New annotation R package (cellbaseR)

melsiddieg commented 7 years ago

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melsiddieg commented 7 years ago

Hi hpages

I have just pushed an update to my package, and the I received the following build report error

Checking for bioc-devel mailing list subscription... Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached

I know this is not a real error as much as it is a short timeout issue with the curl package caused by slow DNS lookup of the test machines

Best regards

On Wed, Oct 12, 2016 at 1:41 PM, hpages notifications@github.com wrote:

Hi Mohammed,

I've been trying to access the cellbase webservice several times in the last 24 hours but I always get an HTTP error 404:

library(cellbaseR) cb <- CellBaseR() Error in open.connection(con, "rb") : HTTP error 404.

Is the service down? Any ETA for when the service will be available again?

Thanks, H.

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

54e1d9a version bump

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Received a valid push; starting a build. Commits are:

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

0dcdcbe added getSnpByGene function 9dc90c1 getSnpByGene man page 1d657bd version bump

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hpages commented 7 years ago

Hi Mohammed,

Glad to hear that the CellBase service is up and running again. Thanks for drastically reducing the dependencies of cellbaseR (from 80 to only 32 packages). That makes a big difference when I load the package on my laptop: now library(cellbaseR) takes < 3 sec. instead of > 20 sec. :-)

About issue 2): you went to the extreme with man page titles that are now exactly the same as the name of the function. For example, the title for AnnotateVcf man page is AnnotateVcf. That is not exactly what I was trying to convey when I wrote that "Title should fit in 1 line, be as short as possible, and not be made of several sentences". A typical title for AnnotateVcf would be more like "Annotate a VCF file". The reason good titles are important is that they show up in the browser when people use the HTML browser interface to navigate the documentation of your package. See by yourself by starting the HTML interface with help.start(), then click on Packages, then on cellbaseR. That displays the list of all the man pages in your package in a 2-column table (aliases in the 1st column, man pages titles in the 2nd column). In your case the 2nd column is almost identical to the 1st column so is not very informative. Having titles that are a little bit more informative would help the user find what s/he's looking for.

About issue 3): AnnotateVcf still doesn't have examples.

About issue 7): I still think that the CellBaseR() constructor function should check the validity of the supplied species. Otherwise, when later on a get* function (e.g. getGene()) gives me back a 0-row data.frame, I have no way to tell if that's because I specified invalid genes or if I created a CellBaseR object pointing to a species that is not supported. And since I don't seem to have a way to know what species are supported, I'm a little bit in the dark as to what species I can supply when I call CellBaseR().

Issue 8) was not addressed.

Other issues:

11) It looks like many of your get* functions ignore the object and filters arguments:

> getConservationByRegion
function (region, object = NULL, filters = NULL) 
{
    cb <- CellBaseR()
    res <- getRegion(object = cb, ids = region, resource = "conservation")
    res
}
<environment: namespace:cellbaseR>
> getGeneInfo
function (gene, object = NULL, filters = NULL) 
{
    cb <- CellBaseR()
    res <- getGene(object = cb, ids = gene, resource = "info")
    res
}
<environment: namespace:cellbaseR>
> getVariantAnnotation
function (variant, object = NULL, filters = NULL) 
{
    cb <- CellBaseR()
    res <- getVariant(object = cb, ids = variant, resource = "annotation")
    res
}
<environment: namespace:cellbaseR>

12) They would also need to present a more consistent interface:

> args(getGene)
function (object, ids, resource, filters = NULL, ...) 
NULL

13) Also why make some of them ordinary functions (e.g. getGeneInfo) and others generic functions with a method for CellBaseR objects (e.g. getGene).

14) You have a stale man page for Annovcf (that function doesn't seem to exist anymore).

Thanks, H.

melsiddieg commented 7 years ago

Hi Hpages

issue 7 we are still working on this issue 8 Here I catually took my guidance from this. stackoverflow recommendation http://stackoverflow.com/questions/28370249/correct-way-to-specifiy-optional-arguments-in-r-functions | Sometimes you want to add a non-trivial default value, which might take several lines of code to compute. Instead of inserting that code in the function | definition, you could use missing() to conditionally compute it if needed. However, this makes it hard to know which arguments are required and which are optional | without carefully reading the documentation. Instead, I usually set the default value to NULL and use is.null() to check if the argument was supplied.

issue 11 That was a work in progress when saw them, now they do not ignore the object and filters

issue 13 I Think there is some misunderstanding here: All the core library of cellbaseR, ie, all the S4 methods that used to start with cb has been renamed to getGene, getProtein, getRegion, etc. We added many convenience functions that has the By in their name like getSnpByGene, getClinicalByRegion, etc. All these functions are merely wrapper functions around the S4 methods as you can see, with fewer arguments and more direct approach. however like the biomaRt package we don't plan to wrap everything and we still prefer people use the library methods itself as this is more flexible, and maintianable and is a more honest represntationo of the CellBase Api as it is nicely docuemnted here http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/ Better we provide very useful tips and up-to-date documentation for using the Cellbase methods through the cbHelp function, for example you can see all the avaiable resurces for a particular sucategory- gene, region, variant, etc- through | cbHelp(object=cb, subactegory="gene")

