DO lost!

[sergiocontrino]

now, when looking for a study 'more details' in the web interface, the attached digital objects (DO) appear to be empty/missing

something like this is displayed:

DATA OBJECTS

No type name !!
Display title: 
No display title???
Managing organisation: 
Year Published: Not provided
Access Type: 
No access type provided!
Access details: 
Further information at: 
Object Data Provenance

No provenance string

[michelescarlato]

@sergiocontrino Thanks for this assignment.

May I ask @Swarnalathaa Swarna if it is possible to have a screenshot and brief step-by-step instructions to help me visualize the error on MDR FuiPortal directly?

If you need a password to access the FuiPortal, please feel free to email it to me at michele.ecrin@gmail.com. I will take care of this issue as soon as I have this information.

(I don't know if @cudillal Leopold can help here, but if you can, feel free to send me the login instructions and how to visualize the error on the UI, please)

[sergiocontrino]

hi @michelescarlato , just go to https://crmdr.ecrin.org/ click on search and do whatever search by kw (e.g. diabetes) you will get a list of studies, just click on one.

or just go directly to a study, e.g. https://crmdr.ecrin.org/Study/4

at the bottom you will see the data object part.

[michelescarlato]

Got it, thank you. I am on it.

[michelescarlato]

Display title: "No display title???"

Display title: "No type name !!" , Year Published: Not provided, Access Type: No access type provided! Further information at:

Object Data Provenance

No provenance string

Are added by this portion of the code: Ref. https://github.com/ecrin-github/MDR_FuiPortal/blob/master/Client/StudyPage/ObjectDetails.razor#L283-L311

protected override void OnInitialized()
    {
        if (ob is not null)
        {
            type_name = ob.object_type?.name ?? "No type name !!";
            if (type_name.ToLower() == "journal article - unspecified")
            {
                type_name = "Journal Article";
            }
            display_title = ob.display_title ?? "No display title???";
            doi = ob.doi ?? "";
            year_pub = ob.publication_year.HasValue ? ((int)ob.publication_year).ToString() : "Not provided";

            managing_org = ob.managing_organisation?.name ?? "";
            if (!string.IsNullOrEmpty(ob.managing_organisation?.ror_id))
            {
                managing_org = "<a href=\"" + ob.managing_organisation?.ror_id + "\" target=\"_blank\">" + managing_org + "</a>";
            }

            access_type = ob.access_type?.name ?? "No access type provided!";
            url = ob.access_details?.url ?? "";
            access_description = ob.access_details?.description ?? "";
            version = ob.version ?? "";

            deidentification = ob.dataset_deident_level;
            consent = ob.dataset_consent;
            rec_keys = ob.dataset_record_keys;

            provenance = ob.provenance_string ?? "No provenance string";

So, the object that is trying to display is not null. And it is defined here: https://github.com/ecrin-github/MDR_FuiPortal/blob/master/Client/StudyPage/ObjectDetails.razor#L175

@code {
    [Parameter]
    public JSONFullObject? ob { get; set; }

Since I am still fairly new to the UI, I would suggest trying to fix the Tasks that didn't terminate with exit code 0 on the Windows server.

I will open issues directly on the proper repo, apply code fixes and open the Pull Request. I will then link everything here to show the modifications done.

[michelescarlato]

I fixed the MDR_Coding issues by adding a timeout and handling npgsqlException and common exceptions in the ExecuteSQL function in the ConditionHelper.cs (https://github.com/ecrin-github/MDR_Coder/blob/master/ContextHelpers/ConditionHelper.cs#L29).

This PR, https://github.com/ecrin-github/MDR_Coder/pull/4, fixed the issue created on the MDR_Coder https://github.com/ecrin-github/MDR_Coder/issues/3

Currently re-running the aggregator.

[michelescarlato]

@sergiocontrino ,

you may find useful this Python utils repo that I recently forked into ecrin-github:

https://github.com/ecrin-github/postgres-utils/tree/main/get_db_size

It provides an insight of the current DB status.

Database Name	Size	Number of Tables	Number of Relations	Total Rows
postgres	8125 kB	216	216	21697
anzctr	280 MB	251	251	865351
biolincc	31 MB	248	248	192713
cessda	10 MB	209	209	46150
chictr	751 MB	257	257	2340208
context	2804 MB	335	335	16802282
cris	114 MB	251	251	456447
ctg	15 GB	336	336	56728479
ctri	6862 MB	256	256	23391940
drks	347 MB	252	252	1033794
euctr	703 MB	261	261	2246345
isrctn	332 MB	258	258	926932
jprn	4851 MB	256	256	19462902
lebctr	26 MB	251	251	188148
mdr	33 GB	329	257	74515508
mon	540 MB	230	230	1303671
nntr	466 MB	251	251	1595235
pactr	63 MB	251	251	293217
pubmed	3632 MB	263	263	12460155
rebec	83 MB	251	251	315171
rpcec	33 MB	251	251	205836
rpuec	59 MB	251	251	284096
slctr	31 MB	251	251	196941
test	27 MB	412	412	45289
thctr	186 MB	251	251	658574
yoda	41 MB	248	248	349463
irct	406 MB	251	251	1162253
aggs	15 GB	251	251	99429827
iec	9935 MB	235	235	12473246
itmctr	69 MB	251	251	302541
bbmri	18 MB	216	216	170904
Total	94.94 GB	8080	8008	330465315

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