From 16bad2532611e57c96adf48c2b141e355f7806e4 Mon Sep 17 00:00:00 2001
From: Anweshi Anavadya <anweshianavadya@gmail.com>
Date: Fri, 23 Apr 2021 21:39:40 -0400
Subject: [PATCH] added further testing to ncbi
---
tests/test_ncbi.py | 127 ++++++++++++++++++++++++++++++++++++++++++---
1 file changed, 119 insertions(+), 8 deletions(-)
diff --git a/tests/test_ncbi.py b/tests/test_ncbi.py
index 7bb2737..23d0206 100644
--- a/tests/test_ncbi.py
+++ b/tests/test_ncbi.py
@@ -36,7 +36,7 @@ def test_safe_request():
def test_get_eutil_records():
eutil = "efetch"
_id = "9887103"
- expected_response = [
+ expected = [
{
"<?xm": ['version="1.0" ?>'],
"<!DO": [
@@ -2033,18 +2033,129 @@ def test_get_eutil_records():
},
{"</Pu": ["edArticleSet>"]},
]
- actual_response = _get_eutil_records(eutil, _id)
- assert isinstance(actual_response, types.GeneratorType)
- assert list(actual_response) == expected_response
+ actual = _get_eutil_records(eutil, _id)
+ assert isinstance(actual, types.GeneratorType)
+ assert list(actual) == expected
def test_parse_medline():
text = "\nPMID- 9887103\nOWN - NLM\nSTAT- MEDLINE\nDCOM- 19990225\nLR - 20190516\nIS - 0890-9369 (Print)\nIS - 0890-9369 (Linking)\nVI - 13\nIP - 1\nDP - 1999 Jan 1\nTI - The Drosophila activin receptor baboon signals through dSmad2 and controls cell\n proliferation but not patterning during larval development.\nPG - 98-111\nAB - The TGF-beta superfamily of growth and differentiation factors, including\n TGF-beta, Activins and bone morphogenetic proteins (BMPs) play critical roles in \n regulating the development of many organisms. These factors signal through a\n heteromeric complex of type I and II serine/threonine kinase receptors that\n phosphorylate members of the Smad family of transcription factors, thereby\n promoting their nuclear localization. Although components of TGF-beta/Activin\n signaling pathways are well defined in vertebrates, no such pathway has been\n clearly defined in invertebrates. In this study we describe the role of Baboon\n (Babo), a type I Activin receptor previously called Atr-I, in Drosophila\n development and characterize aspects of the Babo intracellular\n signal-transduction pathway. Genetic analysis of babo loss-of-function mutants\n and ectopic activation studies indicate that Babo signaling plays a role in\n regulating cell proliferation. In mammalian cells, activated Babo specifically\n stimulates Smad2-dependent pathways to induce TGF-beta/Activin-responsive\n promoters but not BMP-responsive elements. Furthermore, we identify a new\n Drosophila Smad, termed dSmad2, that is most closely related to vertebrate Smads \n 2 and 3. Activated Babo associates with dSmad2 but not Mad, phosphorylates the\n carboxy-terminal SSXS motif and induces heteromeric complex formation with Medea,\n the Drosophila Smad4 homolog. Our results define a novel Drosophila\n Activin/TGF-beta pathway that is analogous to its vertebrate counterpart and show\n that this pathway functions to promote cellular growth with minimal effects on\n patterning.\nFAU - Brummel, T\nAU - Brummel T\nAD - Department of Molecular Biology and Biochemistry, University of California,\n Irvine, California 92697, USA.\nFAU - Abdollah, S\nAU - Abdollah S\nFAU - Haerry, T E\nAU - Haerry TE\nFAU - Shimell, M J\nAU - Shimell MJ\nFAU - Merriam, J\nAU - Merriam J\nFAU - Raftery, L\nAU - Raftery L\nFAU - Wrana, J L\nAU - Wrana JL\nFAU - O'Connor, M B\nAU - O'Connor MB\nLA - eng\nSI - GENBANK/AF101386\nGR - GM47462/GM/NIGMS NIH HHS/United States\nPT - Journal Article\nPT - Research Support, Non-U.S. Gov't\nPT - Research Support, U.S. Gov't, P.H.S.