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openphacts / OPS_LinkedDataApi

A repository to host API configuration files, and code extensions
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First API requests fail with incomplete data #13

Open stain opened 9 years ago

stain commented 9 years ago

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:

Warning: curl_multi_getcontent(): 157 is not a valid cURL handle resource in /var/www/html/ops_ims.class.php on line 147

Warning: curl_close(): 157 is not a valid cURL handle resource in /var/www/html/ops_ims.class.php on line 149

Warning: curl_multi_remove_handle(): 157 is not a valid cURL handle resource in /var/www/html/ops_ims.class.php on line 150

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/ops_ims.class.php:147) in /var/www/html/lda-response.class.php on line 578

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/ops_ims.class.php:147) in /var/www/html/lda-response.class.php on line 669

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/ops_ims.class.php:147) in /var/www/html/lda-response.class.php on line 670

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/ops_ims.class.php:147) in /var/www/html/lda-response.class.php on line 671

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/ops_ims.class.php:147) in /var/www/html/lda-response.class.php on line 679

This is followed by the response to the API call, e.g.

<?xml version="1.0" encoding="utf-8"?>
<result format="linked-data-api" version="1.5" href="http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ9Y5Y9"><primaryTopic href="http://identifiers.org/uniprot/Q9Y5Y9"><exactMatch><item href="http://bio2rdf.org/drugbank:BE0004901"><targetForDrug href="http://bio2rdf.org/drugbank:DB00313"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Valproic Acid</genericName><drug_type><item xml:lang="en">approved [drugbank_resource:Approved]</item><item xml:lang="en">investigational [drugbank_resource:Investigational]</item></drug_type></targetForDrug><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><theoreticalPi><item datatype="float">5.42</item><item datatype="float">5.23</item><item datatype="float">8.04</item><item datatype="float">5.49</item><item datatype="float">6.35</item><item datatype="float">4.56</item><item datatype="float">4.72</item><item datatype="float">5.53</item><item datatype="float">6.18</item><item datatype="float">6.98</item><item datatype="float">7.45</item><item datatype="float">5.77</item><item datatype="float">4.35</item></theoreticalPi><cellularLocation><item datatype="string">Membrane; multi-pass membrane protein. It can be translocated to the extracellular membrane through</item><item datatype="string">Membrane; multi-pass membrane protein. Note=In neurite terminals</item><item datatype="string">Membrane</item><item datatype="string">Membrane; multi-pass membrane protein</item></cellularLocation></item><item href="http://bio2rdf.org/drugbank:BE0000177"><targetForDrug><item href="http://bio2rdf.org/drugbank:DB01173"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Orphenadrine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB01161"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Chloroprocaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00297"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Bupivacaine</genericName><drug_type><item xml:lang="en">approved [drugbank_resource:Approved]</item><item xml:lang="en">investigational [drugbank_resource:Investigational]</item></drug_type></item><item