5M,3850
 geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
-geoseeq-0.7.10.dist-info/METADATA,sha256=euOGPcWdDVCzrLVj-YrLJiI7y8OLqT2HQMih6qjvK4k,5653
-geoseeq-0.7.10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-geoseeq-0.7.10.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.7.10.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.7.10.dist-info/RECORD,,
+geoseeq-0.7.11.dist-info/METADATA,sha256=jdyXuZXsHF2KyE5zEHgZLMFCV6PIEBKFDQ8P1aTdf6c,5653
+geoseeq-0.7.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+geoseeq-0.7.11.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.7.11.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.7.11.dist-info/RECORD,,