pyobo 0.11.0__py3-none-any.whl → 0.11.2__py3-none-any.whl

{pyobo-0.11.0.dist-info → pyobo-0.11.2.dist-info}/RECORD

@@ -1,18 +1,18 @@
 pyobo/__init__.py,sha256=k-oIvi7tNzCg0SA8D7jghJ9Q9GW6RXp75kszqsbZ_Xk,1837
 pyobo/__main__.py,sha256=cOYQ2OELxF-9T6nuZ9xnLSu9bLHk6einrsSoz7EcD9M,83
 pyobo/aws.py,sha256=8vg7VumLT3blTX8dyluS13jrBo6bwRHNEpkQw1njhXo,5946
-pyobo/constants.py,sha256=aonqwwtc65p-XgoPzTXL57dwJWkG5vXGK0ULES3u25U,1911
+pyobo/constants.py,sha256=R6ZIJ9JylzEXaGAO70WcMwwwNXezKoTJDEWLskzcYZc,1936
 pyobo/getters.py,sha256=mOrlI8qrI3zHwloXNvpmQnSSxhZZLjBgg5ZUGUwqUK8,15557
-pyobo/gilda_utils.py,sha256=bj_r8WPHL_BuV2yxRcJDNYHqdExNTz973qeSfx4fpNg,8173
+pyobo/gilda_utils.py,sha256=QXSzJmas1-BzT6S1O6XWnzKVjFzO_-vYoPZGi_HoUpw,8246
 pyobo/identifier_utils.py,sha256=UoDXiOeqlqMVXISR4Qhw1zXD0ss7jsw-fPs5Jsx8xyY,4533
 pyobo/mocks.py,sha256=Tivg8tLNFjUsbAF8TiY3iurhBbgmzGtYJmNMg_e6TTo,2422
 pyobo/normalizer.py,sha256=DfDuX2Ed3vCJgaezfHXorYcNui9vfR64AFJFYfF_NWk,8304
-pyobo/obographs.py,sha256=edsB4MF4x98C2EsIJ8ZifuG4oGA3YWXrCkIVd1iTbOg,3761
+pyobo/obographs.py,sha256=3Bdot7c5KlrTPxmgnk3Y7tXmaVf0n9aL8QEs6pIGVHo,3912
 pyobo/plugins.py,sha256=UyEnXxFP2q9IdYp5o7DDXPBrcExvTx4LkvhvWXx-XQc,1227
 pyobo/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyobo/reader.py,sha256=C_-Dz0ScyFdr8DivHTYyDhIVg8SOwS_Y0DIuqKT2EJI,21292
 pyobo/resource_utils.py,sha256=8ZQx8d-HbmPyc_WHUhqx1yjUKFZMF101FopZwZPghoE,4273
-pyobo/version.py,sha256=HPxL1mV3HqbCzveHuGbwWCt4-rh8D-dif3AILKAlX80,919
+pyobo/version.py,sha256=5XT91psNM717pWEmUHFJc4A_TdbD4AvRx-gAxK9qm4Y,919
 pyobo/api/__init__.py,sha256=7_uVqbZVEWrKNBYxVJb86K9-dLsGD2d2H5wjLzIP1wU,1301
 pyobo/api/alts.py,sha256=fYA3S3odeem2-HvzeqUn0jkAFGdmbL1SYXCjIqKmRqs,2836
 pyobo/api/hierarchy.py,sha256=-zgM4n0n0h5v5aPOhG0AR3isOt10Vtpo6EwVYN00ngI,9509
@@ -24,21 +24,6 @@ pyobo/api/species.py,sha256=Ze1yr3n9jCVQVYXmn_hw_FiziTYchddCNTW9ChDH85U,2259
 pyobo/api/typedefs.py,sha256=Z4IZ5ggJe1N7lKMMrng5P8WnZo0nalsaLTMLmQT0w2Y,1130
 pyobo/api/utils.py,sha256=zM56HjlYNPXjnhIe3oS7Yv5mAEfHHbhnf1gpJOnem1M,3274
 pyobo/api/xrefs.py,sha256=InnBazYid5SBoRCMfE3lrBIRtdvwNi2oozjlGaX06ls,6007
-pyobo/apps/__init__.py,sha256=iACi86TkTiGxwneGmfaudZOIEqZ45YjPXng7XjPE38Y,72
-pyobo/apps/cli.py,sha256=gnXBAaESw1T1BvgMpTv-0P26hM2vKCAXPy0SOskgUwU,335
-pyobo/apps/gilda/__init__.py,sha256=jpLIHJOmR_66tdXXUWFP9NiZnpQKvjv5YpCJWoAKnUI,54
-pyobo/apps/gilda/__main__.py,sha256=9EEwzUlwcFHrfAEzveIvmqHiPu52wLt8o4Xe_vFcWf0,124
-pyobo/apps/gilda/app.py,sha256=rHqGR52fnbhqRPWktbIZc8ZZcFEIKp6rq7ledFuN_Lg,1315
-pyobo/apps/gilda/cli.py,sha256=OteTZy060Elmg38sl091kHfaHjjLTJaAtLdUpWgr6ug,702
-pyobo/apps/gilda/templates/base.html,sha256=MxFNPgWW4wYzXXS3RwXMcMJAc1_lUhguQvVYQYjSjLY,888
-pyobo/apps/gilda/templates/home.html,sha256=ZAqegzBGgVct9UzmfC0dfGJ6_jbDSCpbwqe2WB-00AA,273
