path: root/python-massql.spec

%global _empty_manifest_terminate_build 0
Name:		python-massql
Version:	0.0.15
Release:	1
Summary:	Mass spectrometry query language python implementation
License:	MIT License
URL:		https://github.com/mwang87/MassQueryLanguage
Source0:	https://mirrors.aliyun.com/pypi/web/packages/57/e5/d316d7584cde312cb0f61db08a48b5620885310b3cc112bb803e30a6b80e/massql-0.0.15.tar.gz
BuildArch:	noarch

Requires:	python3-pymzml
Requires:	python3-lark-parser
Requires:	python3-pandas
Requires:	python3-pyarrow
Requires:	python3-tqdm
Requires:	python3-py-expression-eval
Requires:	python3-matchms
Requires:	python3-pyteomics
Requires:	python3-psims
Requires:	python3-plotly
Requires:	python3-kaleido
Requires:	python3-pydot

%description
# Mass Spec Query Language

[![Unit Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml)
[![NF Workflow Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml)

The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to
express a query in a mass spectrometry centric fashion. It is inspired by SQL,
but it attempts to bake in assumptions of mass spectrometry to make querying much more
natural for mass spectrometry users. Broadly we attempt to design it according to several principles:

1. Expressiveness - Capture complex mass spectrometry patterns that the community would like to look for
1. Precision - Exactly prescribe how to find data without ambiguity
2. Scalable - Easily facilitating the querying of one spectrum all the way up to entire repositories of data
3. Relatively Natural - MassQL should be relatively easy to read and write and even use to communicate ideas about mass
   spectrometry, you know like a language.

## Repository Structure

This is the repository to define the language and reference implementation. This contains several parts

1. Language Grammar
1. Reference Implementation Python API
1. Command line Utility to execute
1. NextFlow Workflow For Large Scale Analysis
1. ProteoSAFe workflow
1. Dash interactive exploration

## Developers/Contact

Mingxun Wang is the main creator and developer of MassQL. Contact me for contributing or using it!

## Language Specification/Documentation

Checkout specifics for the language, examples, and design patterns at the documentation.

[Documentation Link](https://mwang87.github.io/MassQueryLanguage_Documentation/)

## Python API

To install massql

```
pip install massql
```

Here is the most basic operation you can do

```
from massql import msql_engine

results_df = msql_engine.process_query(input_query, input_filename)
```

If you want to push in a data frame you already have, you can specify it

```
from massql import msql_engine
from massql import msql_fileloading

# Loading Data
ms1_df, ms2_df = msql_fileloading.load_data(input_filename)

# Executing Query
results_df = msql_engine.process_query(input_query, input_filename, ms1_df=ms1_df, ms2_df=ms2_df)
```

## Command Line Tool

You can use the command line tool ```massql``` to query things or put things into a pipeline.

A few examples of what you can do

```
massql test.mzML "QUERY scaninfo(MS2DATA)" --output_file results.tsv
```

## Web API

### API Version

```/api```

### Parsing query into intermediate JSON string

```/parse?query=<query string>```

[Example Link](https://msql.ucsd.edu/parse?query=QUERY%20MS2DATA%20WHERE%20MS1MZ=100)

### Visualization of Query

Visualization image of MS1 spectra

```/visualize/ms1```

[Example Link](https://msql.ucsd.edu/visualize/ms1?query=QUERY+scaninfo%28MS1DATA%29+WHERE+MS1MZ%3DX%3ATOLERANCEMZ%3D0.1%3AINTENSITYPERCENT%3D25%3AINTENSITYMATCH%3DY%3AINTENSITYMATCHREFERENCE+AND+%0AMS1MZ%3DX%2B2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+%0AMS1MZ%3DX-2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+MS1MZ%3DX%2B4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS1MZ%3DX-4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS2PREC%3DX&filename=GNPS00002_A3_p.mzML&x_axis=&y_axis=&facet_column=&scan=&x_value=572.828&y_value=0.64&ms1_usi=mzspec%3AGNPS%3ATASK-f6e8346934904399ae6742723762b2cb-f.MSV000084691%2Fccms_peak%2F1810E-II.mzML%3Ascan%3A474&ms2_usi=)

Visualization image of MS2 spectra

