# SCRI_db
* ## Description
SCRI_db is a python based application to handle, store, and access data on projects, and associated samples, stored on AWS. Read the [***documentation***](https://awnimo.github.io/SCRI_db/). The application is split into two parts:
1. A *reporting interface*.
2. *Command line tools* to process and update the database registry.
* #### The Reporting Interface
This is a web based interactive R-shiny user friendly interface, to pull reports and summaries, on projects and samples, stored in our database. Once installed, the user can use the package associated notebook, to establish a connection to the database. Through the interface, the user can use the different selectors and filters, to view the desired results. It also allows downloading a `.csv` formatted image of the resulting table.
* #### The Command Line Tools
The ***Command Line Tools*** module has methods to parse ***iLabs*** `HTML` project initiation forms, and sample submission forms. It also has built in methods to collect meta data from these forms, and construct a `MySQL INSERT` statements to push the data to our database on AWS.
* ## System Requirements
1. Python >= 3.6
2. R 3.0.1+. If you don't already have R, download it <a href=http://cran.rstudio.com/>here</a>.
3. mysql-connector-python Version: 8.0.13, install
$> pip3 install mysql-connector-python
4. Jupyter and ipywidgets:
$> pip3 install -U jupyter
$> pip3 install ipywidgets
$> jupyter nbextension enable --py widgetsnbextension
* ## Installation
If you are an authorized user with access privileges to update and write to the database, install the *Command Line Tools* from `PyPI`:
$> pip install SCRIdb
$> scridb -v
To install the `RShiny` package for the `The Reporting Interface`:
$> git clone https://github.com/dpeerlab/SCRI_db.git
$> cd SCRI_db
$> python3 setup.py RShiny
If you are a front-end user that only needs access to the database to view reports, you can skip the previous step. The `RShiny` setup command assumes `R` platform is installed and exists in `$PATH`. For a customized path to `R`, provide the command line with `--R-path=<path/to/R>` (`python3 setup.py RShiny -h`).
Contact a database `admin` for a `username` and `password` before start using the new platform.
* ## Usage
* ### The Reporting Interface
Activate the notebook:
$> cd notebook
$> jupyter notebook samples_db.ipynb
From the main menu choose ***Run All*** from ***Cell***. A dual tab box will appear.
* #### Configuration File Setup
It is optional to setup a configuration file to easily connect to the database. Choose the ***configure*** tab if this is the first time you connect to the database. Check ***Create New Configuration***, and enter your ***New Username*** and ***New Password*** (the same ones provided by the database `admin`), then click ***Submit***. This action will create and store a configuration file for future connections to the databae.
If successful, uncheck the ***Create New Configuration***, and switch back to the ***connect*** tab and click the ***Connect to DB!*** button (no need to provide a ***username*** and ***password***).
* #### Establish Connection Without Configuration Setup
Use a ***username*** and ***password*** in the designated fields in the ***connect*** tab, if you want to skip creating a configuration file, to connect to the database.
Start using the web interface and pull your favotite reports.
* ***Important note:*** it is imperative to close the `Samples Dashbord` page by clicking `Close window` on the left side panel, to properly terminate `RShiny`, and prevent kernel hanging.
* ### The Command Line Tools
Detailed information on usage is on [Wiki](https://github.com/dpeerlab/Dana-Pe-er-Wiki/wiki/Command-Line-Tools).
Intended for users with privileged access to the database (with read/write/update access).
$> scridb -h
scridb [-h] [-c [CONFIG]] [-f [FILE]] [-o [RESULTS_OUTPUT]] [-j [JOBS]]
[-e [EMAIL]] [-p [PEM]] [-dS [DOCKERIZEDSEQC]] [-sc [SCATA]]
{data_submission,process,upload_stats,data_transfer,run} ...
The following will actually build an `HTML` overall report on projects to monitor ongoing projects and their status:
$> projectsHTML_index
A new feature added to update metadata on samples submitted to *IGO* for sequencing:
$> update_IGOdates -h
update_IGOdates [-h] [-s [SEQUENCING_DATE]] [filename]
* ## Release Notes
### Version 1.1.4
Added `Tags` to newly created AWS users, with keys `Name` and `email`.
A minor fix to `upload_stats`.
### Version 1.1.3
The `CLI` can be installed now from [`PyPI`](https://pypi.org/project/SCRIdb/), no need to clone or sync local repository with remote one.
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资源分类:Python库 所属语言:Python 资源全名:SCRIdb-1.1.6.tar.gz 资源来源:官方 安装方法:https://lanzao.blog.csdn.net/article/details/101784059
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