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authorCoprDistGit <infra@openeuler.org>2023-05-15 05:05:21 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-15 05:05:21 +0000
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tree4841d0dda16bc74a3ee33efb50a8d0a80291fdd6 /python-bioclients.spec
parent81cc5881af48e3231fc9e7e96b47785b59bc6cb7 (diff)
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+%global _empty_manifest_terminate_build 0
+Name: python-BioClients
+Version: 0.2.11
+Release: 1
+Summary: Clients for online biomedical resources, usually REST APIs.
+License: MIT License
+URL: https://github.com/jeremyjyang/BioClients
+Source0: https://mirrors.nju.edu.cn/pypi/web/packages/5b/3b/d8e72d59166c43ba184fb4ea3d040a6b5b0b6408d88e2e232c882aa53d92/BioClients-0.2.11.tar.gz
+BuildArch: noarch
+
+
+%description
+# `BioClients` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="BioClients logo">
+
+Python package for access to online biomedical resources,
+usually via REST APIs. Modules generally include
+`Client.py` for command-line use and `Utils.py` for
+integration into other code. With the advent of HTTP web services,
+first SOAP/XML and then mostly REST/JSON, many online APIs
+require very similar methods for data search, requests
+and transforms into usable formats, often TSV.
+
+## Availability and installation
+
+Source at <https://github.com/jeremyjyang/BioClients>;
+releases available via `pypi.org`:
+<https://pypi.org/project/BioClients/>
+(`pip3 install BioClients`).
+
+However, current development snapshot recommended.
+
+___(First download or clone.)___
+```
+$ cd BioClients
+$ python3 setup.py install
+```
+
+## Dependencies
+
+* Python 3.7+
+* Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc.
+
+## Modules
+
+ [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__Bioregistry__](doc/bioregistry.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CAS__](doc/cas.md) &#8226; [__CDC__](doc/cdc.md) &#8226; [__CFDE__](doc/cfde.md) &#8226; [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226; [__ChEBI__](doc/chebi.md) &#8226; [__ChEMBL__](doc/chembl.md) &#8226; [__ChemIdPlus__](doc/chemidplus.md) &#8226; [__ClinicalTrials.gov__](doc/clinicaltrials.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226; [__DisGeNet__](doc/disgenet.md) &#8226; [__DNorm__](doc/dnorm.md) &#8226; [__DrugCentral__](doc/drugcentral.md) &#8226; [__EMBL-EBI__](doc/emblebi.md) &#8226; [__EnsEMBL__](doc/ensembl.md) &#8226; [__FDA__](doc/fda.md) &#8226; [__Gene Ontology__](doc/geneontology.md) &#8226; [__GTEx__](doc/gtex.md) &#8226; [__GWAS Catalog__](doc/gwascatalog.md) &#8226; [__HUGO__](doc/hugo.md) &#8226; [__HumanBase__](doc/humanbase.md) &#8226; [__iCite__](doc/icite.md) &#8226; [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__Medline__](doc/medline.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md) &#8226; [__MyGene__](doc/mygene.md) &#8226; [__NCBO__](doc/ncbo.md) &#8226; [__NCATS__](doc/ncats.md) &#8226; [__OMIM__](doc/omim.md) &#8226; [__Open Targets__](doc/opentargets.md) &#8226; [__Panther__](doc/panther.md) &#8226; [__PDB__](doc/pdb.md) &#8226; [__PubChem__](doc/pubchem.md) &#8226; [__PubMed__](doc/pubmed.md) &#8226; [__PubTator__](doc/pubtator.md) &#8226; [__Reactome__](doc/reactome.md) &#8226; [__RXNorm__](doc/rxnorm.md) &#8226; [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md)
+
+Miscellaneous utilities: [__UTIL__](doc/util.md)
+
+## Usage Example
+
+```
+$ python3 -m BioClients.pubchem.Client -h
+```
+
+## Design pattern
+
+Generally each module includes command-line app `Client.py` which calls
+functions in a corresponding `Utils.py`, providing all capabilities
+by import of the module. Command-line apps not API clients are generally
+named `App.py`. Functions can write to an output file
+or return a Pandas dataframe (if output file unspecified).
+
+## Data structures and formats, XML, JSON, and TSV
+
+BioClients is designed to be simple and practical, and XML, JSON
+and TSV are likewise simple in many respects, yet a great deal
+of conceptual and technological progress is reflected. XML and JSON
+can represent arbitrarily complex data objects, comprised of nested lists,
+dictionaries, and trees of primary types. TSV represents tables of
+rows and columns, related by common keys, reflecting the development
+of SQL and relational databases. Transforming JSON to TSV, as these
+clients generally do, projects data objects to tables useful for many
+applications (e.g. machine learning).