So you can get various gene data, for example, using the same method rather than using six different wrapper functions.

documentation is still incomplete, but we will push more updates in that regard

Best regards

On Fri, Oct 14, 2016 at 5:41 AM, hpages notifications@github.com wrote:

Hi Mohammed,

Glad to hear that the CellBase service is up and running again. Thanks for drastically reducing the dependencies of cellbaseR (from 80 to only 32 packages). That makes a big difference when I load the package on my laptop: now library(cellbaseR) takes < 3 sec. instead of > 20 sec. :-)

About issue 2): you went to the extreme with man page titles that are now exactly the same as the name of the function. For example, the title for AnnotateVcf man page is AnnotateVcf. That is not exactly what I was trying to convey when I wrote that "Title should fit in 1 line, be as short as possible, and not be made of several sentences". A typical title for AnnotateVcf would be more like "Annotate a VCF file". The reason good titles are important is that they show up in the browser when people use the HTML browser interface to navigate the documentation of your package. See by yourself by starting the HTML interface with help.start(), then click on Packages, then on cellbaseR. That displays the list of all the man pages in your package in a 2-column table (aliases in the 1st column, man pages titles in the 2nd column). In your case the 2nd column is almost identical to the 1st column so is not very informative. Having titles that are a little bit more informative would help the user find what s/he's looking for.

About issue 3): AnnotateVcf still doesn't have examples.

About issue 7): I still think that the CellBaseR() constructor function should check the validity of the supplied species. Otherwise, when later on a get* function (e.g. getGene()) gives me back a 0-row data.frame, I have no way to tell if that's because I specified invalid genes or if I created a CellBaseR object pointing to a species that is not supported. And since I don't seem to have a way to know what species are supported, I'm a little bit in the dark as to what species I can supply when I call CellBaseR().

Issue 8) was not addressed.

Other issues:

11) It looks like many of your get* functions ignore the object and filters arguments:

getConservationByRegion function (region, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getRegion(object = cb, ids = region, resource = "conservation") res }
getGeneInfo function (gene, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getGene(object = cb, ids = gene, resource = "info") res } getVariantAnnotation function (variant, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getVariant(object = cb, ids = variant, resource = "annotation") res }

12) They would also need to present a more consistent interface:

args(getGene) function (object, ids, resource, filters = NULL, ...) NULL

13) Also why make some of them ordinary functions (e.g. getGeneInfo) and others generic functions with a method for CellBaseR objects (e.g. getGene ).

14) You have a stale man page for Annovcf (that function doesn't seem to exist anymore).

Thanks, H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-253695462, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhh7kxOncBVRvweDhtzqf0qvnBoCwks5qzuvBgaJpZM4KE9Po .

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

61cb5bf shorten lines ae9fbaa enable filters for convienence methods 1d712ff modifying version according to species f76e219 version bump

melsiddieg commented 7 years ago

issue 3 I am still looking for small enough vcf file to use in the example, can you recommend one ? I am looking for vcf file of less than 1K variants

On Mon, Oct 17, 2016 at 9:42 PM, mohammed Elsiddieg melsiddieg@gmail.com wrote:

Hi Hpages

issue 7 we are still working on this issue 8 Here I catually took my guidance from this. stackoverflow recommendation http://stackoverflow.com/questions/28370249/correct- way-to-specifiy-optional-arguments-in-r-functions | Sometimes you want to add a non-trivial default value, which might take several lines of code to compute. Instead of inserting that code in the function | definition, you could use missing() to conditionally compute it if needed. However, this makes it hard to know which arguments are required and which are optional | without carefully reading the documentation. Instead, I usually set the default value to NULL and use is.null() to check if the argument was supplied.

issue 11 That was a work in progress when saw them, now they do not ignore the object and filters

issue 13 I Think there is some misunderstanding here: All the core library of cellbaseR, ie, all the S4 methods that used to start with cb has been renamed to getGene, getProtein, getRegion, etc. We added many convenience functions that has the By in their name like getSnpByGene, getClinicalByRegion, etc. All these functions are merely wrapper functions around the S4 methods as you can see, with fewer arguments and more direct approach. however like the biomaRt package we don't plan to wrap everything and we still prefer people use the library methods itself as this is more flexible, and maintianable and is a more honest represntationo of the CellBase Api as it is nicely docuemnted here http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/ Better we provide very useful tips and up-to-date documentation for using the Cellbase methods through the cbHelp function, for example you can see all the avaiable resurces for a particular sucategory- gene, region, variant, etc- through | cbHelp(object=cb, subactegory="gene")

So you can get various gene data, for example, using the same method rather than using six different wrapper functions.

documentation is still incomplete, but we will push more updates in that regard

Best regards

On Fri, Oct 14, 2016 at 5:41 AM, hpages notifications@github.com wrote:

Hi Mohammed,

Glad to hear that the CellBase service is up and running again. Thanks for drastically reducing the dependencies of cellbaseR (from 80 to only 32 packages). That makes a big difference when I load the package on my laptop: now library(cellbaseR) takes < 3 sec. instead of > 20 sec. :-)

