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Issue-232: Fix instrument type parsing for NextSeq2k and iSeq (#233)
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* Issue-232: Fix instrument type parsing for NextSeq2k and iSeq

* Update version history

* Fix travis file
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@ezralanglois
ezralanglois authored Nov 9, 2020
1 parent 9a86237 commit 45a2a17
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Showing 5 changed files with 173 additions and 7 deletions.
9 changes: 3 additions & 6 deletions .travis.yml
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## TODO: Create individual builds for each language

language: cpp
sudo: required

env:
global:
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env: SCRIPT="bash ./tools/package.sh $PWD $PWD/dist travis ON Debug Disable"
- os: linux
compiler: gcc
sudo: required
services:
- docker
env: DEPLOY_BUILD=true DEPLOY_DOCS=true DOCKER_IMAGE=ezralanglois/interop SCRIPT="docker run --rm -v $PWD:/io ezralanglois/interop sh /io/tools/package.sh /io /io/dist travis OFF Release None"
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before_deploy:
- export PATH=/opt/pyenv:/opt/pyenv/shims:$PATH
- if [ "$TRAVIS_OS_NAME != "osx ] ; then sudo env "PATH=$PATH" pyenv install 3.5.4 -s || true; fi
- if [ "$TRAVIS_OS_NAME != "osx ] ; then sudo env "PATH=$PATH" pyenv global 3.5.4; fi
- if [ "$TRAVIS_OS_NAME != "osx ] ; then sudo env "PATH=$PATH" pip install twine; fi
- if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pyenv install 3.5.4 -s || true; fi
- if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pyenv global 3.5.4; fi
- if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pip install twine; fi
- if [ "$TRAVIS_TAG" != "" ] && [ "$DEPLOY_BUILD" == "true" ] ; then twine upload --skip-existing $PWD/dist/*.whl; fi

deploy:
- provider: releases
skip_cleanup: true
api_key: $GITHUB_TOKEN
file_glob: true
file: $PWD/dist/*.*
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7 changes: 7 additions & 0 deletions docs/src/changes.md
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@@ -1,6 +1,13 @@
# Changes {#changes}


## v1.1.13

Date | Description
---------- | -----------
2020-08-25 | Issue-322: Update RunParameters.xml parsing to support iSeq and NextSeq2k


## v1.1.12

Date | Description
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1 change: 1 addition & 0 deletions interop/constants/enums.h
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Expand Up @@ -169,6 +169,7 @@
INTEROP_TUPLE1(MiniSeq), \
INTEROP_TUPLE1(NovaSeq), \
INTEROP_TUPLE1(iSeq), \
INTEROP_TUPLE1(NextSeq1k2k), \
INTEROP_TUPLE1(InstrumentCount), \
INTEROP_TUPLE1(UnknownInstrument)

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6 changes: 6 additions & 0 deletions src/interop/model/run/parameters.cpp
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Expand Up @@ -58,6 +58,7 @@ namespace illumina { namespace interop { namespace model { namespace run
for (xml_node_ptr p_node = p_root->first_node(); p_node; p_node = p_node->next_sibling())
{
set_data(p_node, "Application", application_name);
set_data(p_node, "ApplicationName", application_name);
}

xml_node_ptr p_setup = p_root->first_node("Setup");
Expand Down Expand Up @@ -86,6 +87,11 @@ namespace illumina { namespace interop { namespace model { namespace run
if (application_name.find(instrument_name) != std::string::npos)
{
m_instrument_type = static_cast<constants::instrument_type>(i);
if(constants::NextSeq == m_instrument_type &&
application_name.find("nextseq 1000/2000") != std::string::npos)
{
m_instrument_type = constants::NextSeq1k2k;
}
break;
}
}
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157 changes: 156 additions & 1 deletion src/tests/interop/run/parameters_test.cpp
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Expand Up @@ -350,7 +350,7 @@ TEST(RunParameters, ParseXML_HiSeq)
* @test Confirm NexSeq version of the XML format is properly
*
*/
TEST(RunParameters, ParseXML_NextSeq)
TEST(RunParameters, ParseXML_NextSeq500)
{
std::string xml_file = "<?xml version=\"1.0\"?>\n"
"<RunParameters xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
Expand Down Expand Up @@ -423,3 +423,158 @@ TEST(RunParameters, ParseXML_NextSeq)
test_helper_run_parameter_parse_xml(expected_param, xml_file);
}


