Create a tube manifest and print just the first barcode when selecting option Only First Label failed: Unable to find option "Standard sample" within #<Capybara::Node::Element tag="select" path="/html/body/div/section/section/div/form/fieldset[1]/ol/li[2]/select">

Create a tube manifest and print all the barcodes failed: Unable to find option "Standard sample" within #<Capybara::Node::Element tag="select" path="/html/body/div/section/section/div/form/fieldset[1]/ol/li[2]/select">

Upload a manifest that has mismatched welle failed: expected to find text "Sample cannot be moved between wells" in "Cucumber\nStudies Projects Admin UAT Pipelines Batches Labwhere Reception Lab View Lab search Report Fails\nBarcode Project Study Sample Labware AssetGroup Request Supplier Submission All\nJohn Doe Edit profile\nLogout\nYour sample manifest couldn't be uploaded.\nSample Manifests New and upload\nSample manifest can't be blank\n[\"Row 10 - Cannot find sample manifest for Sanger ID: sample_1\"]\n[\"Row 11 - Cannot find sample manifest for Sanger ID: sample_2\"]\n[\"Row 12 - Cannot find sample manifest for Sanger ID: sample_3\"]\n[\"Row 13 - Cannot find sample manifest for Sanger ID: sample_4\"]\n[\"Row 14 - Cannot find sample manifest for Sanger ID: sample_5\"]\n[\"Row 15 - Cannot find sample manifest for Sanger ID: sample_6\"]\n[\"Row 17 - Cannot find sample manifest for Sanger ID: sample_8\"]\n[\"Row 18 - Cannot find sample manifest for Sanger ID: sample_9\"]\n[\"Row 19 - Cannot find sample manifest for Sanger ID: sample_10\"]\n[\"Row 20 - Cannot find sample manifest for Sanger ID: sample_11\"]\n[\"Row 21 - Cannot find sample manifest for Sanger ID: sample_12\"]\nSample manifest Does not exist. Double check that Sanger sample ids have not been changed.\nThis sample manifest upload screen handles tubes with tag sequences, and plates or tubes with foreign barcodes.\n Override previously uploaded samples\nName Contains Study Supplier Created Updated Created by Manifest Upload Errors State Manifest_4 1 plate Test study Test supplier name 2025-02-12 2025-02-12 john Blank manifest Upload manifest No manifest uploaded\nHelp\nSampleDB Home Create manifest for plates Create manifest for library plates Create manifest for tubes Create manifest for library tubes Create manifest for tube racks Create manifest for multiplexed libraries View all manifests Create supplier View all suppliers Create Study Create Project\nWellcome Sanger Institute A tool from LIMS and Informatics\nSequencescape 0.0.0 [cucumber] HEAD@2588720 LOCAL fv-az1118-492"

Upload a manifest that has mismatched plates failed: expected to find text "Sanger plate barcode has been modified, but it is not a valid foreign barcode format" in "Cucumber\nStudies Projects Admin UAT Pipelines Batches Labwhere Reception Lab View Lab search Report Fails\nBarcode Project Study Sample Labware AssetGroup Request Supplier Submission All\nJohn Doe Edit profile\nLogout\nYour sample manifest couldn't be uploaded.\nSample Manifests New and upload\nSample manifest can't be blank\n[\"Row 10 - Cannot find sample manifest for Sanger ID: sample_1\"]\n[\"Row 11 - Cannot find sample manifest for Sanger ID: sample_2\"]\n[\"Row 12 - Cannot find sample manifest for Sanger ID: sample_3\"]\n[\"Row 13 - Cannot find sample manifest for Sanger ID: sample_4\"]\n[\"Row 14 - Cannot find sample manifest for Sanger ID: sample_5\"]\n[\"Row 15 - Cannot find sample manifest for Sanger ID: sample_6\"]\n[\"Row 17 - Cannot find sample manifest for Sanger ID: sample_8\"]\n[\"Row 18 - Cannot find sample manifest for Sanger ID: sample_9\"]\n[\"Row 19 - Cannot find sample manifest for Sanger ID: sample_10\"]\n[\"Row 20 - Cannot find sample manifest for Sanger ID: sample_11\"]\n[\"Row 21 - Cannot find sample manifest for Sanger ID: sample_12\"]\nSample manifest Does not exist. Double check that Sanger sample ids have not been changed.\nThis sample manifest upload screen handles tubes with tag sequences, and plates or tubes with foreign barcodes.\n Override previously uploaded samples\nName Contains Study Supplier Created Updated Created by Manifest Upload Errors State Manifest_5 1 plate Test study Test supplier name 2025-02-12 2025-02-12 john Blank manifest Upload manifest No manifest uploaded\nHelp\nSampleDB Home Create manifest for plates Create manifest for library plates Create manifest for tubes Create manifest for library tubes Create manifest for tube racks Create manifest for multiplexed libraries View all manifests Create supplier View all suppliers Create Study Create Project\nWellcome Sanger Institute A tool from LIMS and Informatics\nSequencescape 0.0.0 [cucumber] HEAD@2588720 LOCAL fv-az1118-492"

