seqslab-cli 3.3.4__tar.gz → 3.3.6__tar.gz

{seqslab-cli-3.3.4/python/seqslab_cli.egg-info → seqslab-cli-3.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.4
+Version: 3.3.6
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

{seqslab-cli-3.3.4 → seqslab-cli-3.3.6}/python/seqslab/__init__.py

@@ -21,6 +21,6 @@ name = "seqslab"
 __all__ = []
 
 
-__version__ = "3.3.4"
+__version__ = "3.3.6"
 
 LOGGING = {"DIR_PATH": "/var/log/seqslab"}

seqslab-cli-3.3.6/python/seqslab/color.py

@@ -0,0 +1,8 @@
+def color_handler(func):
+    ColorDict = {"yellow": "\033[01;33m", "green": "\033[01;32m", "red": "\033[01;31m"}
+
+    def inner_function(*args, **kwargs):
+        kwargs.update(ColorDict)
+        return func(*args, **kwargs)
+
+    return inner_function

{seqslab-cli-3.3.4 → seqslab-cli-3.3.6}/python/seqslab/drs/api/base.py

@@ -333,9 +333,9 @@ class DRSregister:
             folder_stdin["access_methods"].clear()
             for i, dsts in enumerate(dsts_list):
                 folder_stdin["access_methods"].append(access_method_infos[i])
-                folder_stdin["access_methods"][i]["access_url"][
-                    "url"
-                ] = self.common_root(dsts=dsts, workspace=kwargs.get("workspace"))
+                folder_stdin["access_methods"][i]["access_url"]["url"] = (
+                    self.common_root(dsts=dsts, workspace=kwargs.get("workspace"))
+                )
 
         folder_stdin["name"] = kwargs.get(
             "name",

{seqslab-cli-3.3.4 → seqslab-cli-3.3.6}/python/seqslab/drs/commands.py

@@ -15,10 +15,12 @@ from urllib.parse import unquote
 
 from jsonpath_ng.ext import parse
 from nubia import argument, command, context
+from seqslab.color import color_handler
 from seqslab.drs.utils.atgxmetadata import AtgxMetaData
 from seqslab.drs.utils.progressbar import ProgressBarObject
 from seqslab.exceptions import async_exception_handler, exception_handler
 from seqslab.runsheet.runsheet import RunSheet
+from seqslab.workspace.internal.common import get_factory as get_workspace_factory
 from tabulate import tabulate
 from termcolor import cprint
 from yarl import URL
@@ -57,6 +59,7 @@ class BaseDatahub:
         return context.get_context().args.proxy
 
     @staticmethod
+    @color_handler
     @exception_handler
     def _upload(src: URL, dst: URL, recursive: bool, **kwargs) -> list:
         # copy from local to cloud
@@ -67,33 +70,40 @@ class BaseDatahub:
             if os.path.isdir(paths[0]):
                 if not recursive:
                     raise OSError("--recursive (-r) is Required.")
-                if not str(dst).endswith("/") and not kwargs.get("non_interactive"):
-                    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.")
+                sys.stderr.write(
+                    f"{kwargs['green']}"
+                    + "Destination Path: "
+                    + f"{kwargs['red']}"
+                    + f"{str(dst)}\n"
+                    + f"{kwargs['yellow']}\0"
+                )
                 coro = aiocopy.dir_to_blob(URL(*paths), dst, **kwargs)
             else:
-                if not str(dst).endswith("/") and not kwargs.get("non_interactive"):
+                if str(dst).endswith("/"):
+                    sys.stderr.write(
+                        f"{kwargs['green']}"
+                        + "Destination Path: "
+                        + f"{kwargs['red']}"
+                        + f"{os.path.join(str(dst), os.path.basename(str(src)))} \n"
+                        + f"{kwargs['yellow']}\0"
+                    )
+                else:
                     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): "'
+                        f"{kwargs['green']}"
+                        + "Destination Path: "
+                        + f"{kwargs['red']}"
+                        + f"{str(dst)} \n"
+                        + f"{kwargs['yellow']}\0"
                     )
-                    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"):
-                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.")
+            sys.stderr.write(
+                f"{kwargs['green']}"
+                + "Destination Path: "
+                + f"{kwargs['red']}"
+                + f"cloud://{str(dst)}. \n"
+                + f"{kwargs['yellow']}\0"
+            )
             files = []
             dirs = []
             for p in paths:
@@ -156,6 +166,13 @@ class BaseDatahub:
                 "Stdin format only supports json. Please read the document and make sure the format is valid."
             )
 
