seqslab-cli 3.3.8__tar.gz → 3.3.10__tar.gz

{seqslab-cli-3.3.8/python/seqslab_cli.egg-info → seqslab-cli-3.3.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.8
+Version: 3.3.10
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/__init__.py

@@ -21,6 +21,6 @@ name = "seqslab"
 __all__ = []
 
 
-__version__ = "3.3.8"
+__version__ = "3.3.10"
 
 LOGGING = {"DIR_PATH": "/var/log/seqslab"}

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/drs/api/base.py

@@ -156,6 +156,7 @@ class DRSregister:
         checksum_type: str = None,
         updated_time: str = None,
         deleted_time: str = None,
+        access_methods: dict = {},
         **kwargs,
     ) -> dict:
         """
@@ -175,6 +176,7 @@ class DRSregister:
             checksums=checksums,
             updated_time=updated_time,
             deleted_time=deleted_time,
+            access_methods=access_methods,
         )
         return template
 

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/drs/commands.py

@@ -600,8 +600,8 @@ class BaseDatahub:
         type=str,
         description="Specify the access methods of the object that you want to register. "
         "(optional in stdin mode, otherwise required)"
-        'For example, [{"type":"https","access_url":{"url":"https://storage.url","headers":{'
-        '"Authorization":authorization}},"access_tier":"hot","region":"westus3"}, ... ]',
+        'For example, \'[{"type":"https","access_url":{"url":"https://storage.url","headers":{'
+        '"Authorization":authorization}},"access_tier":"hot","region":"westus3"}, ... ]\'',
     )
     @argument(
         "checksum",
@@ -939,36 +939,63 @@ class BaseDatahub:
 
     @command
     @argument(
-        "names",
+        "tags",
         type=List[str],
         positional=False,
         description="Locate a DRS object using a list of names " "(optional).",
     )
     @argument(
-        "tags",
+        "keyword",
+        type=str,
+        positional=False,
+        description="Locate a DRS object with keyword search " "(optional).",
+    )
+    @argument(
+        "page",
+        type=int,
+        positional=False,
+        description="Page index of the return value (optional, default = 1).",
+    )
+    @argument(
+        "page_size",
+        type=int,
+        positional=False,
+        description="Number of record in a page (optional, default = 25).",
+    )
+    @argument(
+        "file_types",
         type=List[str],
         positional=False,
-        description="Locate a DRS object using a list of labels " "(optional).",
+        description="File Type attributes (optional, default = []]).",
+    )
+    @argument(
+        "owner",
+        type=bool,
+        positional=False,
+        description="Whether to return self-own object only (optional, default = False).",
     )
     def search(
         self,
         tags: List[str] = [],
-        names: List[str] = [],
+        keyword: str = "",
+        page: int = 1,
+        page_size: int = 25,
+        file_types: List[str] = [],
+        owner: bool = False,
     ) -> int:
         """
-        Locate DRS objects either by name or by tag. Do not combine names and labels in a single query.
+        Locate DRS objects either by keyword or by tags.
         """
-        if not names and not tags:
-            cprint("Either give names or tags to do DRS query", "red")
-            return errno.ENOENT
-        if names and tags:
-            cprint(
-                "Search condition names and tags cannot be given at the same time",
-                "red",
-            )
+        if not keyword and not tags:
+            cprint("Either give keyword or tags to do DRS query", "red")
             return errno.ENOENT
-
-        result = asyncio.run(utils.drs_search(names, tags))
+        extra_params = {
+            "page": page,
+            "page_size": page_size,
+            "file_types": file_types,
+            "owner": owner,
+        }
+        result = asyncio.run(utils.drs_keyword_search(keyword, tags, **extra_params))
         cprint(json.dumps(result, indent=4))
 
         return 0
@@ -1329,6 +1356,16 @@ class BaseDatahub:
         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(
+        "access_methods",
+        type=str,
+        positional=False,
+        description="Specify the DRS object access_methods in the format of json string (optional)."
+        'For example, \'[{"id":320230,"type":"abfss","region":"westus2","access_url":{"headers":{'
+        '"Authorization":"st=2025-01-06T060628Z&se=2025-01-09T060628Z00xxx"},'
+        '"url":"abfss://org-epa906yha51qwmj@cgmwus232b21storage.dfs.core.windows.net/drs/user_admin'
+        "/ref/ffseq/pd4615-sup-0008-file1.rdata\"}}]' ",
+    )
     @argument(
         "stdin",
         type=bool,
@@ -1359,13 +1396,26 @@ class BaseDatahub:
                 kwargs = kwargs[0]
         kwargs["workspace"] = workspace
 
