cdiam-cli 0.1.0__tar.gz → 0.1.2__tar.gz

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cdiam-cli
-Version: 0.1.0
+Version: 0.1.2
 Summary: 
 Author: tungtp99
 Author-email: tungtp181199@gmail.com
@@ -13,15 +13,8 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: click (>=8.1.7,<9.0.0)
 Requires-Dist: datetime (>=5.5,<6.0)
 Requires-Dist: idna (==3.4)
-Requires-Dist: numpy (>=1.24.0,<2.0.0)
-Requires-Dist: pandas (>=2.1.0,<3.0.0)
 Requires-Dist: pydantic (==1.10.2)
-Requires-Dist: pymysql (==1.0.2)
 Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
-Requires-Dist: sqlalchemy (==1.4.41)
-Requires-Dist: sqlalchemy2-stubs (==0.0.2a27)
-Requires-Dist: sqlmodel (==0.0.8)
-Requires-Dist: tabulate (>=0.9.0,<0.10.0)
 Requires-Dist: typing-extensions (==4.3.0)
 Description-Content-Type: text/markdown
 
@@ -41,12 +34,12 @@ To get started with this project, follow these steps:
 Run `pip install cdiam-cli` 
 
 ### View CLI command
-Run `cdiam_cli --help`
+Run `cdiam-cli --help`
 
 ## Features
 
-- Save token: `python -m cdiam_cli save-token` must provide server endpoint E.g. https://c-diam.com/api and TOKEN get from CDIAM APP
-- Call API: `python -m cdiam_cli call-api <PATH_TO_YAML_OR_JSON_PARAMS>` more detail about params schemas at `<SERVER_ENPOINT>/schemas/docs` E.g. https://c-diam.com/api/schemas/docs
+- Save token: `cdiam-cli save-token` must provide server endpoint E.g. https://c-diam.com/api and TOKEN get from CDIAM APP
+- Call API: `cdiam-cli call-api <PATH_TO_YAML_OR_JSON_PARAMS>` more detail about params schemas at `<SERVER_ENPOINT>/schemas/docs` E.g. https://c-diam.com/api/schemas/docs
 
 
 

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/README.md

@@ -14,12 +14,12 @@ To get started with this project, follow these steps:
 Run `pip install cdiam-cli` 
 
 ### View CLI command
-Run `cdiam_cli --help`
+Run `cdiam-cli --help`
 
 ## Features
 
-- Save token: `python -m cdiam_cli save-token` must provide server endpoint E.g. https://c-diam.com/api and TOKEN get from CDIAM APP
-- Call API: `python -m cdiam_cli call-api <PATH_TO_YAML_OR_JSON_PARAMS>` more detail about params schemas at `<SERVER_ENPOINT>/schemas/docs` E.g. https://c-diam.com/api/schemas/docs
+- Save token: `cdiam-cli save-token` must provide server endpoint E.g. https://c-diam.com/api and TOKEN get from CDIAM APP
+- Call API: `cdiam-cli call-api <PATH_TO_YAML_OR_JSON_PARAMS>` more detail about params schemas at `<SERVER_ENPOINT>/schemas/docs` E.g. https://c-diam.com/api/schemas/docs
 
 
 

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/cdiam_cli/__main__.py

@@ -1,5 +1,4 @@
 # python
-
 from .main import main_group
 
-main_group()
+main_group()

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/cdiam_cli/api/api_action.py

@@ -4,9 +4,8 @@ from cdiam_cli.helper import yaml_helper, curl_helper
 import subprocess
 from typing import Union, Callable, Any, Dict, overload, Literal
 from .settings import read_api_endpoint, read_api_token
-from cdiam_cli.schemas import AnalysisResult
 from cdiam_cli.schemas import ParamsRequestGetTaskStatus
-from cdiam_cli.schemas import AnalysisResultRead
+from cdiam_cli.schemas.analysis import AnalysisResultRead, AnalysisResult
 from time import sleep
 