-pyobo/apps/gilda/templates/matches.html,sha256=x3mvMCevr8IoXSXmm_aOQlKNBycvMpBedLLCt2znNXQ,934
-pyobo/apps/mapper/__init__.py,sha256=9PK1LtsCTVcQQzSPtpa6f1dgjsoeygq9cAP7AXqEiJY,56
-pyobo/apps/mapper/__main__.py,sha256=XScQCj6oK2OslWyZ8yzcaietLJm_XxDLA22CMoyy6dM,169
-pyobo/apps/mapper/cli.py,sha256=AHPPXqSd3LTMhHIsmhErMB_gpfDeDs6IGlPdHQKMIq0,682
-pyobo/apps/mapper/mapper.py,sha256=yVIHGlTwFNtKEF07K-oqsqy8ggIalN6SfmyzB4E--2I,5787
-pyobo/apps/mapper/templates/base.html,sha256=w9d8e8qKnVy_h7RT5hWV9EwghgPqn0y3xJ-tZw0v9TQ,982
-pyobo/apps/mapper/templates/mapper_home.html,sha256=XugUb76C6B1JGQTCb2tDhZ-XyY-636qeZJODUTrpjdw,2785
 pyobo/cli/__init__.py,sha256=pTiLuzjjpi0P69yVjQ2kE6nBUmZuYFnqdJNDZLDkgvk,71
 pyobo/cli/aws.py,sha256=_S08OhNY-vdx-KIT4ix3Zluey9lVY0RWJhDjwcwrw2M,964
 pyobo/cli/cli.py,sha256=gWEMOWEfjpTdCjxJm1F3Kq73FD1xoGfG9p_8r0YJ4Ro,3522
@@ -53,6 +38,8 @@ pyobo/resources/ncbitaxon.py,sha256=rZtU6ik32UATBb5tRY5i5LU9_kpTA3vmPy9gOfhY_fU,
 pyobo/resources/ncbitaxon.tsv.gz,sha256=43zHjnVt62TA4_lV58X-FCPdMDfLg1B1PvZSr_Xy9hY,22981954
 pyobo/resources/ro.py,sha256=k8JoFKz64T1Pp39FKud1n4I3qPb178B2xSWJbAN8qdU,1461
 pyobo/resources/ro.tsv,sha256=YvlBLPAKy2w4IheYzO9ox1Yg6WkHdMVzMQTikIlECog,26586
+pyobo/resources/so.py,sha256=S-vmQ7L8AJE08FfGVDIJqNQNaLPUmuJ6HC5F4hWHMrA,1466
+pyobo/resources/so.tsv,sha256=UJZKFTEAv_XszYYbun4Wf6b4jovDjSKc1RWRQRcTzDw,82068
 pyobo/sources/README.md,sha256=w2klc3MjUbLL9VZxIZIqFrHMdQshPUGSCoFsYdUReD8,889
 pyobo/sources/__init__.py,sha256=WkyBXj7V1Y90qSijmHwF89GyC8kRj-Jv7DiFAzqX1iA,3811
 pyobo/sources/agrovoc.py,sha256=SJsbJ7KtxdJUG9Rimmb2CfLfzpK9eOzP0wx59gj-6s4,787
@@ -63,26 +50,26 @@ pyobo/sources/cgnc.py,sha256=MSEGwaZ8wOypR5sLALAl5Z3ay7K3RjqMC0GtJd4VvSc,2320
 pyobo/sources/chebi.py,sha256=IrfXfO9-75jxeDCjCBFBgRWe2R7DSQpQBOllgt7MmoI,1202
 pyobo/sources/chembl.py,sha256=5K5gtIrsqHyZSG8uxhqgXuvKjSXAw9i1dg20boZg8Fg,2280
 pyobo/sources/civic_gene.py,sha256=_gC7P8QyRhJF9i_46eEU4_nV8I7i6z7XGKvXD67mwOM,1693
-pyobo/sources/complexportal.py,sha256=Uf3lxgD_jzBWQH5xbcJ11hgbdbxOlMHkdqsC0ySurdE,5993
+pyobo/sources/complexportal.py,sha256=n_ZHWzg7jRA0Trmy1ndQZAFM-ayDl_hFnj6O0ZjZESA,7581
 pyobo/sources/conso.py,sha256=OVcfSUjwMh5biMZuTfidHvREjyPrQE84kmEQOHsinxE,2438
 pyobo/sources/cpt.py,sha256=b7hcULlvu_xa6URwoD37Gc_8VAs8mxawAlXflL1e1LU,1466
 pyobo/sources/credit.py,sha256=gOhD5Q2Xa4CgEnDiwli8CuxjAxLkydZukwFU-l_KTzc,2017
 pyobo/sources/cvx.py,sha256=WglHdUi6uLKFUkzDRxGTuElOxBu4x5By2XcfZNS4LlM,2820
 pyobo/sources/depmap.py,sha256=UKJ63iH7NtzklQ7AIqENMxQIvslNeBocwLW90cR8Tcc,3660
-pyobo/sources/dictybase_gene.py,sha256=n91GwkCIZWhS_O9IaRwGS_LZ3rKSb3tCZBpb_uvx27w,2548
+pyobo/sources/dictybase_gene.py,sha256=57RxdH70S3Rklz4qZS0T_kBEdCH2UVSXYdYwt7Gn2Ds,2810
