seqslab-cli 3.2.7__tar.gz → 3.3.1__tar.gz

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.2.7
+Version: 3.3.1
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/python/seqslab/__init__.py

@@ -23,7 +23,7 @@ __all__ = [
 ]
 
 
-__version__ = "3.2.7"
+__version__ = "3.3.1"
 
 LOGGING = {
     "DIR_PATH": "/var/log/seqslab"

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/python/seqslab/cli.py

@@ -26,8 +26,10 @@ from seqslab.plugin import SQLBPlugin
 
 
 def signal_handler(sig, frame):
-    msg = "Ctrl-c was pressed. Do you really want to exit? [y/n] "
-    ans = input(msg)
+    msg = "\nCtrl-c was pressed. Do you really want to exit? [y/n] "
+    sys.stderr.write(msg)
+    ans = input()
+
     if ans == 'y':
         print("")
         exit(1)

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/python/seqslab/drs/api/base.py

@@ -31,6 +31,7 @@ class CopyResult(NamedTuple):
     tags: list
     checksums: dict
     access_methods: dict
+    deleted_time: str
 
     def __str__(self):
         return json.dumps(
@@ -133,7 +134,7 @@ class DRSregister:
     @staticmethod
     def patch_template(name: str = None, tags: List[str] = [], metadata: dict = {}, checksum: str = None,
                        checksum_type: str = None,
-                       updated_time: str = None, **kwargs) -> dict:
+                       updated_time: str = None, deleted_time: str = None, **kwargs) -> dict:
         """
         return only one template
         :param: drs_type, description, aliases, metadata, tags
@@ -151,7 +152,8 @@ class DRSregister:
                                         tags=tags,
                                         metadata=metadata,
                                         checksums=checksums,
-                                        updated_time=updated_time)
+                                        updated_time=updated_time,
+                                        deleted_time=deleted_time)
         return template
 
     @retry(stop=stop_after_attempt(3), wait=WAIT_TWO_SECOND, reraise=True)
@@ -191,14 +193,25 @@ class DRSregister:
             tags=obj.get('tags'),
             access_methods=obj.get('access_methods'),
             checksums=obj.get('checksums'),
+            deleted_time=obj.get('deleted_time')
         )._asdict() for obj in drs_objects]
         return results
 
     def create_payload(self, stdin: List[dict], type: str, **kwargs) -> List[dict]:
-        if type == 'file-blob':
+        if type == 'file':
             payload = stdin
         else:
             payload = self.folder_blob(stdin, **kwargs)
+        if tags := kwargs.get('tags'):
+            for p in payload:
+                p['tags'] = tags
+        if metadata := kwargs.get('metadata'):
+            for p in payload:
+                p['metadata'] = metadata
+        if deleted_time := kwargs.get('deleted_time'):
+            for p in payload:
+                p['deleted_time'] = deleted_time
+
         return payload
 
     def dst_checking(self, dst: str) -> None:
@@ -344,7 +357,8 @@ class DRSregister:
             aliases=obj.get('aliases'),
             tags=obj.get('tags'),
             access_methods=obj.get('access_methods'),
-            checksums=obj.get('checksums')
+            checksums=obj.get('checksums'),
+            deleted_time=obj.get('deleted_time')
         )._asdict()
         return results
 

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/python/seqslab/drs/commands.py

@@ -71,21 +71,24 @@ class BaseDatahub:
                 if not recursive:
                     raise OSError("--recursive (-r) is Required.")
                 if not str(dst).endswith('/') and not kwargs.get('non_interactive'):
-                    user_input = input(
-                        f"Do you mean to rename the `{os.path.basename(str(src))}` to `{os.path.basename(str(dst))}`？(Y/N): ")
+                    sys.stderr.write(f'f"Do you mean to rename the `{os.path.basename(str(src))}` to '
+                                     f'`{os.path.basename(str(dst))}`？(Y/N): "')
+                    user_input = input()
                     if user_input.lower() != "y":
                         raise InterruptedError("Interrupt all the process.")
                 coro = aiocopy.dir_to_blob(URL(*paths), dst, **kwargs)
             else:
                 if not str(dst).endswith('/') and not kwargs.get('non_interactive'):
-                    user_input = input(
-                        f"Do you mean to rename `{os.path.basename(str(src))}` to `{os.path.basename(str(dst))}`？(Y/N): ")
+                    sys.stderr.write(f'f"Do you mean to rename the `{os.path.basename(str(src))}` to '
+                                     f'`{os.path.basename(str(dst))}`？(Y/N): "')
+                    user_input = input()
                     if user_input.lower() != "y":
                         raise InterruptedError("Interrupt all the process.")
                 coro = aiocopy.file_to_blob([URL(*paths)], dst, **kwargs)
         else:
             if not str(dst).endswith('/') and not kwargs.get('non_interactive'):
-                user_input = input(f"Do you mean to upload all the files into {str(dst)}/？(Y/N): ")
+                sys.stderr.write(f"Do you mean to upload all the files into {str(dst)}/？(Y/N): ")
+                user_input = input()
                 if user_input.lower() != "y":
                     raise InterruptedError("Interrupt all the process.")
             files = []
@@ -356,7 +359,7 @@ class BaseDatahub:
               type=str,
               positional=False,
               description="A DRS object ID (required if there is no self URI).")
-    def share_link(self, workspace: str, id: str) -> int:
+    def share(self, workspace: str, id: str) -> int:
         """
         Generate a share link enabling external users to download the DRS object as a zip archive through web
         browsers. The share link expires either after the first successful download or after a period of three months.
@@ -405,10 +408,10 @@ class BaseDatahub:
     @argument("type",
               type=str,
               positional=True,
-              description="If you want to register a file as a blob, please choose file-blob. "
-                          "If you want to register a directory as a blob, please choose dir-blob "
+              description="If you want to register a file as a blob, please choose file. "
+                          "If you want to register a directory as a blob, please choose dir. "
                           "(required).",
-              choices=['file-blob', 'dir-blob'])
+              choices=['file', 'dir'])
     @argument("name",
               type=str,
               description="Specify the name of the object that you want to register "
@@ -487,6 +490,11 @@ class BaseDatahub:
                           "must therefore contain all the required keys [name, file_type, mime_type, description, "
                           "aliases, tags, created_time, updated_time, size, urls, access_tiers, regions, "
                           "Authorizations, checksum, checksum_type, metadata].")
+    @argument("deleted_time",
+              type=str,
+              positional=False,
+              description="Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS "
+                          "object, for example, 2024-01-01 (optional).")
     @argument("output",
               type=str,
               positional=False,
@@ -552,7 +560,8 @@ class BaseDatahub:
                 "aliases": kwargs.get('aliases'),
                 "metadata": json.loads(kwargs.get('metadata')) if kwargs.get('metadata') else None,
                 "tags": kwargs.get('tags'),
-                "id": kwargs.get('id')
+                "id": kwargs.get('id'),
+                "deleted_time": kwargs.get('deleted_time')
             }]
 
         results = backend.create_drsobjects(drs_type='blob', payloads=payloads)
@@ -593,6 +602,11 @@ class BaseDatahub:
               type=str,
               positional=False,
               description="Specify a custom object ID (optional).")
+    @argument("deleted_time",
+              type=str,
+              positional=False,
+              description="Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS "
+                          "object, for example, 2024-01-01 (optional).")
     @argument("output",
               type=str,
               positional=False,
@@ -635,7 +649,8 @@ class BaseDatahub:
                 "metadata": json.loads(kwargs.get('metadata')) if kwargs.get('metadata') else None,
                 "tags": kwargs.get('tags'),
                 "id": kwargs.get('id'),
-                "contents": drs_ids
+                "contents": drs_ids,
+                "deleted_time": kwargs.get('deleted_time')
             }]
 
         results = backend.create_drsobjects(drs_type='bundle', payloads=payloads)
@@ -940,13 +955,17 @@ class BaseDatahub:
                                   proxy=self.proxy,
                                   non_interactive=non_interactive,
                                   expiry_time=expiry_time
-                                  )[0]
-            result['metadata'] = payload.get('metadata')
-            result['tags'] = payload.get('tags')
-            if payload.get('id'):
-                result['id'] = payload.get('id')
-            ret.append(result)
-            if result['status'] != 'complete':
+                                  )
+            if isinstance(result, list):
+                r = result[0]
+                r['metadata'] = payload.get('metadata')
+                r['tags'] = payload.get('tags')
+                if payload.get('id'):
+                    r['id'] = payload.get('id')
+                ret.append(r)
+                if r['status'] != 'complete':
+                    failed = True
+            else:
                 failed = True
         cprint(json.dumps(ret, indent=4), 'yellow')
 
@@ -991,6 +1010,11 @@ class BaseDatahub:
               description="Specify the timestamp when the DRS object was updated (optional). "
                           "The time format must be in RFC3339. "
                           "For example, 2021-09-13 02:54:03.636044+00:00.")
+    @argument("deleted_time",
+              type=str,
+              positional=False,
+              description="Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS "
+                          "object, for example, 2024-01-01 (optional).")
     @argument("stdin",
               type=bool,
               positional=False,

{seqslab-cli-3.2.7 → seqslab-cli-3.3.1}/python/seqslab/drs/internal/aiocopy.py

@@ -286,7 +286,7 @@ async def file_to_blob(
         while progress < len(files):
             tasks = []
             for p in range(progress, progress + min(multiprocessing, len(files) - progress)):
-                _dst = URL(os.path.join(str(dst), os.path.basename(files[p].path))) if str(dst).endswith('/') else dst
+                _dst = URL(os.path.join(str(dst), os.path.basename(files[p].path)), encoded=True) if str(dst).endswith('/') else dst
                 tasks.append(store.upload(_dst, files[p].path, **optargs))
             resp = await asyncio.gather(*tasks, return_exceptions=True)
 
@@ -354,7 +354,7 @@ async def dir_to_blob(
         while progress < len(files):
             tasks = []
             for p in range(progress, progress + min(multiprocessing, len(files) - progress)):
-                uri = dst.with_path(os.path.join(dst.path.strip("/"), relpath[p].strip("/")))
+                uri = dst.with_path(os.path.join(dst.path.strip("/"), relpath[p].strip("/")), encoded=True)
                 tasks.append(store.upload(uri, files[p].path, **optargs))
 
             resp = await asyncio.gather(*tasks, return_exceptions=True)