/**https://basespace.illumina.com/run/195891710/iSeq-100-Illumina-RNA-Prep-with-Enrichment-and-RVOPv2-SARS-CoV-2-Synthetic-RNA-Control-/details
* @class illumina::interop::model::run::parameters
* @test Confirm NexSeq version of the XML format is properly
*
*/
TEST(RunParameters, ParseXML_iSeq)
{
std::string xml_file = "<?xml version=\"1.0\"?>\n"
"<RunParameters xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
" <InstrumentId>FS10000106</InstrumentId>\n"
" <RunId>20200624_FS10000106_66_BPA73105-2609</RunId>\n"
" <RunCounter>66</RunCounter>\n"
" <ApplicationName>iSeq Control Software</ApplicationName>\n"
" <ApplicationVersion>1.4.0.500</ApplicationVersion>\n"
" <ClientVersion>1.4.0.1589</ClientVersion>\n"
" <FirmwareVersion>1.3.0</FirmwareVersion>\n"
" <Pdb1FirmwareVersion>1.3.0</Pdb1FirmwareVersion>\n"
" <Pdb2FirmwareVersion>1.3.0</Pdb2FirmwareVersion>\n"
" <SibFpgaVersion>0x1300000a</SibFpgaVersion>\n"
" <SibBoardRevision>PilotvA</SibBoardRevision>\n"
" <Pdb1BoardRevision>4</Pdb1BoardRevision>\n"
" <Pdb2BoardRevision>3</Pdb2BoardRevision>\n"
" <IdbBoardRevision>1</IdbBoardRevision>\n"
" <RtaVersion>2.12.5.0</RtaVersion>\n"
" <ExperimentName>RNAEnrichment_RVOPv2_iSeq_2</ExperimentName>\n"
" <RecipeRelativeFilePath>Protocol\\2Read2Index.xml</RecipeRelativeFilePath>\n"
" <RecipeFolder>C:\\ProgramData\\Illumina\\iSeq Control Software\\Recipe</RecipeFolder>\n"
" <RecipeName>2Read2Index</RecipeName>\n"
" <RecipeVersion>P2BL_6.1.4</RecipeVersion>\n"
" <LibraryPoolId>X</LibraryPoolId>\n"
" <LocalRunManagerRunId xsi:nil=\"true\" />\n"
" <UcsRunId>16F6A4F1C86D7C50</UcsRunId>\n"
" <ReadType>PairedEnd</ReadType>\n"
" <RtaSaveThumbnailImages>true</RtaSaveThumbnailImages>\n"
" <PlannedCycles>\n"
" <Read1>76</Read1>\n"
" <Index1>10</Index1>\n"
" <Index2>10</Index2>\n"
" <Read2>76</Read2>\n"
" </PlannedCycles>\n"
" <CompletedCycles>\n"
" <Read1>76</Read1>\n"
" <Index1>10</Index1>\n"
" <Index2>10</Index2>\n"
" <Read2>76</Read2>\n"
" </CompletedCycles>\n"
" <SequencingMetrics>\n"
" <Q30Read1>95.26854</Q30Read1>\n"
" <Q30Read2>93.96231</Q30Read2>\n"
" <ClusterPf>75.57266</ClusterPf>\n"
" <Occupancy>88.21739</Occupancy>\n"
" <ProjectedYield>0.9760842 G</ProjectedYield>\n"
" </SequencingMetrics>\n"
" <RunFolderPath>D:\\Illumina\\iSeq Runs\\20200624_FS10000106_66_BPA73105-2609</RunFolderPath>\n"
" <OutputFolder>D:\\SequencingRuns\\20200624_FS10000106_66_BPA73105-2609</OutputFolder>\n"
" <SampleSheetPath>\\\\ussd-prd-isi04\\Holodeck\\Runs\\SampleSheets\\iSeq_RNAEnr_RVOPv2_2.csv</SampleSheetPath>\n"
" <FlowcellEEPROMTag>\n"
" <SerialNumber>BPA73105-2609</SerialNumber>\n"
" <PartNumber>20009555</PartNumber>\n"
" <LotNumber>20411871</LotNumber>\n"
" <ExpirationDate>2020-11-05T00:00:00</ExpirationDate>\n"
" </FlowcellEEPROMTag>\n"
" <ReagentKitRFIDTag>\n"
" <SerialNumber>FY0027716-FC6</SerialNumber>\n"
" <PartNumber>20025914</PartNumber>\n"
" <LotNumber>20405542</LotNumber>\n"
" <ExpirationDate>2020-11-27T00:00:00</ExpirationDate>\n"
" </ReagentKitRFIDTag>\n"
" <RunStartDate>2020-06-24T18:29:14-07:00</RunStartDate>\n"
" <RunEndDate>2020-06-25T07:12:29-07:00</RunEndDate>\n"
" <BaseSpaceParameters>\n"
" <EnvironmentName>use1-prod</EnvironmentName>\n"
" <DomainName />\n"
" <BaseSpaceRunId>195891710</BaseSpaceRunId>\n"
" <Mode>UserAndIlluminaHealth</Mode>\n"
" <WorkgroupName>Personal</WorkgroupName>\n"
" </BaseSpaceParameters>\n"
"</RunParameters>";