 pyobo/sources/drugbank.py,sha256=W-Qa8Cttk07PtndbdJHc1yrAMYZHT-4r1bxeRrXgqHE,11032
 pyobo/sources/drugbank_salt.py,sha256=DXqz5rEw8QUipPkDeuwg-MU9OvnSrBM62k3JeSeq4kM,1768
-pyobo/sources/drugcentral.py,sha256=5k-Fy1Khn_vqtuO5Sy33RsQLB51rcNgUA-K-PVaQOW0,3576
-pyobo/sources/expasy.py,sha256=MpkQ1snWdWAff5xVBpP-c1RQ3JXeFEKJ4J1Taufrtoo,10040
+pyobo/sources/drugcentral.py,sha256=YXd6d2y62ILNrWg5rqi9jDfmB-MTacCZA26itDgETmY,3751
+pyobo/sources/expasy.py,sha256=2MUKkPIiww97e14sTMH-FQa7tSxFym7Gz49D08wmZYI,10771
 pyobo/sources/famplex.py,sha256=oyNbnAbRuc72nap_xWpiZR8mcWWj7O5GliL89kwF9mQ,5787
-pyobo/sources/flybase.py,sha256=tSUbtg7XUnLFi5CKallNQIjwa0zX5rWiuh2vn-k0smA,5747
+pyobo/sources/flybase.py,sha256=8-_8AfS-_rho4OThchHjqDG0y07owq02rlmQjGmuBkY,5817
 pyobo/sources/geonames.py,sha256=uNwrVBXGaPvMS7bwUAof_plSrV3F999Va2YSWbNwAKA,8563
 pyobo/sources/gmt_utils.py,sha256=aPPVAtoyPOzoyGFOAf3RwlgpdARAU0RHkDWnp_ZFgl4,1391
 pyobo/sources/go.py,sha256=SDRZtT28gY6T3k3z_3PMSDdsQkb4vJDAchw1dL6x40Q,1250
 pyobo/sources/gwascentral_phenotype.py,sha256=EDxcAC6ONhZj-Amo4PsT7ruO1-CzqsJvYXug4eeFX5A,1873
 pyobo/sources/gwascentral_study.py,sha256=njSRd9YxMWvXXg4cyILPL704LrtIeg-_63cR120jgyc,2814
-pyobo/sources/hgnc.py,sha256=WDu6O3WCzok1NVOr6cR6WiIprAmTg2fm12yTTpdCewo,15902
-pyobo/sources/hgncgenefamily.py,sha256=StZ9GhhU5SfMrzIJe444SP-PKU-8cZpx9Gv2SlcbHrc,3623
+pyobo/sources/hgnc.py,sha256=C6Av1SIgP4XNyxcKKjZfEEvrPRu8lKUD-rNMYAmSC7Y,16298
+pyobo/sources/hgncgenefamily.py,sha256=jecrhlcBSXMnoFKlKHyS8zkWfqSqr5UHXZT7h_cY4oU,3755
 pyobo/sources/icd10.py,sha256=FqCrB3f1OGukQDcvgLGffbSNyaA9D62ufTQkgMLeE4I,2283
 pyobo/sources/icd11.py,sha256=IaJ6fV_7humYu7AKvn_93y355FL_XMjtMyyMClYBUjI,2831
 pyobo/sources/icd_utils.py,sha256=Ub5LH4fDRHrGWwb7iP8I2KEFNl6I-viqxvLUyxGz2nM,3156
@@ -90,33 +77,33 @@ pyobo/sources/interpro.py,sha256=8IhVie_VrQSHFZmxpQVPQXm6ISFV435UjhDA41qBuk8,488
 pyobo/sources/itis.py,sha256=jJF5oGuaewl4SH882AMhzr7HX5Ekpp2fyqAwT3nY6G4,2951
 pyobo/sources/mesh.py,sha256=02VCo6t4g3kp0BhLb_2pykK1428xyfY40zQ3xCPK_eY,12116
 pyobo/sources/mgi.py,sha256=nIizvAtIG7genT1iETkdKZmS6mCQmQZCSR-_kRMg7_s,5750
-pyobo/sources/mirbase.py,sha256=7bE6XVBn9na82p8Kr6Vs4xjy67MEJK8Ac1ZsQxmC4oA,6327
+pyobo/sources/mirbase.py,sha256=SfXyLt0_EVp_9mTApKC13-9cFTGs2qfi8J7KekKv5d4,6511
 pyobo/sources/mirbase_constants.py,sha256=5DjcwX_FRSzFYbTf50yvkPamSIH70Rw3I8q-Ds0zHVs,1998
 pyobo/sources/mirbase_family.py,sha256=qWAp1PUN5pJCArTPx-rhMGi6UG0LfoZNg5URQdXhDps,2151
 pyobo/sources/mirbase_mature.py,sha256=UbAdGEzLiS3GjeCnGKjapUKrL1WxTgxF25hdwx7pmV4,1488
 pyobo/sources/msigdb.py,sha256=lzQ9Bfuv53UVaN3He1NCkGg4ChWfo_9OPOK8NW6bl_s,5010
 pyobo/sources/ncbigene.py,sha256=jeQRJnLnU4Q1_U-FKOOeQjkqlc-iamUUn0zZqEmiaiI,5028
-pyobo/sources/npass.py,sha256=yMqkAkfOiNeQBXBIRR0qFrtcxBKrIqYH86MXPJC3e9U,2798