About issue 2): you went to the extreme with man page titles that are now exactly the same as the name of the function. For example, the title for AnnotateVcf man page is AnnotateVcf. That is not exactly what I was trying to convey when I wrote that "Title should fit in 1 line, be as short as possible, and not be made of several sentences". A typical title for AnnotateVcf would be more like "Annotate a VCF file". The reason good titles are important is that they show up in the browser when people use the HTML browser interface to navigate the documentation of your package. See by yourself by starting the HTML interface with help.start(), then click on Packages, then on cellbaseR. That displays the list of all the man pages in your package in a 2-column table (aliases in the 1st column, man pages titles in the 2nd column). In your case the 2nd column is almost identical to the 1st column so is not very informative. Having titles that are a little bit more informative would help the user find what s/he's looking for.

About issue 3): AnnotateVcf still doesn't have examples.

About issue 7): I still think that the CellBaseR() constructor function should check the validity of the supplied species. Otherwise, when later on a get* function (e.g. getGene()) gives me back a 0-row data.frame, I have no way to tell if that's because I specified invalid genes or if I created a CellBaseR object pointing to a species that is not supported. And since I don't seem to have a way to know what species are supported, I'm a little bit in the dark as to what species I can supply when I call CellBaseR().

Issue 8) was not addressed.

Other issues:

11) It looks like many of your get* functions ignore the object and filters arguments:

getConservationByRegion function (region, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getRegion(object = cb, ids = region, resource = "conservation") res }
getGeneInfo function (gene, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getGene(object = cb, ids = gene, resource = "info") res } getVariantAnnotation function (variant, object = NULL, filters = NULL) { cb <- CellBaseR() res <- getVariant(object = cb, ids = variant, resource = "annotation") res }

12) They would also need to present a more consistent interface:

args(getGene) function (object, ids, resource, filters = NULL, ...) NULL

13) Also why make some of them ordinary functions (e.g. getGeneInfo) and others generic functions with a method for CellBaseR objects (e.g. getGene).

14) You have a stale man page for Annovcf (that function doesn't seem to exist anymore).

Thanks, H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-253695462, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhh7kxOncBVRvweDhtzqf0qvnBoCwks5qzuvBgaJpZM4KE9Po .

bioc-issue-bot commented 7 years ago

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hpages commented 7 years ago

Hi Mohammed,

Should I take a look at the latest version of cellbaseR (0.99.27)?

I forgot to say earlier that the HTML version of the vignette (cellbaseR.html) should be removed from the git tree. It will automatically be generated when we build the source tarball with R CMD build.

About issue 8: I agree with Hadley's recommendation to use a NULL default when the default value is non-trivial. By non-trivial he means an expression that is not a single constant. However that doesn't apply to the CellBaseR() constructor function where all the default values would be single constants (except maybe for api and tags which are mysterious arguments, poorly documented, and seem to be ignored by the current implementation). Having these constants in the signature of the function and seeing them in the \usage section of the man page will add transparency/readability.

Thanks, H.

melsiddieg commented 7 years ago

HI Hpages

Not yet, I am still rewriting many functions to accommodate your comments and ironing some bugs, I expect to finish this in the coming few days

Best wishes

On Fri, Dec 9, 2016 at 10:53 AM, hpages notifications@github.com wrote:

Hi Mohammed,

Should I take a look at the latest version of cellbaseR (0.99.27)?

I forgot to say earlier that the HTML version of the vignette (cellbaseR.html) should be removed from the git tree. It will automatically be generated when we build the source tarball with R CMD build.

About issue 8: I agree with Hadley's recommendation to use a NULL default when the default value is non-trivial. By non-trivial he means an expression that is not a single constant. However that doesn't apply to the CellBaseR() constructor function where all the default values would be single constants (except maybe for api and tags which are mysterious arguments, poorly documented, and seem to be ignored by the current implementation). Having these constants in the signature of the function and seeing them in the \usage section of the man page will add transparency/readability.

Thanks, H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-265954584, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhkweBGcq4PBPwYtuyqMSMKrZbzsDks5rGQj-gaJpZM4KE9Po .

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

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hpages commented 7 years ago

Hi Mohammed,

Should I take a look at the latest version of cellbaseR (0.99.28)?

Thanks, H.

melsiddieg commented 7 years ago

Go ahead. I will push new updates very shortly

On Jan 20, 2017 9:59 PM, "hpages" notifications@github.com wrote:

Hi Mohammed,

Should I take a look at the latest version of cellbaseR (0.99.28)?

Thanks, H.

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hpages commented 7 years ago

I'll wait for the updates then. Thanks! H.

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Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_20170210133305.html

hpages commented 7 years ago

Hi Mohamed,

Did you push all your updates? Should I go ahead and take a look at the latest version of cellbaseR (0.99.29)? Please make sure all the issues I reported earlier are addressed. Thanks!

H.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

3e9c5bf check valid species names fixes issue no 7

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_20170219120859.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

2a77aff version bump

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

eb9d6e1 update DESCRIPTION file

Bioconductor / Contributions

New annotation R package (cellbaseR) #138