const run::parameters::uint_t Version = 0;
const run::parameters::instrument_type_t ApplicationName_and_SupportMultipleSurfacesInUI=constants::iSeq;
const run::parameters expected_param(Version,
ApplicationName_and_SupportMultipleSurfacesInUI);

test_helper_run_parameter_parse_xml(expected_param, xml_file);
}

/**6471489_213Bin1R0I
* @class illumina::interop::model::run::parameters
* @test Confirm NexSeq version of the XML format is properly
*
*/
TEST(RunParameters, ParseXML_NextSeq2k)
{
std::string xml_file = "<?xml version=\"1.0\"?>\n"
"<RunParameters xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">\n"
" <SampleSheetFilePath>/usr/local/illumina/runs/setup/2020-06-02_00-50-45_VH00120/SampleSheetImport/SampleSheet.csv</SampleSheetFilePath>\n"
" <PlannedCycles>\n"
" <Read1>101</Read1>\n"
" <Index1>10</Index1>\n"
" <Index2>10</Index2>\n"
" <Read2>101</Read2>\n"
" </PlannedCycles>\n"
" <CompletedCycles>\n"
" <Read1>101</Read1>\n"
" <Index1>10</Index1>\n"
" <Index2>10</Index2>\n"
" <Read2>101</Read2>\n"
" </CompletedCycles>\n"
" <InstrumentSerialNumber>VH00120</InstrumentSerialNumber>\n"
" <ApplicationName>NextSeq 1000/2000 Control Software</ApplicationName>\n"
" <ApplicationVersion>1.1.0.27334</ApplicationVersion>\n"
" <FlowCellSerialNumber>AAACWM2M5</FlowCellSerialNumber>\n"
" <FlowCellPartNumber>20034693</FlowCellPartNumber>\n"
" <FlowCellLotNumber>20444017-D</FlowCellLotNumber>\n"
" <FlowCellExpirationDate>2020-10-12</FlowCellExpirationDate>\n"
" <CartridgeSerialNumber>EC0003549-EC05</CartridgeSerialNumber>\n"
" <CartridgePartNumber>20042419</CartridgePartNumber>\n"
" <CartridgeLotNumber>20452046</CartridgeLotNumber>\n"
" <CartridgeExpirationDate>2020-11-18</CartridgeExpirationDate>\n"
" <ExperimentName>NFE_CEX_Exome_v2</ExperimentName>\n"
" <RecipeName>MO-Seq_NoPrePurge</RecipeName>\n"
" <RecipeVersion>1.6</RecipeVersion>\n"
" <RtaVersion>3.6.14</RtaVersion>\n"
" <RunStartTime>2020-06-02T01:46:25.8840085Z</RunStartTime>\n"
" <RunEndTime>2020-06-03T00:58:01.1511824Z</RunEndTime>\n"
" <RunCounter>33</RunCounter>\n"
" <CimVersion>[email protected]</CimVersion>\n"
" <ChmVersion>[email protected]</ChmVersion>\n"
" <ImbVersion>[email protected]</ImbVersion>\n"
" <CibFpgaVersion>0x3200000a</CibFpgaVersion>\n"
" <CopyServiceRunId>16E4948F3B43122F</CopyServiceRunId>\n"
" <CopyServiceVersion>2.0.8.695</CopyServiceVersion>\n"
" <BaseSpaceRunId>195525362</BaseSpaceRunId>\n"
" <PlannedRunId>srn.7efcd556e3fc4f5eb1ce1bc123834ec4</PlannedRunId>\n"
" <BsshMode>RunMonitoringAndStorage</BsshMode>\n"
" <SecondaryAnalysisPlatformVersion>3.5.8</SecondaryAnalysisPlatformVersion>\n"
" <SecondaryAnalysisWorkflow>Cloud_DragenEnrichment</SecondaryAnalysisWorkflow>\n"
" <RunSetupMode>CloudOrchestrated</RunSetupMode>\n"
" <SecondaryAnalysisMode>Cloud</SecondaryAnalysisMode>\n"
" <OutputFolder>/mnt/Vega/SequencingRuns/200602_VH00120_33_AAACWM2M5</OutputFolder>\n"
" <PurgeReagentCartridge>false</PurgeReagentCartridge>\n"
"</RunParameters>";


const run::parameters::uint_t Version = 0;
const run::parameters::instrument_type_t ApplicationName_and_SupportMultipleSurfacesInUI=constants::NextSeq1k2k;
const run::parameters expected_param(Version,
ApplicationName_and_SupportMultipleSurfacesInUI);

test_helper_run_parameter_parse_xml(expected_param, xml_file);
}

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