+pyobo/sources/npass.py,sha256=0jHHGX0gk2PZFhv5jhEsbN-khTaJu0cE3sbMedZe3UU,2799
 pyobo/sources/omim_ps.py,sha256=fcMNrFBtc5u3HHaLpQVML4amHvgMErTS--pOlg074A4,1004
-pyobo/sources/pathbank.py,sha256=xf3e8MvSOUcV_z-fMJuhakuKksL3cGcw2lnNljrX50E,4968
+pyobo/sources/pathbank.py,sha256=5sM_8dgriKE5YawxeGq3A6bpdC1kFS0KZXeaF-k-IYA,5471
 pyobo/sources/pfam.py,sha256=T9rZNIXUTw8XajUSNoPscDUN9wG4bae171xQepYqhQI,1830
 pyobo/sources/pfam_clan.py,sha256=Qk4q8jEwFR9NcLXeGR3p9TjA2oK40KkkFS0wMA1UirA,1324
 pyobo/sources/pid.py,sha256=iVoZ3yUgfTccun2baEDQ-mTwLYJ8kdWMoT9H3Q6xREc,4541
-pyobo/sources/pombase.py,sha256=byAaa4Gwla48y3sglcbfjpXCxVvVR5SAsbUBUiDRnIs,3585
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 pyobo/sources/pubchem.py,sha256=SgC56EBUHT6Cgwm7BUc3Kgw8b-kdg80JHm8D-TKdEzg,5284
-pyobo/sources/reactome.py,sha256=LHtv5dqremVixw4ASVIPM3Aq4feNqXVJ1R5kNQ93z9g,5063
-pyobo/sources/rgd.py,sha256=dleXkB5zQHpjOcj0u2rvSjsXm5S7GRuxQ-DupTN5BKk,5399
+pyobo/sources/reactome.py,sha256=yp0JZkdZvtSlwl9ki2L4ziEfaPo3YDolPeXTbQkmrnA,5720
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 pyobo/sources/rhea.py,sha256=qlQj6wHuY08QeEGwVHubh8oLD-E12dbqNCJ57v_uKW4,7776
 pyobo/sources/ror.py,sha256=U6sQ1IBs0nxENF02bnkUVA8rx04o4Y9dZ2YwKu6rtj4,7377
 pyobo/sources/sgd.py,sha256=kQ_kof0F50RB0TrL2Eorqc7nUyv2kibAdf4Hp99ijKo,2134
-pyobo/sources/slm.py,sha256=EbMv4SIpNbIyWmN4t6rDGji0ziIuLnaqjLR9r8V6LfA,3788
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 pyobo/sources/utils.py,sha256=RLo6z5BKLdofu4bLstDOJMOEiMDEmJdYrE12PeJEKtc,1091
 pyobo/sources/wikipathways.py,sha256=cd_0uRjwi5Q5SpBHTUF2QqLxj67-ZhuqdxEIGHcoB0U,2710
-pyobo/sources/zfin.py,sha256=yHRtpT1JtcP9kq9cPLsuLVainap4vZ9m5gl6ZJi55bk,4998
+pyobo/sources/zfin.py,sha256=6Mh-JhTKXy3g9xed-AgzmZlhIoWnBoEUJK9bsjQUahA,5369
 pyobo/sources/kegg/__init__.py,sha256=hVP0tuwVpiNMikFv_bNPrzuYv-HA1_bPdCvNx-fm5Fg,219
 pyobo/sources/kegg/api.py,sha256=nwHuKPsYbWhHEgBZzJ92XQAibQp8XEVQ6xglzWxyWY4,4709
 pyobo/sources/kegg/genes.py,sha256=T9ct-E_q43MZT4v7I2-liokxhNiRCI-HMZwKgBPwxz4,3707
-pyobo/sources/kegg/genome.py,sha256=0MfKjgbnKNvW_HM2FCufw5p_bj351_rBKIRPfdrAeVA,3968
+pyobo/sources/kegg/genome.py,sha256=9KSpBffM1Wv2pwTG8g0Lve9Zhu1Eur-Alvnjnry2N5o,4321
 pyobo/sources/kegg/pathway.py,sha256=ZvKBXLieL1w5kwaHg5wxvtFAAYAnWF1TalhGo_G6puc,6176
 pyobo/sources/selventa/__init__.py,sha256=cIIDlWL9znL2r0aZIJ2r1FN3NM9io74w-He2egzJwX8,254
 pyobo/sources/selventa/schem.py,sha256=Ct6Ut3AB99eylGhZco57ueoRcsyUmHATpFPRR8cbG8g,1313
@@ -129,7 +116,7 @@ pyobo/sources/umls/get_synonym_types.py,sha256=KU3CQxQBV2xYcX3SjqMrfRNU9nESYGDA7
 pyobo/sources/umls/synonym_types.tsv,sha256=z--ngeAqA_Kk8ft2YD8qOU_XUxhnTxF0OhL8jRd5xqo,8551
 pyobo/sources/umls/umls.py,sha256=WM2vNSX1asHn8hcVjV8sdkxE3Id3xOXwiRdLqb7Jnxk,4297
