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added further testing to ncbi
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@Anwesh1
Anwesh1 committed Apr 24, 2021
1 parent 1cc907d commit 16bad25
Showing 1 changed file with 119 additions and 8 deletions.
127 changes: 119 additions & 8 deletions tests/test_ncbi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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

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