Upload a csv manifest with empty samples failed: Tables were not identical:

Upload a manifest with invalid cell line failed: expected to find text "DNA source is not included in the list" in "Cucumber\nStudies Projects Admin UAT Pipelines Batches Labwhere Reception Lab View Lab search Report Fails\nBarcode Project Study Sample Labware AssetGroup Request Supplier Submission All\nJohn Doe Edit profile\nLogout\nYour sample manifest couldn't be uploaded.\nSample Manifests New and upload\nSample manifest can't be blank\n[\"Row 10 - Cannot find sample manifest for Sanger ID: sample_1\"]\n[\"Row 11 - Cannot find sample manifest for Sanger ID: sample_2\"]\n[\"Row 12 - Cannot find sample manifest for Sanger ID: sample_3\"]\n[\"Row 13 - Cannot find sample manifest for Sanger ID: sample_4\"]\n[\"Row 14 - Cannot find sample manifest for Sanger ID: sample_5\"]\n[\"Row 15 - Cannot find sample manifest for Sanger ID: sample_6\"]\n[\"Row 16 - Cannot find sample manifest for Sanger ID: sample_7\"]\nSample manifest Does not exist. Double check that Sanger sample ids have not been changed.\nThis sample manifest upload screen handles tubes with tag sequences, and plates or tubes with foreign barcodes.\n Override previously uploaded samples\nName Contains Study Supplier Created Updated Created by Manifest Upload Errors State Manifest_7 1 plate Test study Test supplier name 2025-02-12 2025-02-12 john Blank manifest Upload manifest No manifest uploaded\nHelp\nSampleDB Home Create manifest for plates Create manifest for library plates Create manifest for tubes Create manifest for library tubes Create manifest for tube racks Create manifest for multiplexed libraries View all manifests Create supplier View all suppliers Create Study Create Project\nWellcome Sanger Institute A tool from LIMS and Informatics\nSequencescape 0.0.0 [cucumber] HEAD@2588720 LOCAL fv-az1118-492"

Upload a manifest with invalid cell line failed: Tables were not identical:

Upload some empty samples, reupload with samples but without override set failed: Tables were not identical:

Upload some empty samples, reupload with samples but with override set failed: Tables were not identical:

Updating of sample accession numbers failed: Tables were not identical:

The job was canceled because "_2_0" failed.

Previewing the assignment of the bait libraries failed: Cannot find search "Find assets by barcode"

Assigning bait libraries failed: Cannot find search "Find assets by barcode"

Dealing with the MX library tube at the end of the pipeline failed: Cannot find plate purpose "ILB_STD_INPUT"

A submission should error if you set an incorrect request option on construction failed: Could not find pulldown_isc

A submission should not error if you create it without required options, but does if you build it failed: Could not find pulldown_isc

A submission for a pulldown pipeline that uses bait libraries failed: Could not find pulldown_isc

Attempting to set the fragment sizes to anything other than the default values should use the specified values failed: Could not find pulldown_isc