 pyobo/sources/uniprot/__init__.py,sha256=HVrjUxKjixqagsOYvVJkZ7nyIPlWAhLaUWa8sR0gLqA,200
-pyobo/sources/uniprot/uniprot.py,sha256=7Z-K35YVZAFlIGbae7JRlFyEEezubUYuztXYrsnvUrw,6130
+pyobo/sources/uniprot/uniprot.py,sha256=Qi329uy0PWRglmZGoEtSlzXy0Gs7nFVPIFroJA0H0VM,6206
 pyobo/sources/uniprot/uniprot_ptm.py,sha256=8hbGP_5Rh-HhB6iBIJZ7qhXBdcCKD9sUKtwYKUhczHU,3552
 pyobo/ssg/__init__.py,sha256=j_5ZWISXGMNLjJRiT-OBhdJ7MQpRQF69fMLWMaDidVQ,5410
 pyobo/ssg/base.html,sha256=_vldUCa-gL2YTNY6GgAuxNT3TgaED585vF_q7TrrjYs,2844
@@ -137,9 +124,9 @@ pyobo/ssg/index.html,sha256=zDGkwIQBtbpnhCYALXQ0vr7qsVmAqDtbwOyPqU3hZ8s,3993
 pyobo/ssg/term.html,sha256=QU6piGOq4dq8zlNhJvLFxqFjhVQyWlkiG31I0Sg5frg,3559
 pyobo/ssg/typedef.html,sha256=KrdqzB6xjt689bG33D26AL-11JrvNuEkoxNNI-EG-Tg,2038
 pyobo/struct/__init__.py,sha256=DwGtSEPepZdgB49UvxG470g12XIFdhMdKZ44DoZMg6g,646
-pyobo/struct/reference.py,sha256=JPrFspoCVXzDDW9yPbeWu62eP8Q9ForaDJcsQ247k5g,5587
-pyobo/struct/struct.py,sha256=OOzp2b4BkhBqR5DeY1fl90bP7wpdbGSzx4StAHUGcaU,54564
-pyobo/struct/typedef.py,sha256=Oyubk6VfUUDijG2C-l5LOdhdoLKFps6mm5ek5YphAQ8,13869
+pyobo/struct/reference.py,sha256=-SJaXMSDOrQ7SyU12UYquwwUdqoFoxrb6WypVtbGxOs,5661
+pyobo/struct/struct.py,sha256=5GJl4hEY2L5C3iM_vexdsPxiJANwNh_1KakjDMorXDs,55019
+pyobo/struct/typedef.py,sha256=MA62XSS-Me4kSmVs25fQbW1nGss1C8zhAQ5diidCSzs,14009
 pyobo/struct/utils.py,sha256=ETsjZDtlGI3iEMHlYkgHcSNGeo3agwlLK3QL74gqTc8,790
 pyobo/utils/__init__.py,sha256=CANSY8vGq_6v8rWhWRIdnk-Wo5LA2R9Wjg1nqbWqLOw,17
 pyobo/utils/cache.py,sha256=fED68uExWkruXsrqYWe4iAZNZEN4MapEPYmrTBgA7U0,2996
@@ -163,9 +150,8 @@ pyobo/xrefdb/sources/intact.py,sha256=l2gqxm9OLPpQqhNqAIT_jk7AHx61itsUCz-5dowwMb
 pyobo/xrefdb/sources/ncit.py,sha256=QTo9BSGuurvy9M54viS6_v6dF36O8DbUGU6iiyqKsPI,3729
 pyobo/xrefdb/sources/pubchem.py,sha256=VK_yPCaoa-CKQNkq9iAF0Zh0D_zxqa92YG4OBbvnA9c,771
 pyobo/xrefdb/sources/wikidata.py,sha256=JSrl3YWMQA_gxw7IXJRnxWWetcAV82aM5-5J3IHFzoQ,3562
-pyobo-0.11.0.dist-info/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.11.0.dist-info/METADATA,sha256=ydZIch8oh6smWoaZ7SATHqOxIgqWrsRyeDVZaGTAW3U,25208
-pyobo-0.11.0.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-pyobo-0.11.0.dist-info/entry_points.txt,sha256=YfZYzQyXBZ5dGiy4GsOUCOKKlNRNDcmR4vnlpD50q08,41
-pyobo-0.11.0.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
-pyobo-0.11.0.dist-info/RECORD,,
+pyobo-0.11.2.dist-info/METADATA,sha256=OhM135rj_cy5fzwcUBqk0Hfm4ItzYdR7DjKVt5pX8Hg,24916
+pyobo-0.11.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pyobo-0.11.2.dist-info/entry_points.txt,sha256=YfZYzQyXBZ5dGiy4GsOUCOKKlNRNDcmR4vnlpD50q08,41
+pyobo-0.11.2.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.11.2.dist-info/RECORD,,

