Supplyment Information page not working on bulk with E-PROT experiments
Closed this issue · 6 comments
According to @irisdianauy report.
Many E-PROT experiments have nothing under the Supplementary Information tab. Doesn’t seem like by design, because when you do click on the Supplementary Information tab of one such experiment, all the other tabs disappear (as opposed to just having an empty tab). Examples are E-PROT-13, E-PROT-106, E-PROT-23.
I found the following problem with a quick look at the content's payload: the Unicode content is invalid.
Here is one:
Please see \u003ca href\u003d\"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/pipeline.pdf\"\u003eWorkflow\u003c/a\u003e and \u003ca href\u003d\"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/methods.pdf\"\u003eMethods\u003c/a\u003e for more information.
This is going to become:
Please see <a href=%"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/pipeline.pdf%">Workflow</a> and <a href=%"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/methods.pdf%">Methods</a> for more information.
As this value is inside a "" the " in the resolved text is going to crash the UI.
Here is the content from E-PROT-13.
{
content: {
"experimentAccession": "E-PROT-13",
"experimentType": "PROTEOMICS_BASELINE",
"accessKey": "",
"species": "mus musculus",
"disclaimer": "",
"tabs": [
{
"type": "heatmap",
"name": "Results",
"props": {
"groups": [
{
"name": "ORGANISM_PART",
"primary": false,
"selected": "all",
"groupings": [
[
"brain",
[
"g1"
]
],
[
"brown adipose tissue",
[
"g2"
]
],
[
"heart",
[
"g3"
]
],
[
"kidney",
[
"g4"
]
],
[
"lung",
[
"g5"
]
],
[
"liver",
[
"g6"
]
],
[
"pancreas",
[
"g7"
]
],
[
"spleen",
[
"g8"
]
],
[
"testis",
[
"g9"
]
]
]
},
{
"name": "ORGANISM",
"primary": false,
"selected": "all",
"groupings": [
[
"Mus musculus",
[
"g1",
"g2",
"g3",
"g4",
"g5",
"g6",
"g7",
"g8",
"g9"
]
]
]
},
{
"name": "STRAIN",
"primary": false,
"selected": "all",
"groupings": [
[
"Swiss Webster",
[
"g1",
"g2",
"g3",
"g4",
"g5",
"g6",
"g7",
"g8",
"g9"
]
]
]
},
{
"name": "SEX",
"primary": false,
"selected": "all",
"groupings": [
[
"male",
[
"g1",
"g2",
"g3",
"g4",
"g5",
"g6",
"g7",
"g8",
"g9"
]
]
]
},
{
"name": "AGE",
"primary": false,
"selected": "all",
"groupings": [
[
"3 week",
[
"g1",
"g2",
"g3",
"g4",
"g5",
"g6",
"g7",
"g8",
"g9"
]
]
]
}
],
"genesDistributedByCutoffUrl": "json/experiments/E-PROT-13/genedistribution?experimentType\u003dPROTEOMICS_BASELINE",
"availableDataUnits": [
]
}
},
{
"type": "experiment-design",
"name": "Experiment Design",
"props": {
"table": {
"headers": [
{
"name": "",
"values": [
"Run"
]
},
{
"name": "Sample Characteristics",
"values": [
"organism",
"strain",
"sex",
"age",
"organism part"
]
},
{
"name": "Experimental Variables",
"values": [
"organism part"
]
}
],
"data": [
{
"properties": {
"analysed": true
},
"values": [
[
"Brain_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"brain"
],
[
"brain"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"BrownFat_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"brown adipose tissue"
],
[
"brown adipose tissue"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Heart_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"heart"
],
[
"heart"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Kidney_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"kidney"
],
[
"kidney"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Liver_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"liver"
],
[
"liver"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Lung_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"lung"
],
[
"lung"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Pancreas_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"pancreas"
],
[
"pancreas"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Spleen_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"spleen"
],
[
"spleen"
]
]
},
{
"properties": {
"analysed": true
},
"values": [
[
"Testis_Huttlin_NA"
],
[
"Mus musculus",
"Swiss Webster",
"male",
"3 week",
"testis"
],
[
"testis"
]
]
}
]
},
"downloadUrl": "experiments-content/E-PROT-13/resources/experiment-design"
}
},
{
"type": "multipart",
"name": "Supplementary Information",
"props": {
"sections": [
{
"type": "static-table",
"name": "Analysis Methods",
"props": {
"data": [
[
"Pipeline ",
"Please see \u003ca href\u003d\"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/pipeline.pdf\"\u003eWorkflow\u003c/a\u003e and \u003ca href\u003d\"ftp://ftp.pride.ebi.ac.uk/pride/data/expression-atlas/docs/methods.pdf\"\u003eMethods\u003c/a\u003e for more information."