 
@@ -120,12 +119,5 @@ def call_api(params: str):
         Exception: If the API call fails.
     """
 
-    process = run(params)
-    return_code = process.returncode
-
-    if return_code == 0:
-        click.echo(process.stdout.decode())
-        return process.stdout.decode()
-    else:
-        click.echo(process.stdout.decode())
-        raise Exception(process.stderr.decode())
+    data = run(params)
+    print(json.dumps(data, indent=4, sort_keys=True))

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/cdiam_cli/api/download.py

@@ -1,6 +1,5 @@
 import click
 import requests
-import pandas as pd
 from urllib.request import urlopen
 from .settings import read_api_endpoint, read_api_token
 
@@ -8,7 +7,7 @@ from .settings import read_api_endpoint, read_api_token
 @click.command()
 @click.argument("object_id", type=str)
 def download_data(object_id: str):
-    """This api download data of given objec_id"""
+    """This api download data of given object_id"""
     res = requests.get(
         f"{read_api_endpoint()}/data/data/download-file/{object_id}",
         cookies={"cdiam_session_token": read_api_token()},

cdiam_cli-0.1.2/cdiam_cli/command/__init__.py

@@ -0,0 +1,2 @@
+from . import project
+from . import data

cdiam_cli-0.1.2/cdiam_cli/command/data.py

@@ -0,0 +1,33 @@
+from typing import Any
+
+import click
+
+from cdiam_cli import api
+from cdiam_cli.schemas.base import MessageResponseError, MessageResponseSuccess
+
+
+@click.group('data')
+@click.pass_context
+def data_cli(ctx):
+    """
+    This command group provides various commands to show and manage data related to projects.
+    Use the subcommands under this group to interact with project effectively.
+    """
+    pass
+
+
+@data_cli.command('list')
+@click.argument('project_id')
+def list_all_data(project_id: str):
+    """
+        This command lists all available data in given project id.
+    """
+    try:
+        response: Any = api.api_action.run({
+            "api": "list_data",
+            "project_id": project_id
+        })
+        output = MessageResponseSuccess(data=response)
+    except Exception as e:
+        output = MessageResponseError(error=str(e))
+    click.echo(output.json())

cdiam_cli-0.1.2/cdiam_cli/command/project.py

@@ -0,0 +1,29 @@
+from typing import Any
+
+import click
+
+from cdiam_cli import api
+from cdiam_cli.schemas.base import MessageResponseError, MessageResponseSuccess
+
+
+@click.group('project')
+@click.pass_context
+def project_cli(ctx):
+    """
+    This command group provides various commands to show and manage data related to projects.
+    Use the subcommands under this group to interact with project effectively.
+    """
+    pass
+
+
+@project_cli.command('list')
+def list_all_project():
+    """
+        This command lists all the projects available in the system.
+    """
+    try:
+        response: Any = api.api_action.run({"api": 'list_project'})
+        output = MessageResponseSuccess(data=response)
+    except Exception as e:
+        output = MessageResponseError(error=str(e))
+    click.echo(output.json())

cdiam_cli-0.1.2/cdiam_cli/main.py

@@ -0,0 +1,22 @@
+import click
+
+from cdiam_cli import api
+from cdiam_cli.command import data, project
+
+
+@click.group()
+@click.pass_context
+def main_group(ctx):
+    pass
+
+
+# Groups
+main_group.add_command(project.project_cli)
+main_group.add_command(data.data_cli)
+
+# Single command
+main_group.add_command(api.call_api)
+main_group.add_command(api.save_token)
+
+if __name__ == "__main__":
+    main_group()

cdiam_cli-0.1.2/cdiam_cli/schemas/analysis.py

@@ -0,0 +1,60 @@
+from datetime import datetime
+from typing import Optional, List
+
+from pydantic import BaseModel
+
+
+class TaskStatus(BaseModel):
+    status: str = "UNKNOWN"
+
+
+class AnalysisResultBase(BaseModel):
+    result_id: str
+    data_id: str
+    analysis: int
+    task_id: str
+    args: str
+    project_id: str
+    user_email: Optional[str]
+
+
+class AnalysisCatalogBase(BaseModel):
+    name: str
+    description: Optional[str]
+
+
+class AnalysisCatalog(AnalysisCatalogBase):
+    """
+    This table stores available analyses type
+    that the App supports.
+    """
+
+    id: int
+    time_created: datetime
+    time_modified: datetime
+    """A list of all analysis results of this type"""
+    results: List["AnalysisResult"]
+
+
+class AnalysisResultRead(AnalysisResultBase):
+    """
+    A response model of an anlysis result
+    """
+
+    time_created: datetime
+    time_modified: datetime
+    task: Optional[TaskStatus]
+    result_data_status: Optional[str]
+
+
+class AnalysisResult(AnalysisResultBase):
+    """
+    This table stores all analyses that had been produced for a data
+    The analysis reference points to the description of the analysis.
+    The result_id reference points to the detail result of the analysis
+    """
+
+    time_created: datetime
+    time_modified: datetime
+    """An object of the analysis type"""
+    analysis_orm: AnalysisCatalog

cdiam_cli-0.1.2/cdiam_cli/schemas/base.py

@@ -0,0 +1,28 @@
+from enum import Enum
+from typing import Any
+
+from pydantic import BaseModel
+
+
+class MessageStatusEnum(str, Enum):
+    SUCCESS = "success"
+    ERROR = "error"
+
+
+class MessageResponse(BaseModel):
+    status: MessageStatusEnum
+    error: str
+    data: Any
+
+    class Config:
+        allow_population_by_field_name = True
+
+
+class MessageResponseSuccess(MessageResponse):
+    status: MessageStatusEnum = MessageStatusEnum.SUCCESS
+    error: str = ""
+
+
+class MessageResponseError(MessageResponse):
+    status: MessageStatusEnum = MessageStatusEnum.ERROR
+    data: Any = None

cdiam_cli-0.1.2/cdiam_cli/schemas/project.py

@@ -0,0 +1,36 @@
+from datetime import datetime
+from typing import Optional
+
+from pydantic import validator
+from cdiam_cli.schemas import ProjectSettings
+from pydantic import BaseModel
+
+
+class ProjectBase(BaseModel):
+    name: str
+
+
+class Project(ProjectBase):
+
+    id: str
+    tombstone: Optional[bool]
+    time_created: datetime
+    is_public: bool
+    delete_date: Optional[datetime]
+    settings: Optional[str]
+    storage_used: int
+    created_by: str
+
+    @validator("settings")
+    def validate_settings(cls, v: str):
+        if v == "nan":
+            v = "{}"
+        if v is None:
+            v = "{}"
+        return ProjectSettings.encode_settings(ProjectSettings.decode_setting(v))
+
+    @validator("tombstone")
+    def validate_tombstone(cls, v):
+        if not v:
+            return False
+        return v

cdiam_cli-0.1.2/cdiam_cli/schemas/schemas.py

@@ -0,0 +1,36 @@
+from typing import Literal
+from pydantic import BaseModel
+from typing import Union, List, Dict, Any
+import json
+
+
+class ProjectSettings(BaseModel):
+    class Config:
+        orm_mode = True
+
+    cpdb: List[str] = []
+    enrichment: List[str] = []
+
+    @staticmethod
+    def encode_settings(settings: Union[Dict[str, Any], "ProjectSettings"]) -> str:
+        return ProjectSettings.parse_obj(settings).json()
+
+    @staticmethod
+    def decode_setting(settings: str) -> "ProjectSettings":
+        if settings is None:
+            settings = "{}"
+        return ProjectSettings.parse_obj(json.loads(settings))
+
+
+class ParamsRequestGetTaskStatus(BaseModel):
+    """
+    Represents the parameters for a request to get the status of an analysis task.
+
+    :param api: The API endpoint being called, which should be "get_task_status".
+    :param task_id: The unique identifier of the analysis task.
+    """
+
+    api: Literal["get_task_status"]
+    task_id: str
+
+

{cdiam_cli-0.1.0 → cdiam_cli-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cdiam-cli"
-version = "0.1.0"
+version = "0.1.2"
 description = ""
 authors = ["tungtp99 <tungtp181199@gmail.com>"]
 readme = "README.md"
@@ -13,19 +13,13 @@ cdiam-cli = "cdiam_cli.main:main_group"
 python = "^3.9"
 click = "^8.1.7"
 pyyaml = "^6.0.1"
-tabulate = "^0.9.0"
 
 
 datetime = "^5.5"
-numpy = "^1.24.0"
-pandas = "^2.1.0"
 pydantic = "1.10.2"
-sqlmodel = "0.0.8"
 typing-extensions = "4.3.0"
-sqlalchemy = "1.4.41"
-sqlalchemy2-stubs = "0.0.2a27"
-pymysql = "1.0.2"
 idna = "3.4"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

cdiam_cli-0.1.0/cdiam_cli/main.py

@@ -1,15 +0,0 @@
-import click
-from . import api
-
-
-@click.group
-def main_group():
-    pass
-
-
-main_group.add_command(api.save_token)
-main_group.add_command(api.call_api)
-
-
-if __name__ == "__main__":
-    main_group()

cdiam_cli-0.1.0/cdiam_cli/schemas/schemas.py

@@ -1,213 +0,0 @@
-from pydantic import BaseModel
-from typing import Literal, Optional
-from sqlmodel import (
-    Field,
-    SQLModel,
-    ForeignKeyConstraint,
-    Column,
-    DateTime,
-    func,
-    Relationship,
-    UniqueConstraint,
-    BigInteger,
-)
-import sqlalchemy as sa
-from pydantic import validator, BaseModel
-from datetime import datetime
-from typing import Union, Callable, ClassVar, Optional, List, Dict, Any
-import json
-
-
-class ProjectSettings(BaseModel):
-    class Config:
-        orm_mode = True
-
-    cpdb: List[str] = []
-    enrichment: List[str] = []
-
-    @staticmethod
-    def encode_settings(settings: Union[Dict[str, Any], "ProjectSettings"]) -> str:
-        return ProjectSettings.parse_obj(settings).json()
-
-    @staticmethod
-    def decode_setting(settings: str) -> "ProjectSettings":
-        if settings is None:
-            settings = "{}"
-        return ProjectSettings.parse_obj(json.loads(settings))
-
-
-class ProjectBase(SQLModel):
-    name: str = Field(max_length=128, nullable=False)
-
-
-class Project(ProjectBase, table=True):
-    __tablename__: ClassVar[Union[str, Callable[..., str]]] = "project"
-    id: str = Field(
-        max_length=128, nullable=False, primary_key=True, index=True, unique=True
-    )
-    tombstone: Optional[bool] = Field(
-        default=False,
-        nullable=False,
-        description="Deleted marker of the project. True = deleted",
-    )
-    time_created: datetime = Field(
-        default=None,
-        sa_column=Column(DateTime(timezone=True), server_default=func.now()),
-        description="Time added",
-    )
-    is_public: bool = Field(
-        default=False,
-        nullable=False,
-        description="If the project is public",
-    )
-    delete_date: Optional[datetime] = Field(
-        default=None, sa_column=Column(sa.DateTime(timezone=True), nullable=True)
-    )
-    settings: Optional[str] = Field(
-        default=None,
-        max_length=10240,
-        nullable=True,
-    )
-    storage_used: int = Field(
-        sa_column=Column(BigInteger),
-        nullable=True,
-        description="Non-zero expression values",
-    )
-    created_by: str = Field(
-        max_length=128,
-        nullable=False,
-        index=True,
-        foreign_key="user.email",
-    )
-
-    @validator("settings")
-    def validate_settings(cls, v: str):
-        if v == "nan":
-            v = "{}"
-        if v is None:
-            v = "{}"
-        return ProjectSettings.encode_settings(ProjectSettings.decode_setting(v))
-
-    @validator("tombstone")
-    def validate_tombstone(cls, v):
-        if not v:
-            return False
-        return v
-
-
-class ParamsRequestGetTaskStatus(BaseModel):
-    """