```/visualize/ms2```

## Testing

To run tests, you'll need to first fetch some fixtures that are not bundled with the git repo:
```cd tests && sh ./get_data.sh```

You will also want to install the extra requirements for the test suite:
```pip install -r requirements_test.txt```

## License

MIT License


%package -n python3-massql
Summary:	Mass spectrometry query language python implementation
Provides:	python-massql
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-massql
# Mass Spec Query Language

[![Unit Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml)
[![NF Workflow Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml)

The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to
express a query in a mass spectrometry centric fashion. It is inspired by SQL,
but it attempts to bake in assumptions of mass spectrometry to make querying much more
natural for mass spectrometry users. Broadly we attempt to design it according to several principles:

1. Expressiveness - Capture complex mass spectrometry patterns that the community would like to look for
1. Precision - Exactly prescribe how to find data without ambiguity
2. Scalable - Easily facilitating the querying of one spectrum all the way up to entire repositories of data
3. Relatively Natural - MassQL should be relatively easy to read and write and even use to communicate ideas about mass
   spectrometry, you know like a language.

## Repository Structure

This is the repository to define the language and reference implementation. This contains several parts

1. Language Grammar
1. Reference Implementation Python API
1. Command line Utility to execute
1. NextFlow Workflow For Large Scale Analysis
1. ProteoSAFe workflow
1. Dash interactive exploration

## Developers/Contact

Mingxun Wang is the main creator and developer of MassQL. Contact me for contributing or using it!

## Language Specification/Documentation

Checkout specifics for the language, examples, and design patterns at the documentation.

[Documentation Link](https://mwang87.github.io/MassQueryLanguage_Documentation/)

## Python API

To install massql

```
pip install massql
```

Here is the most basic operation you can do

```
from massql import msql_engine

results_df = msql_engine.process_query(input_query, input_filename)
```

If you want to push in a data frame you already have, you can specify it

```
from massql import msql_engine
from massql import msql_fileloading

# Loading Data
ms1_df, ms2_df = msql_fileloading.load_data(input_filename)

# Executing Query
results_df = msql_engine.process_query(input_query, input_filename, ms1_df=ms1_df, ms2_df=ms2_df)
```

## Command Line Tool

You can use the command line tool ```massql``` to query things or put things into a pipeline.

A few examples of what you can do

```
massql test.mzML "QUERY scaninfo(MS2DATA)" --output_file results.tsv
```

## Web API

### API Version

```/api```

### Parsing query into intermediate JSON string

```/parse?query=<query string>```

[Example Link](https://msql.ucsd.edu/parse?query=QUERY%20MS2DATA%20WHERE%20MS1MZ=100)

### Visualization of Query

Visualization image of MS1 spectra

```/visualize/ms1```

[Example Link](https://msql.ucsd.edu/visualize/ms1?query=QUERY+scaninfo%28MS1DATA%29+WHERE+MS1MZ%3DX%3ATOLERANCEMZ%3D0.1%3AINTENSITYPERCENT%3D25%3AINTENSITYMATCH%3DY%3AINTENSITYMATCHREFERENCE+AND+%0AMS1MZ%3DX%2B2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+%0AMS1MZ%3DX-2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+MS1MZ%3DX%2B4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS1MZ%3DX-4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS2PREC%3DX&filename=GNPS00002_A3_p.mzML&x_axis=&y_axis=&facet_column=&scan=&x_value=572.828&y_value=0.64&ms1_usi=mzspec%3AGNPS%3ATASK-f6e8346934904399ae6742723762b2cb-f.MSV000084691%2Fccms_peak%2F1810E-II.mzML%3Ascan%3A474&ms2_usi=)

Visualization image of MS2 spectra

```/visualize/ms2```

## Testing

To run tests, you'll need to first fetch some fixtures that are not bundled with the git repo:
```cd tests && sh ./get_data.sh```

You will also want to install the extra requirements for the test suite:
```pip install -r requirements_test.txt```

## License

MIT License


%package help
Summary:	Development documents and examples for massql
Provides:	python3-massql-doc
%description help
# Mass Spec Query Language

