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Bioconductor / AnnotationHub

Client for the Bioconductor AnnotationHub web resource
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Accessing a resource with a snapshotDate() before it was available gives a cryptic error #11

Closed mtmorgan closed 4 years ago

mtmorgan commented 4 years ago

In the current 'devel' version of AnnotationHub, record "AH75194" exists

> hub = AnnotationHub()
snapshotDate(): 2019-10-25
> hub[["AH75194"]]
downloading 0 resources
loading from cache
                                                 AH75194 : 81940
"/Users/ma38727/Library/Caches/AnnotationHub/d90d285daf8e_81940"

but trying to access it from a snapshotDate() before it was available gives a cryptic message

> snapshotDate(hub) <- "2019-05-02"
> hub[["AH75194"]]
Error: Public

Also, I'm not sure why we're told downloading 0 resources or the internal information AH75194 : 81940, which makes it hard to know, from the return object, what the original, user-facing, AH id was (i.e., the name should just be AH75194).

lshep commented 4 years ago

I thought I got rid of the id information so I'll check on that implementation.

We do display the download information but maybe if it doesn't download anything we should change the message.

I don't think I ever tested trying to download a resource that is added after a snapshot date. I'll look into this. Thanks for reporting it.

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From: Martin Morgan notifications@github.com Sent: Sunday, October 27, 2019 6:44:07 PM To: Bioconductor/AnnotationHub AnnotationHub@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Bioconductor/AnnotationHub] Accessing an existing resource with a snapshotDate() before it was available gives a cryptic error (#11)

In the current 'devel' version of AnnotationHub, record "AH75194" exists

hub = AnnotationHub() snapshotDate(): 2019-10-25 hub[["AH75194"]] downloading 0 resources loading from cache AH75194 : 81940 "/Users/ma38727/Library/Caches/AnnotationHub/d90d285daf8e_81940"

but trying to access it from a snapshotDate() before it was available gives a cryptic message

snapshotDate(hub) <- "2019-05-02" hub[["AH75194"]] Error: Public

Also, I'm not sure why we're told downloading 0 resources or the internal information AH75194 : 81940, which makes it hard to know, from the return object, what the original, user-facing, AH id was (i.e., the name should just be AH75194).

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lshep commented 4 years ago

@mtmorgan - so a few different options for the snapshot date access issue - Currently when a resource isn't available it only prints out Error: along with the status message (assuming there are a few other statuses that define removal or deprecation of a resource) If the resource has been removed removed then there is a message that its been removed from the database

> hub = AnnotationHub()
> hub[["AH1"]]
Error: record not found in database
> snapshotDate(hub) <- "2019-05-02"
> hub[["AH75194"]]
Error: Public

Currently recordStatus is used in the ERROR message - I could do a few different things - I could print out additional information about the resources by using getInfoOnIds or internally .IdsInfo so that date added / date remove information is also printed with the status instead of using recordStatus

> getInfoOnIds(hub, "AH75194")
         ah_id fetch_id               title rdataclass status biocversion
291151 AH75194    81940 PANTHER.db database     SQLite Public        3.10
       rdatadateadded rdatadateremoved file_size
291151     2019-10-22             <NA> 501149696

Or I can check that if the status is public compared to the rdatadateadded is after the snapshot date to have a specific error message for this case - something like resource addeds after currently snapshot date and include the two dates .....

Or some combination of both?

lshep commented 4 years ago

The other two issues have been addressed - now only labelled with AH_id and if 0 resources are downloaded it skips this message.