+
+
+
+
+%package -n python3-BioClients
+Summary: Clients for online biomedical resources, usually REST APIs.
+Provides: python-BioClients
+BuildRequires: python3-devel
+BuildRequires: python3-setuptools
+BuildRequires: python3-pip
+%description -n python3-BioClients
+# `BioClients` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="BioClients logo">
+
+Python package for access to online biomedical resources,
+usually via REST APIs. Modules generally include
+`Client.py` for command-line use and `Utils.py` for
+integration into other code. With the advent of HTTP web services,
+first SOAP/XML and then mostly REST/JSON, many online APIs
+require very similar methods for data search, requests
+and transforms into usable formats, often TSV.
+
+## Availability and installation
+
+Source at <https://github.com/jeremyjyang/BioClients>;
+releases available via `pypi.org`:
+<https://pypi.org/project/BioClients/>
+(`pip3 install BioClients`).
+
+However, current development snapshot recommended.
+
+___(First download or clone.)___
+```
+$ cd BioClients
+$ python3 setup.py install
+```
+
+## Dependencies
+
+* Python 3.7+
+* Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc.
+
+## Modules
+
+ [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__Bioregistry__](doc/bioregistry.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CAS__](doc/cas.md) &#8226; [__CDC__](doc/cdc.md) &#8226; [__CFDE__](doc/cfde.md) &#8226; [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226; [__ChEBI__](doc/chebi.md) &#8226; [__ChEMBL__](doc/chembl.md) &#8226; [__ChemIdPlus__](doc/chemidplus.md) &#8226; [__ClinicalTrials.gov__](doc/clinicaltrials.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226; [__DisGeNet__](doc/disgenet.md) &#8226; [__DNorm__](doc/dnorm.md) &#8226; [__DrugCentral__](doc/drugcentral.md) &#8226; [__EMBL-EBI__](doc/emblebi.md) &#8226; [__EnsEMBL__](doc/ensembl.md) &#8226; [__FDA__](doc/fda.md) &#8226; [__Gene Ontology__](doc/geneontology.md) &#8226; [__GTEx__](doc/gtex.md) &#8226; [__GWAS Catalog__](doc/gwascatalog.md) &#8226; [__HUGO__](doc/hugo.md) &#8226; [__HumanBase__](doc/humanbase.md) &#8226; [__iCite__](doc/icite.md) &#8226; [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__Medline__](doc/medline.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md) &#8226; [__MyGene__](doc/mygene.md) &#8226; [__NCBO__](doc/ncbo.md) &#8226; [__NCATS__](doc/ncats.md) &#8226; [__OMIM__](doc/omim.md) &#8226; [__Open Targets__](doc/opentargets.md) &#8226; [__Panther__](doc/panther.md) &#8226; [__PDB__](doc/pdb.md) &#8226; [__PubChem__](doc/pubchem.md) &#8226; [__PubMed__](doc/pubmed.md) &#8226; [__PubTator__](doc/pubtator.md) &#8226; [__Reactome__](doc/reactome.md) &#8226; [__RXNorm__](doc/rxnorm.md) &#8226; [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md)
+
+Miscellaneous utilities: [__UTIL__](doc/util.md)
+
+## Usage Example
+
+```
+$ python3 -m BioClients.pubchem.Client -h
+```
+
+## Design pattern
+
+Generally each module includes command-line app `Client.py` which calls
+functions in a corresponding `Utils.py`, providing all capabilities
+by import of the module. Command-line apps not API clients are generally
+named `App.py`. Functions can write to an output file
+or return a Pandas dataframe (if output file unspecified).
+
+## Data structures and formats, XML, JSON, and TSV
+
+BioClients is designed to be simple and practical, and XML, JSON
+and TSV are likewise simple in many respects, yet a great deal
+of conceptual and technological progress is reflected. XML and JSON
+can represent arbitrarily complex data objects, comprised of nested lists,
+dictionaries, and trees of primary types. TSV represents tables of
+rows and columns, related by common keys, reflecting the development
+of SQL and relational databases. Transforming JSON to TSV, as these
+clients generally do, projects data objects to tables useful for many
+applications (e.g. machine learning).
+
+
+
+
+%package help
+Summary: Development documents and examples for BioClients
+Provides: python3-BioClients-doc
+%description help
+# `BioClients` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="BioClients logo">
+
+Python package for access to online biomedical resources,
+usually via REST APIs. Modules generally include
+`Client.py` for command-line use and `Utils.py` for
+integration into other code. With the advent of HTTP web services,
+first SOAP/XML and then mostly REST/JSON, many online APIs
+require very similar methods for data search, requests
+and transforms into usable formats, often TSV.