{pyobo-0.11.0.dist-info → pyobo-0.11.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyobo/apps/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""A collection of web apps built on PyOBO."""

pyobo/apps/cli.py

@@ -1,24 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO apps."""
-
-import click
-
-from .gilda.cli import main as gilda_main
-from .mapper.cli import main as mapper_main
-
-__all__ = [
-    "main",
-]
-
-
-@click.group(name="apps")
-def main():
-    """Apps."""
-
-
-main.add_command(gilda_main)
-main.add_command(mapper_main)
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Gilda Service."""

pyobo/apps/gilda/__main__.py

@@ -1,8 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Gilda Service."""
-
-from .cli import main
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/app.py

@@ -1,48 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Gilda Service."""
-
-from typing import Iterable, Union
-
-import flask
-from flask_bootstrap import Bootstrap
-from flask_wtf import FlaskForm
-from wtforms.fields import StringField, SubmitField
-from wtforms.validators import DataRequired
-
-from pyobo.gilda_utils import get_grounder
-
-
-class Form(FlaskForm):
-    """Form for submitting a query."""
-
-    text = StringField("Text", validators=[DataRequired()])
-    submit = SubmitField()
-
-    def make_response(self):
-        """Make a response with the text."""
-        return flask.redirect(flask.url_for("ground", text=self.text.data))
-
-
-def get_app(prefix: Union[str, Iterable[str]]):
-    """Make an app for grounding the text."""
-    grounder = get_grounder(prefix)
-
-    app = flask.Flask(__name__)
-    app.config["WTF_CSRF_ENABLED"] = False
-    Bootstrap(app)
-
-    @app.route("/", methods=["GET", "POST"])
-    def home():
-        """Ground the given text."""
-        form = Form()
-        if form.validate_on_submit():
-            return form.make_response()
-        return flask.render_template("home.html", form=form)
-
-    @app.route("/ground/<text>")
-    def ground(text: str):
-        """Ground the given text."""
-        return flask.jsonify([scored_match.to_json() for scored_match in grounder.ground(text)])
-
-    return app

pyobo/apps/gilda/cli.py

@@ -1,36 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Gilda Service."""
-
-import click
-from more_click import (
-    host_option,
-    port_option,
-    run_app,
-    verbose_option,
-    with_gunicorn_option,
-    workers_option,
-)
-
-__all__ = [
-    "main",
-]
-
-
-@click.command(name="gilda")
-@click.argument("prefix", nargs=-1)
-@verbose_option
-@host_option
-@workers_option
-@port_option
-@with_gunicorn_option
-def main(prefix: str, host: str, port: str, with_gunicorn: bool, workers: int):
-    """Run the Gilda service for this database."""
-    from .app import get_app
-
-    app = get_app(prefix)
-    run_app(app, host=host, port=port, with_gunicorn=with_gunicorn, workers=workers)
-
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/templates/base.html

@@ -1,33 +0,0 @@
-<!doctype html>
-<html lang="en">
-<head>
-    {% block head %}
-        <!-- Required meta tags -->
-        <meta charset="utf-8">
-        <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-
-        {% block styles %}
-            <!-- Bootstrap CSS -->
-            {{ bootstrap.load_css() }}
-        {% endblock %}
-
-        <script src="https://kit.fontawesome.com/4c86883252.js" crossorigin="anonymous"></script>
-
-        <title>{% block title %}{% endblock %}</title>
-    {% endblock %}
-</head>
-<body>
-<div class="container" style="margin-top: 50px; margin-bottom: 50px">
-    <div class="row">
-        <div class="card">
-            <!-- Your page content -->
-            {% block content %}{% endblock %}
-        </div>
-    </div>
-</div>
-{% block scripts %}
-    <!-- Optional JavaScript -->
-    {{ bootstrap.load_js() }}
-{% endblock %}
-</body>
-</html>

