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@@ -0,0 +1 @@ +/massql-0.0.15.tar.gz diff --git a/python-massql.spec b/python-massql.spec new file mode 100644 index 0000000..6460beb --- /dev/null +++ b/python-massql.spec @@ -0,0 +1,417 @@ +%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 + +[](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml) +[](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 + +[](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml) +[](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 + +[](https://github.com/mwang87/MassQueryLanguage/actions/workflows/test-unit.yml) +[](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 @@ -0,0 +1 @@ +5426f3e7e49620b9624e3c1df0230bc6 massql-0.0.15.tar.gz |