\nPL - United States\nTA - Genes Dev\nJT - Genes & development\nJID - 8711660\nRN - 0 (Bone Morphogenetic Proteins)\nRN - 0 (DNA-Binding Proteins)\nRN - 0 (Drosophila Proteins)\nRN - 0 (RNA, Messenger)\nRN - 0 (Receptors, Growth Factor)\nRN - 0 (Smad2 Protein)\nRN - 0 (Trans-Activators)\nRN - EC 2.7.11.30 (Activin Receptors)\nRN - EC 2.7.11.30 (Activin Receptors, Type I)\nRN - EC 2.7.11.30 (Babo protein, Drosophila)\nSB - IM\nMH - Activin Receptors\nMH - Activin Receptors, Type I\nMH - Amino Acid Sequence\nMH - Animals\nMH - Bone Morphogenetic Proteins/genetics\nMH - Cell Division\nMH - Cloning, Molecular\nMH - DNA-Binding Proteins/chemistry/*genetics\nMH - Drosophila/*embryology\nMH - Drosophila Proteins\nMH - Gene Expression Regulation, Developmental\nMH - In Situ Hybridization\nMH - Larva/genetics/*growth & development\nMH - Molecular Sequence Data\nMH - Phosphorylation\nMH - RNA, Messenger/genetics\nMH - Receptors, Growth Factor/*genetics/metabolism\nMH - Sequence Alignment\nMH - Sequence Analysis, DNA\nMH - Signal Transduction/*physiology\nMH - Smad2 Protein\nMH - Trans-Activators/chemistry/*genetics\nMH - Wings, Animal/growth & development\nPMC - PMC316373\nEDAT- 1999/01/14 00:00\nMHDA- 1999/01/14 00:01\nCRDT- 1999/01/14 00:00\nPHST- 1999/01/14 00:00 [pubmed]\nPHST- 1999/01/14 00:01 [medline]\nPHST- 1999/01/14 00:00 [entrez]\nAID - 10.1101/gad.13.1.98 [doi]\nPST - ppublish\nSO - Genes Dev. 1999 Jan 1;13(1):98-111. doi: 10.1101/gad.13.1.98.\n"
- # checking if generator is returned, need to check integrity of the returned value
- assert isinstance(_parse_medline(text), types.GeneratorType)
+ expected = [
+ {
+ "PMID": "9887103",
+ "OWN": "NLM",
+ "STAT": "MEDLINE",
+ "DCOM": "19990225",
+ "LR": "20190516",
+ "IS": "0890-9369 (Print) 0890-9369 (Linking)",
+ "VI": "13",
+ "IP": "1",
+ "DP": "1999 Jan 1",
+ "TI": "The Drosophila activin receptor baboon signals through dSmad2 and controls cell proliferation but not patterning during larval development.",
+ "PG": "98-111",
+ "AB": "The TGF-beta superfamily of growth and differentiation factors, including TGF-beta, Activins and bone morphogenetic proteins (BMPs) play critical roles in regulating the development of many organisms. These factors signal through a heteromeric complex of type I and II serine/threonine kinase receptors that phosphorylate members of the Smad family of transcription factors, thereby promoting their nuclear localization. Although components of TGF-beta/Activin signaling pathways are well defined in vertebrates, no such pathway has been clearly defined in invertebrates. In this study we describe the role of Baboon (Babo), a type I Activin receptor previously called Atr-I, in Drosophila development and characterize aspects of the Babo intracellular signal-transduction pathway. Genetic analysis of babo loss-of-function mutants and ectopic activation studies indicate that Babo signaling plays a role in regulating cell proliferation. In mammalian cells, activated Babo specifically stimulates Smad2-dependent pathways to induce TGF-beta/Activin-responsive promoters but not BMP-responsive elements. Furthermore, we identify a new Drosophila Smad, termed dSmad2, that is most closely related to vertebrate Smads 2 and 3. Activated Babo associates with dSmad2 but not Mad, phosphorylates the carboxy-terminal SSXS motif and induces heteromeric complex formation with Medea, the Drosophila Smad4 homolog. Our results define a novel Drosophila Activin/TGF-beta pathway that is analogous to its vertebrate counterpart and show that this pathway functions to promote cellular growth with minimal effects on patterning.",
+ "FAU": [
+ "Brummel, T",
+ "Abdollah, S",
+ "Haerry, T E",
+ "Shimell, M J",
+ "Merriam, J",
+ "Raftery, L",
+ "Wrana, J L",
+ "O'Connor, M B",
+ ],
+ "AU": [
+ "Brummel T",
+ "Abdollah S",
+ "Haerry TE",
+ "Shimell MJ",
+ "Merriam J",
+ "Raftery L",
+ "Wrana JL",
+ "O'Connor MB",
+ ],
+ "AD": [
+ "Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA."