pyobo/apps/gilda/templates/home.html

@@ -1,11 +0,0 @@
-{% extends "base.html" %}
-
-{% block content %}
-    <h5 class="card-header">Gilda</h5>
-    <div class="card-body">
-        <p>
-            This is the Gilda grounding service.
-        </p>
-        {{ wtf.quick_form(form, form_type='horizontal') }}
-    </div>
-{% endblock %}

pyobo/apps/gilda/templates/matches.html

@@ -1,32 +0,0 @@
-{% extends "base.html" %}
-
-{% block content %}
-    <h5 class="card-header">Gilda</h5>
-    <div class="card-body">
-        <p>
-            Results for <code>{{ form.text.data }}</code>
-            {% if form.context.data %} with context
-                <i>{{ form.context.data }}</i>{% endif %}
-        </p>
-    </div>
-    <table class="table table-striped table-hover">
-        <thead>
-        <tr>
-            <th>Database</th>
-            <th>Identifier</th>
-            <th>Name</th>
-            <th>Score</th>
-        </tr>
-        </thead>
-        <tbody>
-        {% for match in matches %}
-            <tr>
-                <td>{{ match['term']['db'] }}</td>
-                <td>{{ match['term']['id'] }}</td>
-                <td>{{ match['term']['entry_name'] }}</td>
-                <td class="text-right">{{ match['score'] | round(4) }}</td>
-            </tr>
-        {% endfor %}
-        </tbody>
-    </table>
-{% endblock %}

pyobo/apps/mapper/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Mapping Service."""

pyobo/apps/mapper/__main__.py

@@ -1,11 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``
-"""
-
-from .cli import main
-
-if __name__ == "__main__":
-    main()

pyobo/apps/mapper/cli.py

@@ -1,37 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``.
-"""
-
-import click
-from more_click import (
-    host_option,
-    port_option,
-    run_app,
-    verbose_option,
-    with_gunicorn_option,
-)
-
-__all__ = [
-    "main",
-]
-
-
-@click.command(name="mapper")
-@click.option("-x", "--mappings-file")
-@port_option
-@host_option
-@with_gunicorn_option
-@verbose_option
-def main(mappings_file, host: str, port: str, with_gunicorn: bool):
-    """Run the mappings app."""
-    from .mapper import get_app
-
-    app = get_app(mappings_file)
-    run_app(app=app, host=host, port=port, with_gunicorn=with_gunicorn)
-
-
-if __name__ == "__main__":
-    main()

