First API requests fail with incomplete data #13
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I now changed the docker image to silence those warnings: |
stain
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Jul 23, 2015
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Silencing the warning does not hide the problem. Now the first request does not include IMS-based information. So if I restart memcached, http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json says just: {
"format": "linked-data-api",
"version": "1.5",
"result": {
"_about": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json",
"definition": "http://heater.cs.man.ac.uk:3002/api-config",
"extendedMetadataVersion": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite",
"linkPredicate": "http://www.w3.org/2004/02/skos/core#exactMatch",
"activeLens": "Default",
"primaryTopic": {
"_about": "http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
"exactMatch": [
{
"_about": "http://rdf.ebi.ac.uk/resource/chembl/target/CHEMBL5451",
"hasTargetComponent": {
"_about": "http://rdf.ebi.ac.uk/resource/chembl/targetcomponent/CHEMBL_TC_3744",
"description": "Sodium channel protein type 10 subunit alpha",
"inDataset": "http://www.ebi.ac.uk/chembl"
},
"inDataset": "http://www.ebi.ac.uk/chembl",
"type": "http://rdf.ebi.ac.uk/terms/chembl#SingleProtein",
"label": "Sodium channel protein type X alpha subunit"
},
{
"_about": "http://purl.uniprot.org/uniprot/Q9Y5Y9",
"Function_Annotation": "Tetrodotoxin-resistant channel that mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which sodium ions may pass in accordance with their electrochemical gradient. Plays a role in neuropathic pain mechanisms.",
"alternativeName": [
"Voltage-gated sodium channel subunit alpha Nav1.8",
"Sodium channel protein type X subunit alpha",
"Peripheral nerve sodium channel 3"
],
"classifiedWith": [
"http://purl.uniprot.org/go/0086069",
"http://purl.uniprot.org/keywords/597",
"http://purl.uniprot.org/keywords/225",
"http://purl.uniprot.org/keywords/621",
"http://purl.uniprot.org/keywords/677",
"http://purl.uniprot.org/go/0086067",
"http://purl.uniprot.org/go/0060371",
"http://purl.uniprot.org/go/0034765",
"http://purl.uniprot.org/go/0035725",
"http://purl.uniprot.org/go/0055117",
"http://purl.uniprot.org/keywords/325",
"http://purl.uniprot.org/go/0006814",
"http://purl.uniprot.org/keywords/894",
"http://purl.uniprot.org/go/0086010",
"http://purl.uniprot.org/go/0005248",
"http://purl.uniprot.org/go/0001518",
"http://purl.uniprot.org/go/0019233",
"http://purl.uniprot.org/go/0070062",
"http://purl.uniprot.org/go/0019228",
"http://purl.uniprot.org/keywords/851",
"http://purl.uniprot.org/go/0002027",
"http://purl.uniprot.org/keywords/832",
"http://purl.uniprot.org/go/0044299",
"http://purl.uniprot.org/keywords/1133",
"http://purl.uniprot.org/keywords/1185",
"http://purl.uniprot.org/go/0007600"
],
"existence": "http://purl.uniprot.org/core/Evidence_at_Protein_Level_Existence",
"mass": 220626,
"organism": "http://purl.uniprot.org/taxonomy/9606",
"sequence": "MEFPIGSLETNNFRRFTPESLVEIEKQIAAKQGTKKAREKHREQKDQEEKPRPQLDLKACNQLPKFYGELPAELIGEPLEDLDPFYSTHRTFMVLNKGRTISRFSATRALWLFSPFNLIRRTAIKVSVHSWFSLFITVTILVNCVCMTRTDLPEKIEYVFTVIYTFEALIKILARGFCLNEFTYLRDPWNWLDFSVITLAYVGTAIDLRGISGLRTFRVLRALKTVSVIPGLKVIVGALIHSVKKLADVTILTIFCLSVFALVGLQLFKGNLKNKCVKNDMAVNETTNYSSHRKPDIYINKRGTSDPLLCGNGSDSGHCPDGYICLKTSDNPDFNYTSFDSFAWAFLSLFRLMTQDSWERLYQQTLRTSGKIYMIFFVLVIFLGSFYLVNLILAVVTMAYEEQNQATTDEIEAKEKKFQEALEMLRKEQEVLAALGIDTTSLHSHNGSPLTSKNASERRHRIKPRVSEGSTEDNKSPRSDPYNQRRMSFLGLASGKRRASHGSVFHFRSPGRDISLPEGVTDDGVFPGDHESHRGSLLLGGGAGQQGPLPRSPLPQPSNPDSRHGEDEHQPPPTSELAPGAVDVSAFDAGQKKTFLSAEYLDEPFRAQRAMSVVSIITSVLEELEESEQKCPPCLTSLSQKYLIWDCCPMWVKLKTILFGLVTDPFAELTITLCIVVNTIFMAMEHHGMSPTFEAMLQIGNIVFTIFFTAEMVFKIIAFDPYYYFQKKWNIFDCIIVTVSLLELGVAKKGSLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTIILAIIVFVFALVGKQLLGENYRNNRKNISAPHEDWPRWHMHDFFHSFLIVFRILCGEWIENMWACMEVGQKSICLILFLTVMVLGNLVVLNLFIALLLNSFSADNLTAPEDDGEVNNLQVALARIQVFGHRTKQALCSFFSRSCPFPQPKAEPELVVKLPLSSSKAENHIAANTARGSSGGLQAPRGPRDEHSDFIANPTVWVSVPIAEGESDLDDLEDDGGEDAQSFQQEVIPKGQQEQLQQVERCGDHLTPRSPGTGTSSEDLAPSLGETWKDESVPQVPAEGVDDTSSSEGSTVDCLDPEEILRKIPELADDLEEPDDCFTEGCIRHCPCCKLDTTKSPWDVGWQVRKTCYRIVEHSWFESFIIFMILLSSGSLAFEDYYLDQKPTVKALLEYTDRVFTFIFVFEMLLKWVAYGFKKYFTNAWCWLDFLIVNISLISLTAKILEYSEVAPIKALRTLRALRPLRALSRFEGMRVVVDALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFWRCINYTDGEFSLVPLSIVNNKSDCKIQNSTGSFFWVNVKVNFDNVAMGYLALLQVATFKGWMDIMYAAVDSREVNMQPKWEDNVYMYLYFVIFIIFGGFFTLNLFVGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKFQGFVFDIVTRQAFDITIMVLICLNMITMMVETDDQSEEKTKILGKINQFFVAVFTGECVMKMFALRQYYFTNGWNVFDFIVVVLSIASLIFSAILKSLQSYFSPTLFRVIRLARIGRILRLIRAAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMSSFPHVRWEAGIDDMFNFQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGTRGDCGSPAVGIIFFTTYIIISFLIMVNMYIAVILENFNVATEESTEPLSEDDFDMFYETWEKFDPEATQFITFSALSDFADTLSGPLRIPKPNRNILIQMDLPLVPGDKIHCLDILFAFTKNVLGESGELDSLKANMEEKFMATNLSKSSYEPIATTLRWKQEDISATVIQKAYRSYVLHRSMALSNTPCVPRAEEEAASLPDEGFVAFTANENCVLPDKSETASATSFPPSYESVTRGLSDRVNMRTSSSIQNEDEATSMELIAPGP",
"inDataset": "http://purl.uniprot.org",
"molecularWeight": 220626
}
],
"isPrimaryTopicOf": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json"
}
}
}While a Ctrl-R gives the expected, IMS-complete results: {
"format": "linked-data-api",
"version": "1.5",
"result": {
"_about": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json",
"definition": "http://heater.cs.man.ac.uk:3002/api-config",
"extendedMetadataVersion": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite",
"linkPredicate": "http://www.w3.org/2004/02/skos/core#exactMatch",
"activeLens": "Default",
"primaryTopic": {
"_about": "http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
"inDataset": "http://www.conceptwiki.org",
"exactMatch": [
"http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
{
"_about": "http://bio2rdf.org/drugbank:BE0000177",
"cellularLocation": "Membrane; multi-pass membrane protein. It can be translocated to the extracellular membrane through",
"theoreticalPi": 5.77,
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
"targetForDrug": [
{
"_about": "http://bio2rdf.org/drugbank:DB01173",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Orphenadrine",
"genericName": "Orphenadrine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB01161",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Chloroprocaine",
"genericName": "Chloroprocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00297",
"drug_type_en": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"drug_type": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"genericName_en": "Bupivacaine",
"genericName": "Bupivacaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00961",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Mepivacaine",
"genericName": "Mepivacaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00527",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Cinchocaine",
"genericName": "Cinchocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00892",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Oxybuprocaine",
"genericName": "Oxybuprocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB01002",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Levobupivacaine",
"genericName": "Levobupivacaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB06218",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Lacosamide",
"genericName": "Lacosamide",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00296",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Ropivacaine",
"genericName": "Ropivacaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00281",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Lidocaine",
"genericName": "Lidocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00807",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Proparacaine",
"genericName": "Proparacaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00721",
"drug_type_en": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"drug_type": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"genericName_en": "Procaine",
"genericName": "Procaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00645",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Dyclonine",
"genericName": "Dyclonine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00907",
"drug_type_en": [