+ ],
+ "LA": ["eng"],
+ "SI": ["GENBANK/AF101386"],
+ "GR": ["GM47462/GM/NIGMS NIH HHS/United States"],
+ "PT": [
+ "Journal Article",
+ "Research Support, Non-U.S. Gov't",
+ "Research Support, U.S. Gov't, P.H.S.",
+ ],
+ "PL": "United States",
+ "TA": "Genes Dev",
+ "JT": "Genes & development",
+ "JID": "8711660",
+ "RN": [
+ "0 (Bone Morphogenetic Proteins)",
+ "0 (DNA-Binding Proteins)",
+ "0 (Drosophila Proteins)",
+ "0 (RNA, Messenger)",
+ "0 (Receptors, Growth Factor)",
+ "0 (Smad2 Protein)",
+ "0 (Trans-Activators)",
+ "EC 2.7.11.30 (Activin Receptors)",
+ "EC 2.7.11.30 (Activin Receptors, Type I)",
+ "EC 2.7.11.30 (Babo protein, Drosophila)",
+ ],
+ "SB": "IM",
+ "MH": [
+ "Activin Receptors",
+ "Activin Receptors, Type I",
+ "Amino Acid Sequence",
+ "Animals",
+ "Bone Morphogenetic Proteins/genetics",
+ "Cell Division",
+ "Cloning, Molecular",
+ "DNA-Binding Proteins/chemistry/*genetics",
+ "Drosophila/*embryology",
+ "Drosophila Proteins",
+ "Gene Expression Regulation, Developmental",
+ "In Situ Hybridization",
+ "Larva/genetics/*growth & development",
+ "Molecular Sequence Data",
+ "Phosphorylation",
+ "RNA, Messenger/genetics",
+ "Receptors, Growth Factor/*genetics/metabolism",
+ "Sequence Alignment",
+ "Sequence Analysis, DNA",
+ "Signal Transduction/*physiology",
+ "Smad2 Protein",
+ "Trans-Activators/chemistry/*genetics",
+ "Wings, Animal/growth & development",
+ ],
+ "PMC": "PMC316373",
+ "EDAT": "1999/01/14 00:00",
+ "MHDA": "1999/01/14 00:01",
+ "CRDT": ["1999/01/14 00:00"],
+ "PHST": [
+ "1999/01/14 00:00 [pubmed]",
+ "1999/01/14 00:01 [medline]",
+ "1999/01/14 00:00 [entrez]",
+ ],
+ "AID": ["10.1101/gad.13.1.98 [doi]"],
+ "PST": "ppublish",
+ "SO": "Genes Dev. 1999 Jan 1;13(1):98-111. doi: 10.1101/gad.13.1.98.",
+ }
+ ]
+ actual = _parse_medline(text)
+ assert isinstance(actual, types.GeneratorType)
+ assert list(actual) == expected
def test_uids_to_docs():
uids = ["9887103"]
- # checking if generator is returned, need to check integrity of the returned value
- assert isinstance(uids_to_docs(uids), types.GeneratorType)
+ expected = [
+ [
+ {
+ "uid": "9887103",
+ "text": "The Drosophila activin receptor baboon signals through dSmad2 and controls cell proliferation but not patterning during larval development. The TGF-beta superfamily of growth and differentiation factors, including TGF-beta, Activins and bone morphogenetic proteins (BMPs) play critical roles in regulating the development of many organisms. These factors signal through a heteromeric complex of type I and II serine/threonine kinase receptors that phosphorylate members of the Smad family of transcription factors, thereby promoting their nuclear localization. Although components of TGF-beta/Activin signaling pathways are well defined in vertebrates, no such pathway has been clearly defined in invertebrates. In this study we describe the role of Baboon (Babo), a type I Activin receptor previously called Atr-I, in Drosophila development and characterize aspects of the Babo intracellular signal-transduction pathway. Genetic analysis of babo loss-of-function mutants and ectopic activation studies indicate that Babo signaling plays a role in regulating cell proliferation. In mammalian cells, activated Babo specifically stimulates Smad2-dependent pathways to induce TGF-beta/Activin-responsive promoters but not BMP-responsive elements. Furthermore, we identify a new Drosophila Smad, termed dSmad2, that is most closely related to vertebrate Smads 2 and 3. Activated Babo associates with dSmad2 but not Mad, phosphorylates the carboxy-terminal SSXS motif and induces heteromeric complex formation with Medea, the Drosophila Smad4 homolog. Our results define a novel Drosophila Activin/TGF-beta pathway that is analogous to its vertebrate counterpart and show that this pathway functions to promote cellular growth with minimal effects on patterning.",
+ }
+ ]
+ ]
+ actual = uids_to_docs(uids)
+ assert isinstance(actual, types.GeneratorType)
+ assert list(actual) == expected