],
[
"Protein to Gene Mapping",
" Ensembl 89/Genome assembly: GRCm38.p5 (Genome Reference Consortium Mouse Reference 38)"
]
]
}
},
{
"type": "resources",
"name": "Resources",
"props": {
"url": "json/experiments/E-PROT-13/resources/SUPPLEMENTARY_INFORMATION"
}
}
]
}
},
{
"type": "resources",
"name": "Downloads",
"props": {
"url": "json/experiments/E-PROT-13/resources/DATA"
}
}
]
}
}
Not all E-PROT experiments have the same issue, for instance E-PROT-1. It just happens on some particular experiments.
According to the content value for the experiments loading well. They all have the same format, i.e. "" the ", I think the it is not the problem that crashes the UI. Take E-PROT-1 as an example:
{"type":"multipart","name":"Supplementary Information","props":{"sections":[{"type":"static-table","name":"Analysis Methods","props":{"data":[["Pipeline ","Please see \u003ca href\u003d\"https://www.ebi.ac.uk/gxa/experiments/E-PROT-1/analysis-methods/HumanDataAnalysisFigure.pdf\"\u003eWorkflow\u003c/a\u003e and \u003ca href\u003d\"https://www.ebi.ac.uk/gxa/experiments/E-PROT-1/analysis-methods/HumanDataAnalysisMethods.pdf\"\u003eMethods\u003c/a\u003e for more information."],["Protein to Gene Mapping"," Ensembl 76/GENCODE 20 (GRCh38)"]]}},
I think the endpoint has some issues which returns 500. Unfortunatelly, we don't have any experiment in local having the same issue, so I will try to remotely debug on this instead.
Another interesting example for experiment E-PROT-106 which is not working the content data is as below, where no parsing format.
{
"type": "multipart",
"name": "Supplementary Information",
"props": {
"sections": [
{
"type": "static-table",
"name": "Analysis Methods",
"props": {
"data": [
[
"Samples used in this study",
"Data included in this study is based on the re-analysis of raw mass spectrometry data originally submitted to the PRIDE database."
],
[
"Data processing protocol",
"Raw mass spectrometry data was manually curated in order to map the raw files to the samples (see “Experimental Design” tab) and then processed using MaxQuant (version 2.1.0.0) using a label-free approach. The human UniProt reference Proteome One Protein sequence per Gene Set (September 2020) was used as the search database together with the contaminants.fasta database included in MaxQuant. Additionally, match between runs was set on, protein and peptide FDR values were set to 1% and iBAQ (intensity-based absolute quantification) values were calculated. Only protein groups with two or more peptide evidences were considered."
],
[
"Post-processing analysis",
"Protein groups with contaminants, reverse decoys and with no mappings or mapping to more than one Ensembl gene IDs were removed. Protein abundance values were normalized per sample by “parts per billion”."
],
[
"Protein to Gene Mapping",
"The R package ‘mygene’ (version 1.20.0) was used to map UniProt accessions to Ensembl gene ID, gene symbol. The data resource used was Ensembl 99/Genome assembly: GRCh38 (Genome Reference Consortium Human Reference 38)."
]
]
}
},
{
"type": "resources",
"name": "Resources",
"props": {
"url": "json/experiments/E-PROT-106/resources/SUPPLEMENTARY_INFORMATION"
}
}
]
}
},
@lingyun1010 I am sorry, but I don't think this is done yet.
A tiny bit is missing. We need a commit to bulk that point to the latest core (where you actually fixed this issue), create a tiny Pr and merge that to develop. Then it is done. 😉
Thanks
@lingyun1010 I am sorry, but I don't think this is done yet. A tiny bit is missing. We need a commit to
bulkthat point to the latestcore(where you actually fixed this issue), create a tiny Pr and merge that todevelop. Then it is done. 😉 Thanks
Yes. That's right! I will make it.