pyobo/apps/mapper/mapper.py

@@ -1,187 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``.
-"""
-
-import logging
-from functools import lru_cache
-from typing import Any, Dict, Iterable, List, Mapping, Optional, Union
-
-import bioregistry
-import pandas as pd
-from flasgger import Swagger
-from flask import (
-    Blueprint,
-    Flask,
-    abort,
-    current_app,
-    jsonify,
-    render_template,
-    url_for,
-)
-from flask_bootstrap import VERSION_BOOTSTRAP, Bootstrap
-from werkzeug.local import LocalProxy
-
-from pyobo import Canonicalizer
-from pyobo.constants import PROVENANCE, SOURCE_PREFIX, TARGET_PREFIX
-from pyobo.identifier_utils import normalize_curie
-from pyobo.resource_utils import ensure_inspector_javert_df
-
-__all__ = [
-    "get_app",
-]
-
-logger = logging.getLogger(__name__)
-
-summary_df = LocalProxy(lambda: current_app.config["summary"])
-canonicalizer: Canonicalizer = LocalProxy(lambda: current_app.config["canonicalizer"])
-
-
-@lru_cache()
-def _single_source_shortest_path(curie: str) -> Optional[Mapping[str, List[Mapping[str, str]]]]:
-    return canonicalizer.single_source_shortest_path(curie=curie)
-
-
-@lru_cache()
-def _all_shortest_paths(source_curie: str, target_curie: str) -> List[List[Mapping[str, str]]]:
-    return canonicalizer.all_shortest_paths(source_curie=source_curie, target_curie=target_curie)
-
-
-#: The blueprint that gets added to the app
-search_blueprint = Blueprint("search", __name__)
-
-
-@search_blueprint.route("/")
-def home():
-    """Show the home page."""
-    return render_template("mapper_home.html")
-
-
-@search_blueprint.route("/mappings/<curie>")
-def single_source_mappings(curie: str):
-    """Return all length xrefs from the given identifier."""
-    if curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(curie=curie),
-            message="could not find curie",
-        )
-    return jsonify(_single_source_shortest_path(curie))
-
-
-@search_blueprint.route("/mappings/<source_curie>/<target_curie>")
-def all_mappings(source_curie: str, target_curie: str):
-    """Return all shortest paths of xrefs between the two identifiers."""
-    if source_curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(source_curie=source_curie, target_curie=target_curie),
-            message="could not find source curie",
-        )
-    if target_curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(source_curie=source_curie, target_curie=target_curie),
-            message="could not find target curie",
-        )
-
-    return jsonify(_all_shortest_paths(source_curie, target_curie))
-
-
-@search_blueprint.route("/mappings/summarize")
-def summarize():
-    """Summarize the mappings."""
-    return summary_df.to_html(index=False)
-
-
-@search_blueprint.route("/mappings/summarize_by/<prefix>")
-def summarize_one(prefix: str):
-    """Summarize the mappings."""
-    norm_prefix = bioregistry.normalize_prefix(prefix)
-    if norm_prefix is None:
-        return abort(500, f"invalid prefix: {prefix}")
-    in_df = summary_df.loc[summary_df[TARGET_PREFIX] == norm_prefix, [SOURCE_PREFIX, "count"]]
-    out_df = summary_df.loc[summary_df[SOURCE_PREFIX] == norm_prefix, [TARGET_PREFIX, "count"]]
-    return f"""
-    <h1>Incoming Mappings to {norm_prefix}</h1>
-    {in_df.to_html(index=False)}
-    <h1>Outgoing Mappings from {norm_prefix}</h1>
-    {out_df.to_html(index=False)}
-    """
-
-
-@search_blueprint.route("/canonicalize/<curie>")
-def canonicalize(curie: str):
-    """Return the best CURIE."""
-    # TODO maybe normalize the curie first?
-    norm_prefix, norm_identifier = normalize_curie(curie)
-    if norm_prefix is None or norm_identifier is None:
-        return jsonify(
-            query=curie,
-            normalizable=False,
-        )
-
-    norm_curie = f"{norm_prefix}:{norm_identifier}"
-
-    rv: Dict[str, Any] = dict(query=curie)
-    if norm_curie != curie:
-        rv["norm_curie"] = norm_curie
-
-    if norm_curie not in canonicalizer.graph:
-        rv["found"] = False
-    else:
-        result_curie = canonicalizer.canonicalize(norm_curie)
-        rv.update(
-            found=True,
-            result=result_curie,
-            mappings=url_for(
-                f".{all_mappings.__name__}",
-                source_curie=norm_curie,
-                target_curie=result_curie,
-            ),
-        )
-
-    return jsonify(rv)
-
-
-def get_app(paths: Union[None, str, Iterable[str]] = None) -> Flask:
-    """Build the Flask app."""
-    app = Flask(__name__)
-    Swagger(app)
-
-    logger.info("using bootstrap_flask %s", VERSION_BOOTSTRAP)
-    Bootstrap(app)
-
-    if paths is None:
-        df = ensure_inspector_javert_df()
-    elif isinstance(paths, str):
-        df = pd.read_csv(paths, sep="\t", dtype=str)
-    else:
-        df = pd.concat(pd.read_csv(path, sep="\t", dtype=str) for path in paths)
-
-    app.config["summary"] = summarize_xref_df(df)
-    app.config["summary_provenances"] = summarize_xref_provenances_df(df)
-    # TODO allow for specification of priorities in the canonicalizer
-    app.config["canonicalizer"] = Canonicalizer.from_df(df)
-    app.register_blueprint(search_blueprint)
-    return app
-
-
-def summarize_xref_df(df: pd.DataFrame) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    return _summarize(df, [SOURCE_PREFIX, TARGET_PREFIX])
-
-
-def summarize_xref_provenances_df(df: pd.DataFrame) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    return _summarize(df, [SOURCE_PREFIX, TARGET_PREFIX, PROVENANCE])
-
-
-def _summarize(df: pd.DataFrame, columns) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    rv = df[columns].groupby(columns).size().reset_index()
-    rv.columns = [*columns, "count"]
-    rv.sort_values("count", inplace=True, ascending=False)
-    return rv

pyobo/apps/mapper/templates/base.html

@@ -1,35 +0,0 @@
-<!doctype html>
-<html lang="en">
-<head>
-    {% block head %}
-        <!-- Required meta tags -->
-        <meta charset="utf-8">
-        <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-
-        {% block styles %}
-            <!-- Bootstrap CSS -->
-            {{ bootstrap.load_css() }}
-        {% endblock %}
-
-        <script src="https://kit.fontawesome.com/4c86883252.js" crossorigin="anonymous"></script>
-
-        <title>{% block title %}{% endblock %}</title>
-    {% endblock %}
-</head>
-<body>
-<div class="container" style="margin-top: 25px; margin-bottom: 25px">
-    <div class="row justify-content-center">
-        <div class="col-md-8 col-lg-8">
-            <div class="card">
-                <!-- Your page content -->
-                {% block content %}{% endblock %}
-            </div>
-        </div>
-    </div>
-</div>
-{% block scripts %}
-    <!-- Optional JavaScript -->
-    {{ bootstrap.load_js() }}
-{% endblock %}
-</body>
-</html>