Can I see and add a reference genome when creating a study failed: expected to find text "Your study has been created" in "Cucumber\nStudies\nProjects\nAdmin\nUAT\nPipelines\nBatches\nLabwhere Reception\nLab View\nLab search\nReport Fails\nBarcode\nProject\nStudy\nSample\nLabware\nAssetGroup\nRequest\nSupplier\nSubmission\nAll\nProblems creating your new study\nStudy Create\nTo register a new study, complete the form below. Required fields are marked with .\nYour study has not been created.\nStudy metadata study type can't be blank\nStudy metadata data release study type can't be blank\nStudy metadata program can't be blank\nStudy name\nStudy owner name\nSelect an owner...\nSelect an owner...\nProperties\nFaculty Sponsor\nJack Sponsor\nJack Sponsor\nProgram\nNumber of gigabases per sample (minimum 0.15)\nPrelim ID\nPrelim ID\nReference genome\nDanio_rerio (zv9)\nHomo_sapiens (GRCh37_53)\nMus_musculus (NCBIm37)\nSchistosoma_mansoni (20100601)\nStaphylococcus_aureus (NCTC_8325)\nDanio_rerio (zv9)\nStudy Type\nTitleENA requirement\nTitle of the study as would be used in a publication.\nStudy descriptionENA requirement\nparp parp\nAbstractENA requirement\nBriefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication. For managed access studies, please bear in mind it’s this text in the Abstract section that will be publicly visible on the EGA website.\nStudy Visibility\nStudy VisibilityENA requirement\nHold\nPublic\nMake this ENA project public immediately.\nEBI Library StrategyENA requirement\nRNA-Seq\nChIP-Seq\nWGS\nWXS\nAMPLICON\nCLONE\nPOOLCLONE\nCLONEEND\nBisulfite-Seq\nMNase-Seq\nDNase-Hypersensitivity\nFAIRE-seq\nSELEX\nRIP-Seq\nChIA-PET\nOTHER\nRNA-Seq\nEBI Library SourceENA requirement\nGENOMIC\nTRANSCRIPTOMIC\nMETAGENOMIC\nMETATRANSCRIPTOMIC\nSYNTHETIC\nVIRAL RNA\nOTHER\nGENOMIC\nEBI Library SelectionENA requirement\nRANDOM\nPCR\nRANDOM PCR\nRT-PCR\nHMPR\nMF\nCF-S\nCF-M\nCF-T\nMDA\nMSLL\ncDNA\nChIP\nMNase\nDNAse\nHybrid Selection\nReduced Representation\nRestriction Digest\n5-methylcytidine antibody\nMBD2 protein methyl-CpG binding domain\nRANDOM\nDo any of the samples in this study contain human DNA?\nDo any of the samples in this study contain human DNA?\nYes\nNo\nIf they do, you will be required to upload the relevant documents. This does not apply to samples that are going to have the Human DNA removed prior to analysis.\nDoes this study contain samples that are contaminated with human DNA which must be removed prior to analysis?\nDoes this study contain samples that are contaminated with human DNA which must be removed prior to analysis?\nYes\nNo\nUsually only applicable to pathogen research when human DNA will not be sequenced and therefore does not require ethical approval.\nAre all the samples to be used in this study commercially available, unlinked anonymised cell-lines?\nAre all the samples to be used in this study commercially available, unlinked anonymised cell-lines?\nYes\nNo\nAre all the samples to be used in this study commercially available, anonymised cell-lines or DNA/RNA from commercially available, anonymised cell-lines?\nDoes this study require the removal of X chromosome and autosome sequence?\nDoes this study require the removal of X chromosome and autosome sequence?\nYes\nNo\nApplicable for studies where only mtDNA and Y-chromosomal data will be submitted to EGA.\nDoes this study require y chromosome data to be separated from x and autosomal data before archival?\nApplicable for studies where Y-chromosome data will not be submitted to the EGA, or will be submitted separately from autosomal sequence.\nENA Project IDENA (see help)\nThe required PROJECT_ID accession is generated by the Genome Project database at NCBI and will be valid also at the other archival institutions. Enter 0 if the project id is unknown or not assigned.\nENA Study Accession Numbersee help\nData Release accession Number. Will be filled automatically during submission process. Provide ONLY if the project has already been submitted to EBI.\nStudy

When the data release is standard failed: Couldn't find Study with [WHERE `studies`.`name` = ?]