+
+## Availability and installation
+
+Source at <https://github.com/jeremyjyang/BioClients>;
+releases available via `pypi.org`:
+<https://pypi.org/project/BioClients/>
+(`pip3 install BioClients`).
+
+However, current development snapshot recommended.
+
+___(First download or clone.)___
+```
+$ cd BioClients
+$ python3 setup.py install
+```
+
+## Dependencies
+
+* Python 3.7+
+* Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc.
+
+## Modules
+
+ [__Allen__](doc/allen.md) &#8226; [__AMP-T2D__](doc/amp__t2d.md) &#8226; [__BindingDb__](doc/bindingdb.md) &#8226; [__BioGrid__](doc/biogrid.md) &#8226; [__Bioregistry__](doc/bioregistry.md) &#8226; [__BRENDA__](doc/brenda.md) &#8226; [__CAS__](doc/cas.md) &#8226; [__CDC__](doc/cdc.md) &#8226; [__CFDE__](doc/cfde.md) &#8226; [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) &#8226; [__ChEBI__](doc/chebi.md) &#8226; [__ChEMBL__](doc/chembl.md) &#8226; [__ChemIdPlus__](doc/chemidplus.md) &#8226; [__ClinicalTrials.gov__](doc/clinicaltrials.md) &#8226; [__Disease Ontology__](doc/diseaseontology.md) &#8226; [__DisGeNet__](doc/disgenet.md) &#8226; [__DNorm__](doc/dnorm.md) &#8226; [__DrugCentral__](doc/drugcentral.md) &#8226; [__EMBL-EBI__](doc/emblebi.md) &#8226; [__EnsEMBL__](doc/ensembl.md) &#8226; [__FDA__](doc/fda.md) &#8226; [__Gene Ontology__](doc/geneontology.md) &#8226; [__GTEx__](doc/gtex.md) &#8226; [__GWAS Catalog__](doc/gwascatalog.md) &#8226; [__HUGO__](doc/hugo.md) &#8226; [__HumanBase__](doc/humanbase.md) &#8226; [__iCite__](doc/icite.md) &#8226; [__IDG__](doc/idg.md) &#8226; [__JensenLab__](doc/jensenlab.md) &#8226; [__LINCS__](doc/lincs.md) &#8226; [__MaayanLab__](doc/maayanlab.md) &#8226; [__Medline__](doc/medline.md) &#8226; [__MeSH__](doc/mesh.md) &#8226; [__MONARCH__](doc/monarch.md) &#8226; [__MyGene__](doc/mygene.md) &#8226; [__NCBO__](doc/ncbo.md) &#8226; [__NCATS__](doc/ncats.md) &#8226; [__OMIM__](doc/omim.md) &#8226; [__Open Targets__](doc/opentargets.md) &#8226; [__Panther__](doc/panther.md) &#8226; [__PDB__](doc/pdb.md) &#8226; [__PubChem__](doc/pubchem.md) &#8226; [__PubMed__](doc/pubmed.md) &#8226; [__PubTator__](doc/pubtator.md) &#8226; [__Reactome__](doc/reactome.md) &#8226; [__RXNorm__](doc/rxnorm.md) &#8226; [__STRINGDB__](doc/stringdb.md) &#8226; [__TCGA__](doc/tcga.md) &#8226; [__UMLS__](doc/umls.md) &#8226; [__UniProt__](doc/uniprot.md) &#8226; [__Wikidata__](doc/wikidata.md) &#8226; [__WikiPathways__](doc/wikipathways.md)
+
+Miscellaneous utilities: [__UTIL__](doc/util.md)
+
+## Usage Example
+
+```
+$ python3 -m BioClients.pubchem.Client -h
+```
+
+## Design pattern
+
+Generally each module includes command-line app `Client.py` which calls
+functions in a corresponding `Utils.py`, providing all capabilities
+by import of the module. Command-line apps not API clients are generally
+named `App.py`. Functions can write to an output file
+or return a Pandas dataframe (if output file unspecified).
+
+## Data structures and formats, XML, JSON, and TSV
+
+BioClients is designed to be simple and practical, and XML, JSON
+and TSV are likewise simple in many respects, yet a great deal
+of conceptual and technological progress is reflected. XML and JSON
+can represent arbitrarily complex data objects, comprised of nested lists,
+dictionaries, and trees of primary types. TSV represents tables of
+rows and columns, related by common keys, reflecting the development
+of SQL and relational databases. Transforming JSON to TSV, as these
+clients generally do, projects data objects to tables useful for many
+applications (e.g. machine learning).
+
+
+
+
+%prep
+%autosetup -n BioClients-0.2.11
+
+%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-BioClients -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.11-1
+- Package Spec generated