"illicit [drugbank_resource:Illicit]",
"approved [drugbank_resource:Approved]"
],
"drug_type": [
"illicit [drugbank_resource:Illicit]",
"approved [drugbank_resource:Approved]"
],
"genericName_en": "Cocaine",
"genericName": "Cocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB01086",
"drug_type_en": "approved [drugbank_resource:Approved]",
"drug_type": "approved [drugbank_resource:Approved]",
"genericName_en": "Benzocaine",
"genericName": "Benzocaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
},
{
"_about": "http://bio2rdf.org/drugbank:DB00473",
"drug_type_en": [
"approved [drugbank_resource:Approved]",
"withdrawn [drugbank_resource:Withdrawn]"
],
"drug_type": [
"approved [drugbank_resource:Approved]",
"withdrawn [drugbank_resource:Withdrawn]"
],
"genericName_en": "Hexylcaine",
"genericName": "Hexylcaine",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
}
]
},
{
"_about": "http://bio2rdf.org/drugbank:BE0004901",
"cellularLocation": [
"Membrane; multi-pass membrane protein. It can be translocated to the extracellular membrane through",
"Membrane; multi-pass membrane protein. Note=In neurite terminals",
"Membrane",
"Membrane; multi-pass membrane protein"
],
"theoreticalPi": [
5.42,
5.23,
8.04,
5.49,
6.35,
4.56,
4.72,
5.53,
6.18,
6.98,
7.45,
5.77,
4.35
],
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank",
"targetForDrug": {
"_about": "http://bio2rdf.org/drugbank:DB00313",
"drug_type_en": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"drug_type": [
"approved [drugbank_resource:Approved]",
"investigational [drugbank_resource:Investigational]"
],
"genericName_en": "Valproic Acid",
"genericName": "Valproic Acid",
"inDataset": "http://www.openphacts.org/bio2rdf/drugbank"
}
},
{
"_about": "http://rdf.ebi.ac.uk/resource/chembl/target/CHEMBL5451",
"hasTargetComponent": {
"_about": "http://rdf.ebi.ac.uk/resource/chembl/targetcomponent/CHEMBL_TC_3744",
"description": "Sodium channel protein type 10 subunit alpha",
"inDataset": "http://www.ebi.ac.uk/chembl"
},
"inDataset": "http://www.ebi.ac.uk/chembl",
"type": "http://rdf.ebi.ac.uk/terms/chembl#SingleProtein",
"label": "Sodium channel protein type X alpha subunit"
}
],
"prefLabel_en": "Sodium channel protein type 10 subunit alpha (Homo sapiens)",
"prefLabel": "Sodium channel protein type 10 subunit alpha (Homo sapiens)",
"isPrimaryTopicOf": "http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291&_format=json"
}
}
}Is this something going wrong with multiple IMS requests at once? Still now, if I do Ctrl-Shift-R a couple of times, sometimes Uniprot is included, other times drugbank might be missing. |
stain
changed the title
|
@antonisloizou do you know what this could be caused by..? |
stain
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that referenced
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Aug 17, 2015
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I thinks this might be sensitive to the I was able to work around this on the I'll leave this open until this or a better fix has been added to develop. |
stain
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Nov 21, 2016
from docker branch removed puelia README
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In the Docker installation of OPS_LinkedDataApi (see http://heater.cs.man.ac.uk:3002) , running of the docker branch which is equivalent to the 1.5.0 "branch" always fails on the first request for any identifier with PHP warnings.
For instance, for http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ9Y5Y9 I first time got:
This is followed by the response to the API call, e.g.
The errors cause the HTTP Content-Type to be wrong and obviously breaks parsing.
Later calls hit memcached, and do not give any errors.
If a resource is 404, I always get the error. So you can check this at:
http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fexample.org%2Fnotfound
Compare with with ops2, which do not fail:
http://ops2.few.vu.nl/target?uri=http%3A%2F%2Fexample.org%2Fnotfound
I can configure PHP to not print any warnings, but still this error indicates something is going wrong in the multi-batch call to IMS.
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