+    @staticmethod
+    def _valide_workspace(workspace: str) -> bool:
+        ctx = context.get_context()
+        backend = ctx.args.backend
+        resource = get_workspace_factory().load_resource()
+        return resource.validate_workspace(workspace, backend)
+
     @command(aliases=["copy"])
     @argument(
         "workspace",
@@ -173,7 +190,9 @@ class BaseDatahub:
         "dst",
         type=str,
         positional=False,
-        description="Specify the destination directory, file path, or DRS URL (optional, default ='MyDir/'). ",
+        description="Specify the destination directory, file path, or DRS URL. Paths with leading slashes, leading "
+        "backslashes, or dot-only segments are invalid. Additionally, paths should not contain characters other than "
+        "[0-9a-zA-Z-._:/]. If not provided, the default is the current Linux epoch timestamp (optional).",
     )
     @argument(
         "recursive",
@@ -194,15 +213,13 @@ class BaseDatahub:
         "multiprocessing",
         type=int,
         positional=False,
-        description="Specify the number of files that you want to upload at any given time. "
-        "Changing the default value is not recommended (default = 1).",
+        description="Specify the number of files that you want to upload at any given time. (default = 1).",
     )
     @argument(
         "chunk_size",
         type=str,
         positional=False,
-        description="Specify the size of each file that you want to upload in megabytes (MB). "
-        "Changing the default value is not recommended (default = 8MB).",
+        description="Specify the size of each file that you want to upload in mebibyte (MiB). (default = 8MiB).",
         choices=["8", "16"],
     )
     @argument(
@@ -212,28 +229,19 @@ class BaseDatahub:
         description="Specify the stdout format (default = json).",
         choices=["json", "table", "tsv"],
     )
-    @argument(
-        "non_interactive",
-        type=bool,
-        positional=False,
-        description="Whether to run in non-interactive mode, i.e. without prompt (default = False).",
-        aliases=["ni"],
-    )
     def upload(
         self,
         workspace: str,
         src: str,
-        dst: str = "MyDir/",
+        dst: str = f"{str(int(datetime.datetime.now().timestamp()))}/",
         recursive: bool = False,
         output: str = "json",
         concurrency: int = 0,
         multiprocessing: int = 1,
         chunk_size: str = "8",
-        expiry_time: str = None,
-        non_interactive: bool = False,
     ) -> int:
         """
-        Upload data from the local file system to a SeqsLab Data Hub cloud service.
+        Upload data from the local file system to a SeqsLab Data Hub cloud service.  This command behaves similarly to gsutil cp command.
         """
 
         def __log(results: List[dict], output: str):
@@ -249,12 +257,26 @@ class BaseDatahub:
                 else:
                     logging.info(msg)
 
-        if not workspace:
-            logging.error("Invalid workspace name")
-            cprint("Enter a valid workspace name.", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint(f"Workspace {workspace} not found.", "red")
             return errno.EINVAL
 
-        if dst.isspace() or len(dst) == 0:
+        if dst:
+            # Standard Library
+            import re
+
+            invalid_patterns = [
+                r"(^|/|\\)\.{1,}($|/|\\|$)|^\s*$|^\/$|^\.$|^/|//",  # ex: ., .., ..., ./, ../, .../, ././. etc
+                r"[^0-9a-zA-Z\-\._:/]+",
+                # ex: Only alphanumeric characters, hyphen, period, colon, and underscore are allowed.
+            ]
+            for pattern in invalid_patterns:
+                if re.search(pattern, dst):
+                    logging.error(f"Invalid dst path {dst}")
+                    cprint(f"Invalid dst path {dst}.", "red")
+                    return errno.EINVAL
+        else:
             logging.error("Invalid dst path")
             cprint("Enter a valid dst path.", "red")
             return errno.EINVAL
@@ -262,19 +284,7 @@ class BaseDatahub:
         if os.path.isdir(src):
             if src.endswith("/"):
                 src = URL(f'{str(src).rstrip("/")}', encoded=True)
-        if expiry_time:
-            # Standard Library
-            import re
 
-            pattern = r"\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}"
-            if not re.fullmatch(pattern, expiry_time):
-                cprint(
-                    "Make sure expiry_time format is correct. e.g. 2023-12-31 00:00:00",
-                    "red",
-                )
-                return errno.EINVAL
-
-        dst = "/" if dst == "." else dst
         result = self._upload(
             src=URL(src, encoded=True),
             dst=URL(dst, encoded=True),
@@ -284,8 +294,6 @@ class BaseDatahub:
             concurrency=concurrency,
             chunk_size=self.size[chunk_size],
             proxy=self.proxy,
-            non_interactive=non_interactive,
-            expiry_time=expiry_time,
         )
         if isinstance(result, int):
             return result
@@ -322,23 +330,20 @@ class BaseDatahub:
         type=int,
         positional=False,
         description="Specify the numbers of chunks that can be transferred concurrently. The download bandwidth "
-        "can be estimated using the formula concurrency * chunk_size. "
-        "Changing the default value is not recommended (optional, default = 120).",
+        "can be estimated using the formula concurrency * chunk_size. (optional, default = 120).",
     )
     @argument(
         "multiprocessing",
         type=int,
         positional=False,
-        description="Specify the number of files that you want to upload at any given time. "
-        "Changing the default value is not recommended (default = 1).",
+        description="Specify the number of files that you want to upload at any given time. (default = 1).",
     )
     @argument(
         "chunk_size",
         type=str,
         positional=False,
         description="Specify the size of chunk in the chunked downloading process. "
-        "If the specified size is greater than 4MB, the md5 hashes are not checked. "
-        "Changing the default value is not recommended (optional, default = 4MB).",
+        "If the specified size is greater than 4MiB, the md5 hashes are not checked. (optional, default = 4MiB).",
         choices=["4", "8", "16", "32"],
     )
     @argument(
@@ -384,9 +389,9 @@ class BaseDatahub:
                     else:
                         logging.info(msg)
 
-        if not workspace:
-            logging.error("Invalid workspace name")
-            cprint("Invalid workspace name", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint(f"Workspace {workspace} not found.", "red")
             return errno.EINVAL
 
         tasks = []
@@ -461,9 +466,9 @@ class BaseDatahub:
         browsers. The share link expires either after the first successful download or after a period of three months.
         """
 
-        if not workspace:
-            logging.error("Invalid workspace name")
-            cprint("Invalid workspace name", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
             return errno.EINVAL
 
         api_backend = drs_register().load_register(workspace)
@@ -663,6 +668,10 @@ class BaseDatahub:
         """
         Register a DRS object as a blob.
         """
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
+            return errno.EINVAL
 