-        if kwargs.get("metadata"):
+        if metadata := kwargs.get("metadata"):
             try:
-                kwargs["metadata"] = json.loads(kwargs.get("metadata"))
+                kwargs["metadata"] = json.loads(metadata)
             except Exception as e:
                 cprint(f"Provided metadata is not a valid json-string: {e}", "red")
                 return errno.EINVAL
 
+        if access_methods := kwargs.get("access_methods"):
+            try:
+                kwargs["access_methods"] = (
+                    json.loads(access_methods)
+                    if isinstance(access_methods, str)
+                    else access_methods
+                )
+            except Exception as e:
+                cprint(
+                    f"Provided access_methods is not a valid json-string: {e}", "red"
+                )
+                return errno.EINVAL
+
         def __log(results: dict):
             self._stdout(results=[results], output="json")
             msg = f"Register {results['id']}  is complete."

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/drs/internal/utils.py

@@ -34,7 +34,7 @@ DRS_OBJECT_URL = f"https://{API_HOSTNAME}/ga4gh/drs/{__version__}/objects/"
 
 
 @async_exception_handler
-async def drs_search(names: List[str], labels: List[str], **kwargs) -> dict:
+async def drs_exact_match(names: List[str], labels: List[str], **kwargs) -> dict:
     if names and labels:
         raise ValueError("one search condition, either name or label, is allowed")
 
@@ -66,6 +66,34 @@ async def drs_search(names: List[str], labels: List[str], **kwargs) -> dict:
     return json.loads(resp)
 
 
+@async_exception_handler
+async def drs_keyword_search(keyword: str, labels: List[str], **kwargs) -> dict:
+    try:
+        token = BaseAuth.get_token().get("tokens").get("access")
+    except KeyError:
+        raise KeyError("No tokens, Please signin first!")
+    params = f'?page_size={kwargs["page_size"]}&page={kwargs["page"]}&'
+    if keyword:
+        params += f"search={keyword}&"
+    if labels:
+        for lb in labels:
+            params += f"label={lb}&"
+    if types := kwargs["file_types"]:
+        for t in types:
+            params += f"file_types={t}&"
+    if kwargs["owner"]:
+        params += "owner=true&"
+    url = f"{DRS_OBJECT_URL}{params}"
+    async with ClientSession(raise_for_status=False).request(
+        method="get",
+        url=url.rstrip("&"),
+        proxy=kwargs.get("proxy", None),
+        headers={"Authorization": f"Bearer {token}"},
+    ) as response:
+        resp = await response.content.read()
+    return json.loads(resp)
+
+
 @async_exception_handler
 async def drs_crud(drs_id: str, method: str, sem: asyncio.Semaphore, **kwargs) -> dict:
     try:
@@ -107,9 +135,9 @@ async def get_by_ids(drs_ids: List[str], **kwargs):
 @async_exception_handler
 async def drs_existence(path: URL, label_check: bool = True) -> bool:
     if label_check:
-        res = await drs_search(names=[], labels=[str(path)])
+        res = await drs_exact_match(names=[], labels=[str(path)])
     else:
-        res = await drs_search(names=[os.path.basename(str(path))], labels=[])
+        res = await drs_exact_match(names=[os.path.basename(str(path))], labels=[])
 
     if not res.get("objects"):
         return False
@@ -119,7 +147,10 @@ async def drs_existence(path: URL, label_check: bool = True) -> bool:
 
 @async_exception_handler
 async def drs_delete(ids: List[str], names: List[str], labels: List[str], **kwargs):
-    search = [drs_search(names=names, labels=[]), drs_search(names=[], labels=labels)]
+    search = [
+        drs_exact_match(names=names, labels=[]),
+        drs_exact_match(names=[], labels=labels),
+    ]
     resps = await asyncio.gather(*search, return_exceptions=False)
     drs_ids = list(
         set([ob.get("id") for res in resps for ob in res.get("objects")] + ids)