[![Unit Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml)
[![NF Workflow Testing](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml/badge.svg)](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-workflow.yml)

The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to
express a query in a mass spectrometry centric fashion. It is inspired by SQL,
but it attempts to bake in assumptions of mass spectrometry to make querying much more
natural for mass spectrometry users. Broadly we attempt to design it according to several principles:

1. Expressiveness - Capture complex mass spectrometry patterns that the community would like to look for
1. Precision - Exactly prescribe how to find data without ambiguity
2. Scalable - Easily facilitating the querying of one spectrum all the way up to entire repositories of data
3. Relatively Natural - MassQL should be relatively easy to read and write and even use to communicate ideas about mass
   spectrometry, you know like a language.

## Repository Structure

This is the repository to define the language and reference implementation. This contains several parts

1. Language Grammar
1. Reference Implementation Python API
1. Command line Utility to execute
1. NextFlow Workflow For Large Scale Analysis
1. ProteoSAFe workflow
1. Dash interactive exploration

## Developers/Contact

Mingxun Wang is the main creator and developer of MassQL. Contact me for contributing or using it!

## Language Specification/Documentation

Checkout specifics for the language, examples, and design patterns at the documentation.

[Documentation Link](https://mwang87.github.io/MassQueryLanguage_Documentation/)

## Python API

To install massql

```
pip install massql
```

Here is the most basic operation you can do

```
from massql import msql_engine

results_df = msql_engine.process_query(input_query, input_filename)
```

If you want to push in a data frame you already have, you can specify it

```
from massql import msql_engine
from massql import msql_fileloading

# Loading Data
ms1_df, ms2_df = msql_fileloading.load_data(input_filename)

# Executing Query
results_df = msql_engine.process_query(input_query, input_filename, ms1_df=ms1_df, ms2_df=ms2_df)
```

## Command Line Tool

You can use the command line tool ```massql``` to query things or put things into a pipeline.

A few examples of what you can do

```
massql test.mzML "QUERY scaninfo(MS2DATA)" --output_file results.tsv
```

## Web API

### API Version

```/api```

### Parsing query into intermediate JSON string

```/parse?query=<query string>```

[Example Link](https://msql.ucsd.edu/parse?query=QUERY%20MS2DATA%20WHERE%20MS1MZ=100)

### Visualization of Query

Visualization image of MS1 spectra

```/visualize/ms1```

[Example Link](https://msql.ucsd.edu/visualize/ms1?query=QUERY+scaninfo%28MS1DATA%29+WHERE+MS1MZ%3DX%3ATOLERANCEMZ%3D0.1%3AINTENSITYPERCENT%3D25%3AINTENSITYMATCH%3DY%3AINTENSITYMATCHREFERENCE+AND+%0AMS1MZ%3DX%2B2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+%0AMS1MZ%3DX-2%3ATOLERANCEMZ%3D0.1%3AINTENSITYMATCH%3DY%2A0.66%3AINTENSITYMATCHPERCENT%3D30+AND+MS1MZ%3DX%2B4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS1MZ%3DX-4%3ATOLERANCEMZ%3D0.2%3AINTENSITYMATCH%3DY%2A0.17%3AINTENSITYMATCHPERCENT%3D40+AND+%0AMS2PREC%3DX&filename=GNPS00002_A3_p.mzML&x_axis=&y_axis=&facet_column=&scan=&x_value=572.828&y_value=0.64&ms1_usi=mzspec%3AGNPS%3ATASK-f6e8346934904399ae6742723762b2cb-f.MSV000084691%2Fccms_peak%2F1810E-II.mzML%3Ascan%3A474&ms2_usi=)

Visualization image of MS2 spectra

```/visualize/ms2```

## Testing

To run tests, you'll need to first fetch some fixtures that are not bundled with the git repo:
```cd tests && sh ./get_data.sh```

You will also want to install the extra requirements for the test suite:
```pip install -r requirements_test.txt```

## License

MIT License


%prep
%autosetup -n massql-0.0.15

%build
%py3_build

%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
	find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
	find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
	find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
	find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
	find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .

%files -n python3-massql -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.15-1
- Package Spec generated