geoseeq 0.7.8__py3-none-any.whl → 0.7.10__py3-none-any.whl

geoseeq/cli/download.py

@@ -21,6 +21,7 @@ from .shared_params import (
     ignore_errors_option,
     folder_ids_arg,
 )
+from tqdm import tqdm
 from geoseeq.result.file_download import download_url
 from geoseeq.utils import download_ftp
 from geoseeq.id_constructors import (
@@ -598,10 +599,10 @@ def cli_download_fastqs(state,
         samples = handle_multiple_sample_ids(knex, sample_ids, proj=proj, alternate_id_col=alt_sample_id)
     else:
         logger.info("Fetching info for all samples in project.")
-        samples = proj.get_samples()
+        samples = list(tqdm(proj.get_samples(), total=proj.samples_count, desc="Fetching Sample Info"))
 
     result_files_with_names = []
-    for sample in samples:
+    for sample in tqdm(samples, desc="Finding Fastq Files in Samples"):
         try:
             result_files_with_names += _get_sample_result_files_with_names(sample, module_name, which_fastqs_mode, file_name_mode)
         except Exception as e:
@@ -620,7 +621,7 @@ def cli_download_fastqs(state,
         progress_tracker_factory=PBarManager().get_new_bar,
         head=head,
     )
-    for result_file, filename, key in result_files_with_names:
+    for result_file, filename, key in tqdm(result_files_with_names, desc="Adding Fastq Files to Download Manager"):
         callback = None
         if head:
             callback = _trim_fastq_to_complete_reads

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

geoseeq/project.py

@@ -191,23 +191,26 @@ class Project(RemoteObject):
             for sample in self._get_sample_cache:
                 yield sample
             return
+        from geoseeq.id_constructors import sample_from_uuid
         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.uuid = sample_blob["uuid"]
-            sample.metadata = sample_blob["metadata"]
-            if fetch:
-                sample.get()
-            sample._modified = False
-            if cache:
-                self._get_sample_cache.append(sample)
+            if sample_blob["owner_project"]["uuid"] != self.uuid:
+                sample = sample_from_uuid(self.knex, sample_blob["uuid"])  # fetch from elsewhere
             else:
-                yield sample
-        if cache:
-            for sample in self._get_sample_cache:
-                yield sample
+                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:
+                    self._get_sample_cache.append(sample)
+            yield sample
 
     def get_sample_uuids(self, cache=True, error_handler=None):
         """Yield samples uuids fetched from the server."""

{geoseeq-0.7.8.dist-info → geoseeq-0.7.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.8
+Version: 0.7.10
 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-0.7.8.dist-info → geoseeq-0.7.10.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=jryxHMx5PdQNaMJWjlzgQmxJt_s2M-HAHARBCPd1Vzc,17075
+geoseeq/project.py,sha256=wtsakR0jZ07rTNtkkzsEug6aWB97eqLjqQ5EZ1XpHo0,17410
 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=RZolqwaIVRa7fkaN9AZxswJ7BSaAg6Itk0SKs_dCjVs,25422
+geoseeq/cli/download.py,sha256=j5y0VsqK5-FSHpkM4kYGJB1OERIB6dsVJuuUJjqub7E,25609
 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=s6iWmXFp7a3C_If5NxTo_mBuRhPqp3VWeN5iXf60fzk,4133
+geoseeq/cli/main.py,sha256=a47KNif6e1y7EqFJ3hF00j41pjPW8MHfu0XxyfKtBKY,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-0.7.8.dist-info/METADATA,sha256=Z-HVBUxxGG8YGY3JSw5PHjkujPgsso9b5vUzfRbrG28,5652
-geoseeq-0.7.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-geoseeq-0.7.8.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.7.8.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.7.8.dist-info/RECORD,,
+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,,