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/drs/storage/azure.py

@@ -4,6 +4,7 @@ import datetime
 import hashlib
 import json
 import os
+import time
 from base64 import b64encode
 from functools import lru_cache
 from hashlib import md5
@@ -375,10 +376,21 @@ class BlobStorage(BaseBlob):
             "x-ms-date": date,
         }
         try:
-            get_block_list = requests.get(
-                url=str(url),
-                headers=headers,
-            )
+            retry = 5
+            while retry:
+                retry -= 1
+                try:
+                    get_block_list = requests.get(
+                        url=str(url),
+                        headers=headers,
+                    )
+                    break
+                except Exception as err:
+                    if progress_bar := kwargs.get("progress_bar"):
+                        progress_bar.print(
+                            f"Get block list failed, trial ${retry}.(Connection failed with error ${err}.)"
+                        )
+                        time.sleep(float(1))
             if get_block_list.status_code == 200:
                 if progress_bar := kwargs.get("progress_bar"):
                     progress_bar.print("Get block list successfully.")

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/drs/utils/biomimetype.py

@@ -21,7 +21,7 @@ class bioMimeTypes(MimeTypes):
                 table[f"{prefix}"] = p_mime_types[i]
                 for j, suffixs in enumerate(suffixs_list):
                     for _, suffix in enumerate(suffixs):
-                        table[f"{'.'.join([prefix,suffix])}"] = s_mime_types[j]
+                        table[f"{'.'.join([prefix, suffix])}"] = s_mime_types[j]
                         table[f"{suffix}"] = s_mime_types[j]
 
         for ext, type in table.items():

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/organization/commands.py

@@ -95,6 +95,8 @@ class BaseOrg:
             keyring.set_password(
                 "net.seqslab.api.tokens.access", user, resp["tokens"]["access"]
             )
+            token = resp["tokens"]["access"]
+
             org_info = get_org(
                 access_token=token, cus_id=Auth._decode(token)["cus_id"], proxy=proxy
             )

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/user/resource/azure.py

@@ -37,7 +37,7 @@ class AzureResource(BaseResource):
 
     @exception_handler
     def admin_consent(self):
-        if self.is_global_admin():
+        if self.is_global_or_org_admin():
             token = BaseAuth.get_token().get("attrs")
             return AzureResource.CONSENT_URL.format(
                 tenant=token.get("tid"),

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/user/resource/base.py

@@ -109,12 +109,11 @@ class BaseResource:
 
     @exception_handler
     @retry(stop=stop_after_attempt(3), wait=wait_fixed(2), reraise=True)
-    def is_global_admin(self, **kwargs) -> bool:
+    def is_global_or_org_admin(self, **kwargs) -> bool:
         token = BaseAuth.get_token()
         response = self.get_user(token.get("attrs").get("user_id"))
-        if "Global administrator" in [
-            item.get("name") for item in response.get("roles")
-        ]:
+        roles = [item.get("name") for item in response.get("roles")]
+        if "Global administrator" in roles or "Organization administrator" in roles:
             return True
 
         return False

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10}/python/seqslab/wes/resource/base.py

@@ -191,7 +191,7 @@ class BaseResource(ABC):
         backend = ctx.args.backend
         token = BaseAuth.get_token().get("tokens").get("access")
         with requests.get(
-            url=f"{self.WES_RUNS_STATUS_URL.format(id=run_id,backend=backend)}",
+            url=f"{self.WES_RUNS_STATUS_URL.format(id=run_id, backend=backend)}",
             headers={"Authorization": f"Bearer {token}"},
         ) as response:
             if response.status_code not in [requests.codes.ok]:
@@ -270,7 +270,7 @@ class BaseResource(ABC):
             backend = ctx.args.backend
             token = BaseAuth.get_token().get("tokens").get("access")
             with requests.get(
-                url=f"{self.WES_RUNS_FILE_URL.format(id=run_id,backend=backend)}",
+                url=f"{self.WES_RUNS_FILE_URL.format(id=run_id, backend=backend)}",
                 headers={"Authorization": f"Bearer {token}"},
             ) as response:
                 if response.status_code not in [requests.codes.ok]:

{seqslab-cli-3.3.8 → seqslab-cli-3.3.10/python/seqslab_cli.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.8
+Version: 3.3.10
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang