معرفی شرکت ها
cidc-cli-0.9.9
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مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
A command-line interface for interacting with the CIDC.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cidc-cli-0.9.9 |
| نام | cidc-cli |
| نسخه کتابخانه | 0.9.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cidc-cli/ |
| مجوز | - |
| Branch | Status | License |
| ------ | ---------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------- |
| Master |  | [](https://opensource.org/licenses/MIT) |
## CIDC-CLI
Command line tool for interfacing with the CIDC API.
## Setup
### Install the CIDC-CLI
```bash
pip3 install cidc-cli
```
### Run the CIDC-CLI
To display the help message for the CLI, run:
```bash
cidc
```
To authenticate with the CIDC API, run:
```bash
cidc login [token]
```
## Development
For local development, first install the development dependencies:
```bash
pip install -r requirements.dev.txt
```
Then, install and configure the pre-commit hooks:
```bash
pre-commit install
```
## JIRA Integration
To set-up the git hook for JIRA integration, run:
```bash
ln -s ../../.githooks/commit-msg .git/hooks/commit-msg
chmod +x .git/hooks/commit-msg
rm .git/hooks/commit-msg.sample
```
This symbolic link is necessary to correctly link files in `.githooks` to `.git/hooks`. Note that setting the `core.hooksPath` configuration variable would lead to [pre-commit failing](https://github.com/pre-commit/pre-commit/issues/1198). The `commit-msg` hook [runs after](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) the `pre-commit` hook, hence the two are de-coupled in this workflow.
To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.
## Admin functions
Under the (hidden) `admin` are several functions meant for CIDC administators / engineers.
### CSMS
```bash
cidc admin test-csms
```
A simple API hit for a test of CSMS connection. Hits API endpoint `/admin/test_csms` which in turn gets CSMS's `/docs`.
This tests that the API is able to successfully make connection with the CSMS, as the `/docs` endpoint requires authorization.
As the API endpoint is protected, only users with role `cidc-admin` can make this request.
### dbedit suite
A set of commands to list / remove data from the database, including shipments, clinical data, and assay/analysis data.
It directly uses Google's cloud SDK to make a direct connection to the postgres cloud sql database, so it requires the user has `cloudsql.instances.connect` IAM permission.
#### Authentication
Authentication uses Application Default Credentials (ADC). Log-in is done via:
```bash
gcloud auth application-default login
```
#### Configuration
Configuration of the environment ie staging versus production is done as above using:
```bash
cidc config get-env
cidc config set-env ENV
```
Configuration of the database username is done via a pair of functions:
```bash
cidc admin get-username
cidc admin set-username USERNAME
```
The password is requested every time you issue a command so as to not store it.
#### Listing data
Under the `list` subcommand of `cidc admin`, you can get descriptions of the data available in the database.
- `cidc admin list clinical TRIAL_ID`
- prints a table describing all shipments for the given trial
- with the following columns:
- `object_url`, `filename`, `num_participants`, `created`, `comment`
- `cidc admin list misc-data TRIAL_ID`
- prints a table describing all misc_data files for the given trial
- with the following columns:
- `batch_id`, `object_url`, `filename`, `created`, `description`
- `cidc admin list shipments TRIAL_ID`
- prints a table describing all shipments for the given trial
- with the following columns:
- `upload_type`, `manifest_id`, `num_samples`, `created`
- `cidc admin list assay TRIAL_ID ASSAY_OR_ANALYSIS`
- prints a table listing all samples for the given assay/analysis and trial
- any of the following values are allowed:
- `clinical_data`, same as `cidc admin list clinical TRIAL_ID`
- `misc_data`, same as `cidc admin list misc-data TRIAL_ID`
- analyses: `atacseq_analysis`, `ctdna_analysis`, `cytof_analysis`, `microbiome_analysis`, `rna_level1_analysis`, `tcr_analysis`, `wes_analysis`, `wes_analysis_old`, `wes_tumor_only_analysis`, `wes_tumor_only_analysis_old`
- assays: `atacseq`, `ctdna`, `cytof`, `hande`, `ihc`, `elisa`, `microbiome`, `mif`, `nanostring`, `olink`, `rna`, `tcr`, `wes`
#### Removing data
Under the `remove` subcommand of `cidc admin`, you can remove a wide variety of data from the JSON blobs.
- `cidc admin remove clinical TRIAL_ID TARGET_ID`
- removes a given clinical data file from a given trial's metadata as well as the file itself from the portal
- `TARGET_ID` is the `filename` of the clinical data to remove, as from `cidc admin list clinical TRIAL_ID`
- special value `'*'` for all files for this trial
- `cidc admin remove shipment TRIAL_ID TARGET_ID`
- removes a given shipment from a given trial's metadata
- `TARGET_ID` is the `manifest_id` of the shipment to remove, as from `cidc admin list shipments TRIAL_ID`
- `cidc admin remove assay TRIAL_ID ASSAY_OR_ANALYSIS TARGET_ID`
- removes a given clinical data file from a given trial's metadata as well as the associated files themselves from the portal
- for `ASSAY_OR_ANALYSIS=clinical_data`, same as `cidc admin remove clinical TRIAL_ID TARGET_ID`
- `TARGET_ID` is a tuple of the ids to find the data to remove, as from `cidc admin list assay TRIAL_ID ASSAY_OR_ANALYSIS`.
- It cannot go past where is divisible in the data, but can end early to remove the whole section.
- Namely:
- `elisa`: requires only `assay_run_id`
- `misc_data`, `olink`: require `batch_id` with an optional `filename`
- `nanostring`: requires `batch_id` and optional `run_id`
- `rna_level1_analysis`, `wes_tumor_only_analysis`, `wes_tumor_only_analysis_old`: requires only `cimac_id`
- `wes_analysis`, `wes_analysis_old`: requires only `run_id`
- otherwise: requires `batch_id` and optional `cimac_id`
نیازمندی
| مقدار | نام |
|---|---|
| ~=8.0.1 | click |
| - | cloud-sql-python-connector[pg8000] |
| ==1.2.4 | pandas |
| ==0.10.3 | python-dotenv |
| ==3.0.1 | python-jose |
| ==1.8.0 | pyperclip |
| ==2.22.0 | requests |
| ~=1.4.0 | sqlalchemy |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl cidc-cli-0.9.9:
pip install cidc-cli-0.9.9.whl
نصب پکیج tar.gz cidc-cli-0.9.9:
pip install cidc-cli-0.9.9.tar.gz