href="http://bio2rdf.org/drugbank:DB00961"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Mepivacaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00527"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Cinchocaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00892"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Oxybuprocaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB01002"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Levobupivacaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB06218"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Lacosamide</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00296"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Ropivacaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00281"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Lidocaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00721"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Procaine</genericName><drug_type><item xml:lang="en">approved [drugbank_resource:Approved]</item><item xml:lang="en">investigational [drugbank_resource:Investigational]</item></drug_type></item><item href="http://bio2rdf.org/drugbank:DB00807"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Proparacaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00645"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Dyclonine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00907"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Cocaine</genericName><drug_type><item xml:lang="en">illicit [drugbank_resource:Illicit]</item><item xml:lang="en">approved [drugbank_resource:Approved]</item></drug_type></item><item href="http://bio2rdf.org/drugbank:DB01086"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Benzocaine</genericName><drug_type xml:lang="en">approved [drugbank_resource:Approved]</drug_type></item><item href="http://bio2rdf.org/drugbank:DB00473"><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><genericName xml:lang="en">Hexylcaine</genericName><drug_type><item xml:lang="en">approved [drugbank_resource:Approved]</item><item xml:lang="en">withdrawn [drugbank_resource:Withdrawn]</item></drug_type></item></targetForDrug><inDataset href="http://www.openphacts.org/bio2rdf/drugbank"/><theoreticalPi datatype="float">5.77</theoreticalPi><cellularLocation datatype="string">Membrane; multi-pass membrane protein. It can be translocated to the extracellular membrane through</cellularLocation></item><item href="http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291"><prefLabel xml:lang="en">Sodium channel protein type 10 subunit alpha (Homo sapiens)</prefLabel><inDataset href="http://www.conceptwiki.org"/></item><item href="http://purl.uniprot.org/uniprot/Q9Y5Y9"><molecularWeight datatype="int">220626</molecularWeight><inDataset href="http://purl.uniprot.org"/><sequence>MEFPIGSLETNNFRRFTPESLVEIEKQIAAKQGTKKAREKHREQKDQEEKPRPQLDLKACNQLPKFYGELPAELIGEPLEDLDPFYSTHRTFMVLNKGRTISRFSATRALWLFSPFNLIRRTAIKVSVHSWFSLFITVTILVNCVCMTRTDLPEKIEYVFTVIYTFEALIKILARGFCLNEFTYLRDPWNWLDFSVITLAYVGTAIDLRGISGLRTFRVLRALKTVSVIPGLKVIVGALIHSVKKLADVTILTIFCLSVFALVGLQLFKGNLKNKCVKNDMAVNETTNYSSHRKPDIYINKRGTSDPLLCGNGSDSGHCPDGYICLKTSDNPDFNYTSFDSFAWAFLSLFRLMTQDSWERLYQQTLRTSGKIYMIFFVLVIFLGSFYLVNLILAVVTMAYEEQNQATTDEIEAKEKKFQEALEMLRKEQEVLAALGIDTTSLHSHNGSPLTSKNASERRHRIKPRVSEGSTEDNKSPRSDPYNQRRMSFLGLASGKRRASHGSVFHFRSPGRDISLPEGVTDDGVFPGDHESHRGSLLLGGGAGQQGPLPRSPLPQPSNPDSRHGEDEHQPPPTSELAPGAVDVSAFDAGQKKTFLSAEYLDEPFRAQRAMSVVSIITSVLEELEESEQKCPPCLTSLSQKYLIWDCCPMWVKLKTILFGLVTDPFAELTITLCIVVNTIFMAMEHHGMSPTFEAMLQIGNIVFTIFFTAEMVFKIIAFDPYYYFQKKWNIFDCIIVTVSLLELGVAKKGSLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTIILAIIVFVFALVGKQLLGENYRNNRKNISAPHEDWPRWHMHDFFHSFLIVFRILCGEWIENMWACMEVGQKSICLILFLTVMVLGNLVVLNLFIALLLNSFSADNLTAPEDDGEVNNLQVALARIQVFGHRTKQALCSFFSRSCPFPQPKAEPELVVKLPLSSSKAENHIAANTARGSSGGLQAPRGPRDEHSDFIANPTVWVSVPIAEGESDLDDLEDDGGEDAQSFQQEVIPKGQQEQLQQVERCGDHLTPRSPGTGTSSEDLAPSLGETWKDESVPQVPAEGVDDTSSSEGSTVDCLDPEEILRKIPELADDLEEPDDCFTEGCIRHCPCCKLDTTKSPWDVGWQVRKTCYRIVEHSWFESFIIFMILLSSGSLAFEDYYLDQKPTVKALLEYTDRVFTFIFVFEMLLKWVAYGFKKYFTNAWCWLDFLIVNISLISLTAKILEYSEVAPIKALRTLRALRPLRALSRFEGMRVVVDALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFWRCINYTDGEFSLVPLSIVNNKSDCKIQNSTGSFFWVNVKVNFDNVAMGYLALLQVATFKGWMDIMYAAVDSREVNMQPKWEDNVYMYLYFVIFIIFGGFFTLNLFVGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKFQGFVFDIVTRQAFDITIMVLICLNMITMMVETDDQSEEKTKILGKINQFFVAVFTGECVMKMFALRQYYFTNGWNVFDFIVVVLSIASLIFSAILKSLQSYFSPTLFRVIRLARIGRILRLIRAAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMSSFPHVRWEAGIDDMFNFQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGTRGDCGSPAVGIIFFTTYIIISFLIMVNMYIAVILENFNVATEESTEPLSEDDFDMFYETWEKFDPEATQFITFSALSDFADTLSGPLRIPKPNRNILIQMDLPLVPGDKIHCLDILFAFTKNVLGESGELDSLKANMEEKFMATNLSKSSYEPIATTLRWKQEDISATVIQKAYRSYVLHRSMALSNTPCVPRAEEEAASLPDEGFVAFTANENCVLPDKSETASATSFPPSYESVTRGLSDRVNMRTSSSIQNEDEATSMELIAPGP</sequence><organism href="http://purl.uniprot.org/taxonomy/9606"/><mass datatype="int">220626</mass><existence href="http://purl.uniprot.org/core/Evidence_at_Protein_Level_Existence"/><classifiedWith><item href="http://purl.uniprot.org/keywords/597"/><item href="http://purl.uniprot.org/keywords/621"/><item href="http://purl.uniprot.org/keywords/677"/><item href="http://purl.uniprot.org/go/0055117"/><item href="http://purl.uniprot.org/keywords/851"/><item href="http://purl.uniprot.org/go/0034765"/><item href="http://purl.uniprot.org/go/0002027"/><item href="http://purl.uniprot.org/go/0005248"/><item href="http://purl.uniprot.org/keywords/325"/><item href="http://purl.uniprot.org/go/0035725"/><item href="http://purl.uniprot.org/go/0007600"/><item href="http://purl.uniprot.org/go/0006814"/><item href="http://purl.uniprot.org/keywords/225"/><item href="http://purl.uniprot.org/go/0019233"/><item href="http://purl.uniprot.org/keywords/1133"/><item href="http://purl.uniprot.org/keywords/1185"/><item href="http://purl.uniprot.org/go/0086069"/><item href="http://purl.uniprot.org/go/0086010"/><item href="http://purl.uniprot.org/go/0086067"/><item href="http://purl.uniprot.org/go/0070062"/><item href="http://purl.uniprot.org/go/0001518"/><item href="http://purl.uniprot.org/keywords/894"/><item href="http://purl.uniprot.org/go/0060371"/><item href="http://purl.uniprot.org/go/0019228"/><item href="http://purl.uniprot.org/keywords/832"/><item href="http://purl.uniprot.org/go/0044299"/></classifiedWith><alternativeName><item>Sodium channel protein type X subunit alpha</item><item>Voltage-gated sodium channel subunit alpha Nav1.8</item><item>Peripheral nerve sodium channel 3</item></alternativeName><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.</Function_Annotation></item></exactMatch></primaryTopic><activeLens>Default</activeLens><linkPredicate href="http://www.w3.org/2004/02/skos/core#exactMatch"/><extendedMetadataVersion href="http://heater.cs.man.ac.uk:3002/target?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ9Y5Y9&amp;_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite"/><definition href="http://heater.cs.man.ac.uk:3002/api-config"/></result>

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.

stain commented 9 years ago

I now changed the docker image to silence those warnings:

root@3127b70f8fa2:/usr/local/etc/php/conf.d# cat ops-warnings.ini
display_errors=0
log_errors=1
html_errors=0
stain commented 9 years ago

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 commented 8 years ago

@antonisloizou do you know what this could be caused by..?

stain commented 8 years ago

I thinks this might be sensitive to the libcurl version.

I was able to work around this on the docker branch by disabling the handleAvailableResponses call - responses are still handled after the big loop.

I'll leave this open until this or a better fix has been added to develop.