-    Represents the parameters for a request to get the status of an analysis task.
-
-    :param api: The API endpoint being called, which should be "get_task_status".
-    :param task_id: The unique identifier of the analysis task.
-    """
-
-    api: Literal["get_task_status"]
-    task_id: str
-
-
-class TaskStatus(BaseModel):
-    status: str = "UNKNOWN"
-
-
-class AnalysisResultBase(SQLModel):
-    result_id: str = Field(
-        max_length=128,
-        nullable=False,
-        primary_key=True,
-        description="ID of the analysis",
-    )
-    data_id: str = Field(max_length=128, nullable=False, description="ID of the data")
-    analysis: int = Field(
-        nullable=False,
-        foreign_key="analysis_catalog.id",
-        description="Reference to the analysis",
-    )
-    task_id: str = Field(
-        max_length=128,
-        nullable=False,
-        sa_column_kwargs={"server_default": ""},
-        description="ID of task in celery",
-    )
-    args: str = Field(
-        max_length=10240,
-        default="{}",
-        nullable=False,
-        description="Args of the analysis",
-        sa_column_kwargs={"server_default": "{}"},
-    )
-    project_id: str = Field(
-        max_length=128,
-        nullable=False,
-        description="ID of project this analysis belong to",
-    )
-    user_email: Optional[str] = Field(max_length=256, nullable=True)
-
-
-class AnalysisCatalogBase(SQLModel):
-    name: str = Field(nullable=False, description="Name of the analysis")
-    description: Optional[str] = Field(
-        max_length=4096, description="Detailed information about this analysis"
-    )
-
-
-class AnalysisCatalog(AnalysisCatalogBase, table=True):
-    """
-    This table stores available analyses type
-    that the App supports.
-    """
-
-    __tablename__: ClassVar[Union[str, Callable[..., str]]] = "analysis_catalog"
-    id: int = Field(primary_key=True)
-    time_created: datetime = Field(
-        sa_column=Column(DateTime(timezone=True), server_default=func.now()),
-        description="Time added",
-    )
-    time_modified: datetime = Field(
-        sa_column=Column(
-            DateTime(timezone=True), server_default=func.now(), onupdate=func.now()
-        ),
-        description="Time modified",
-    )
-    """A list of all analysis results of this type"""
-    results: List["AnalysisResult"] = Relationship(back_populates="analysis_orm")
-
-    __table_args__ = (UniqueConstraint("name", name="_name_analysis_uc"),)
-
-
-class AnalysisResultRead(AnalysisResultBase):
-    """
-    A response model of an anlysis result
-    """
-
-    time_created: datetime
-    time_modified: datetime
-    task: Optional[TaskStatus]
-    result_data_status: Optional[str]
-
-
-class AnalysisResult(AnalysisResultBase, table=True):
-    __tablename__: ClassVar[Union[str, Callable[..., str]]] = "analysis_result"
-    __table_args__ = (
-        ForeignKeyConstraint(
-            ["project_id"], ["project.id"], onupdate="CASCADE", ondelete="CASCADE"
-        ),
-    )
-    """
-    This table stores all analyses that had been produced for a data 
-    The analysis reference points to the description of the analysis.
-    The result_id reference points to the detail result of the analysis
-    """
-    time_created: datetime = Field(
-        sa_column=Column(DateTime(timezone=True), server_default=func.now()),
-        description="Time added",
-    )
-    time_modified: datetime = Field(
-        sa_column=Column(
-            DateTime(timezone=True), server_default=func.now(), onupdate=func.now()
-        ),
-        description="Time modified",
-    )
-    """An object of the analysis type"""
-    analysis_orm: AnalysisCatalog = Relationship(back_populates="results")