         def __log(results: List[dict], output: str):
             self._stdout(results=results, output=output)
@@ -725,17 +734,21 @@ class BaseDatahub:
                     "mime_type": kwargs.get("mime_type"),
                     "file_type": kwargs.get("file_type"),
                     "created_time": kwargs.get("created_time"),
-                    "updated_time": kwargs.get("updated_time")
-                    if kwargs.get("updated_time")
-                    else kwargs.get("created_time"),
+                    "updated_time": (
+                        kwargs.get("updated_time")
+                        if kwargs.get("updated_time")
+                        else kwargs.get("created_time")
+                    ),
                     "size": kwargs.get("size"),
                     "access_methods": json.loads(kwargs.get("access_methods")),
                     "checksums": checksums,
                     "description": kwargs.get("description"),
                     "aliases": kwargs.get("aliases"),
-                    "metadata": json.loads(kwargs.get("metadata"))
-                    if kwargs.get("metadata")
-                    else None,
+                    "metadata": (
+                        json.loads(kwargs.get("metadata"))
+                        if kwargs.get("metadata")
+                        else None
+                    ),
                     "tags": kwargs.get("tags"),
                     "id": kwargs.get("id"),
                     "deleted_time": kwargs.get("deleted_time"),
@@ -828,8 +841,9 @@ class BaseDatahub:
                 msg = f"{r['id']}  has been registered."
                 logging.info(msg)
 
-        if not workspace:
-            cprint("Enter a valid workspace", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
             return errno.EINVAL
 
         results = self._register_bundle(
@@ -856,9 +870,11 @@ class BaseDatahub:
                     "file_type": "bundle",
                     "description": kwargs.get("description"),
                     "aliases": kwargs.get("aliases"),
-                    "metadata": json.loads(kwargs.get("metadata"))
-                    if kwargs.get("metadata")
-                    else None,
+                    "metadata": (
+                        json.loads(kwargs.get("metadata"))
+                        if kwargs.get("metadata")
+                        else None
+                    ),
                     "tags": kwargs.get("tags"),
                     "id": kwargs.get("id"),
                     "contents": drs_ids,
@@ -872,7 +888,7 @@ class BaseDatahub:
 
     @command(aliases=["deregister"])
     @argument(
-        "ids",
+        "id",
         type=List[str],
         positional=False,
         description="Specify the IDs of the DRS objects that you want to delete "
@@ -894,14 +910,14 @@ class BaseDatahub:
     )
     def deregister(
         self,
-        ids: List[str] = [],
+        id: List[str] = [],
         tags: List[str] = [],
         names: List[str] = [],
     ) -> int:
         """
         Deregister DRS objects by DRS ID, DRS name, or DRS tag.
         """
-        if not ids and not names and not tags:
+        if not id and not names and not tags:
             cprint(
                 "Must specify one of the IDs, names or tags to identify DRS objects for deletion",
                 "red",
@@ -909,7 +925,7 @@ class BaseDatahub:
             return errno.ENOENT
 
         resps = asyncio.run(
-            utils.drs_delete(ids, names, tags, query_opts="?backend_content=false")
+            utils.drs_delete(id, names, tags, query_opts="?backend_content=false")
         )
         for r in resps:
             cprint(r, "yellow")
@@ -918,7 +934,7 @@ class BaseDatahub:
 
     @command(aliases=["clean"])
     @argument(
-        "ids",
+        "id",
         type=List[str],
         positional=False,
         description="Specify the IDs of the DRS objects that you want to delete "
@@ -940,14 +956,14 @@ class BaseDatahub:
     )
     def delete(
         self,
-        ids: List[str] = [],
+        id: List[str] = [],
         tags: List[str] = [],
         names: List[str] = [],
     ) -> int:
         """
         Delete DRS objects and the associated files in cloud storage by DRS ID, DRS name, or DRS tag.
         """
-        if not ids and not names and not tags:
+        if not id and not names and not tags:
             cprint(
                 "Must specify one of the IDs, names or tags to identify "
                 "the associated files in cloud storage of DRS objects for deletion",
@@ -956,8 +972,12 @@ class BaseDatahub:
             return errno.ENOENT
 
         resps = asyncio.run(
-            utils.drs_delete(ids, names, tags, query_opts="?backend_content=true")
+            utils.drs_delete(id, names, tags, query_opts="?backend_content=true")
         )
+        if isinstance(resps, int):
+            cprint(f"Delete with return code {resps}", "red")
+            return resps
+
         for r in resps:
             cprint(r, "yellow")
 
@@ -1074,7 +1094,9 @@ class BaseDatahub:
             fq_paths = BaseDatahub.find_fastq_paths(fastq_path, fastq_signature)
 
             if run_sheet.SampleSheet.is_single_end:
-                assert len(fq_paths) == 1
+                assert (
+                    len(fq_paths) == 1
+                ), f"{str(fq_paths)} does not contain exactly one fastq path"
                 sample_meta["Pair"] = "1"
                 upload_info.append(
                     {
@@ -1094,7 +1116,9 @@ class BaseDatahub:
                     )
 
             if run_sheet.SampleSheet.is_paired_end:
-                assert len(fq_paths) == 2
+                assert (
+                    len(fq_paths) == 2
+                ), f"{str(fq_paths)} does not contain exactly two fastq paths"
                 fq_paths.sort()
                 sample_meta["Pair"] = "1"
                 upload_info.append(
@@ -1202,24 +1226,15 @@ class BaseDatahub:
         "multiprocessing",
         type=int,
         positional=False,
-        description="Specify the number of files that you want to upload at any given time. "
-        "Changing the default value is not recommended (optional, default = 1).",
+        description="Specify the number of files that you want to upload at any given time. (optional, default = 1).",
     )
     @argument(
         "chunk_size",
         type=str,
         positional=False,
-        description="Specify the size of each file that you want to upload in megabytes (MB). "
-        "Changing the default value is not recommended (default = 8MB).",
+        description="Specify the size of each file that you want to upload in mebibyte (MiB). (default = 8MiB).",
         choices=["8", "16"],
     )
-    @argument(
-        "non_interactive",
-        type=bool,
-        positional=False,
-        description="Whether to run in non-interactive mode, i.e. without prompt (default = False).",
-        aliases=["ni"],
-    )
     @argument(
         "seq_run_id",
         type=str,
@@ -1237,17 +1252,16 @@ class BaseDatahub:
         concurrency: int = 0,
         multiprocessing: int = 1,
         chunk_size: str = "8",
-        expiry_time: str = None,
-        non_interactive: bool = False,
         seq_run_id: str = "",
     ) -> int:
         """
         Upload samples based on the Run Sheet and FASTQ path information.
         """
-        if not workspace:
-            logging.error("Invalid workspace name")
-            cprint("Invalid workspace name", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
             return errno.EINVAL
+
         failed = False
         if not upload_dst:
             upload_dst = int(datetime.datetime.timestamp(datetime.datetime.now()))
@@ -1282,8 +1296,7 @@ class BaseDatahub:
                 concurrency=concurrency,
                 chunk_size=self.size[chunk_size],
                 proxy=self.proxy,
-                non_interactive=non_interactive,
-                expiry_time=expiry_time,
+                non_interactive=False,
             )
             if isinstance(result, list):
                 r = result[0]
@@ -1375,8 +1388,9 @@ class BaseDatahub:
         """
         Update a DRS object.
         """
-        if not workspace:
-            cprint("Enter a valid workspace", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
             return errno.EINVAL
 
         if stdin:
@@ -1427,8 +1441,9 @@ class BaseDatahub:
         """
         Get a DRS object.
         """
-        if not workspace:
-            cprint("Enter a valid workspace", "red")
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
             return errno.EINVAL
 
         def __log(results: dict):
@@ -1448,6 +1463,122 @@ class BaseDatahub:
         api_backend = drs_register().load_register(workspace)
         return api_backend.get_drs(drs_id=id)
 
+    @exception_handler
+    def _patch_add_read_drs(self, add_reads_id: str, workspace: str, tag: str):
+        results = self._get(add_reads_id, workspace)
+        if isinstance(results, int):
+            return results
+        cprint(f"Found Add Reads target DRS object {add_reads_id}", color="yellow")
+        tags = [item["name"] for item in results["tags"]] + [tag]
+        patch_payload = {"tags": tags}
+        results = self._change(add_reads_id, **patch_payload)
+        if isinstance(results, int):
+            return results
+        cprint(
+            f"Add Reads target DRS object {add_reads_id} patched with tags {tags}",
+            color="yellow",
+        )
+        return add_reads_id
+
+    @command(aliases=["add-reads"])
+    @argument(
+        "workspace",
+        type=str,
+        positional=False,
+        description="Specify the workspace based on the signed in account (required).",
+    )
+    @argument(
+        "run_sheet",
+        type=str,
+        positional=False,
+        description="Specify the Run Sheet file path (required).",
+    )
+    @argument(
+        "seq_run_id",
+        type=str,
+        positional=False,
+        description="Specify a runsheet header field as a sequencer run identifier; the specified value will be "
+        "used as a sequencer run specific label for future dataset management (optional).",
+    )
+    def add_reads_runsheet(
+        self,
+        workspace,
+        run_sheet: str,
+        seq_run_id: str = "",
+    ) -> int:
+        """
+        Identify and Patch existing DRS object with add-reads runsheet label for runsheet-based run triggering for
+        DRS auto-matching
+        """
+        if not self._valide_workspace(workspace):
+            logging.error("Workspace not found")
+            cprint("Workspace not found.", "red")
+            return errno.EINVAL
+
+        # SampleSheetV2 based RunSheet SeqsLab fields
+        seqslab_section = "SeqsLabRunSheet"
+        seqslab_format = "SeqsLabColumnFormat"
+        seqslab_sep = "#"
+        rs = RunSheet(run_sheet, seqslab_section, seqslab_format, seqslab_sep)
+
+        # set base tags
+        base_tgs = ""
+        try:
+            if seq_run_id:
+                base_tgs = f"{rs.SampleSheet.Header[seq_run_id]}/"
+        except KeyError:
+            print(
+                f"Given base_label_field not found in SampleSheet Header {seq_run_id}"
+            )
+            return errno.EINVAL
+
+        add_reads = False
+        for sa in rs.SampleSheet.samples:
+            if rs.SampleSheet.is_single_end:
+                assert (
+                    sa.to_json().get("Add_Read2_ID") == ""
+                    and sa.to_json().get("Add_Read2_Label") == ""
+                ), "columns Add_Read2_ID and Add_Read2_Label should be blank for single_end sequencer run"
+                if (add_read1_id := sa.to_json().get("Add_Read1_ID")) and (
+                    add_read1_label := sa.to_json().get("Add_Read1_Label")
+                ):
+                    add_reads = True
+                    ret = self._patch_add_read_drs(
+                        add_read1_id,
+                        workspace,
+                        f"{base_tgs}{sa.get('Run_Name', rs.SampleSheet.Header.Date)}/"
+                        f"{add_read1_label}",
+                    )
+                    if isinstance(ret, int):
+                        return ret
+            if rs.SampleSheet.is_paired_end:
+                if (add_read1_id := sa.to_json().get("Add_Read1_ID")) and (
+                    add_read1_label := sa.to_json().get("Add_Read1_Label")
+                ):
+                    add_reads = True
+                    ret = self._patch_add_read_drs(
+                        add_read1_id,
+                        workspace,
+                        f"{base_tgs}{sa.get('Run_Name', rs.SampleSheet.Header.Date)}/{add_read1_label}",
+                    )
+                    if isinstance(ret, int):
+                        return ret
+                if (add_read2_id := sa.to_json().get("Add_Read2_ID")) and (
+                    add_read2_label := sa.to_json().get("Add_Read2_Label")
+                ):
+                    add_reads = True
+                    ret = self._patch_add_read_drs(
+                        add_read2_id,
+                        workspace,
+                        f"{base_tgs}{sa.get('Run_Name', rs.SampleSheet.Header.Date)}/{add_read2_label}",
+                    )
+                    if isinstance(ret, int):
+                        return ret
+
+        if not add_reads:
+            cprint("No DRS object is patched in this operation", color="yellow")
+        return 0
+
 
 @command
 class Datahub(BaseDatahub):