SpectraQL package to support MassQL on Bioconductor's mass spectrometry objects #3525

jorainer · 2024-08-21T11:22:53Z

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bioc-issue-bot · 2024-08-21T11:22:57Z

Hi @jorainer

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: SpectraQL
Title: MassQL support for Spectra
Version: 0.99.0
Description: The Mass Spec Query Language (MassQL) is a domain-specific
    language enabling to express a query and retrieve mass spectrometry (MS)
    data in a more natural and understandable way for MS users. It is inspired
    by SQL and is by design programming language agnostic. The SpectraQL
    package adds support for the MassQL query language to R, in particular
    to MS data represented by Spectra objects. Users can thus apply MassQL
    expressions to analyze and retrieve specific data from Spectra objects.
Authors@R: c(person(given = "Johannes", family = "Rainer",
          email = "Johannes.Rainer@eurac.edu",
          role = c("aut", "cre"),
          comment = c(ORCID = "0000-0002-6977-7147")),
	     person(given = "Andrea", family = "Vicini",
          email = "andrea.vicini@eurac.edu",
          role = "aut"),
   person(given = "Sebastian", family = "Gibb",
          email = "mail@sebastiangibb.de",
          role = "ctb",
          comment = c(ORCID = "0000-0001-7406-4443"))
		    )
Depends:
    R (>= 4.4.0),
    ProtGenerics (>= 1.25.1)
Imports:
    Spectra (>= 1.5.6),
    MsCoreUtils,
    methods
Suggests:
    testthat,
    msdata (>= 0.19.3),
    roxygen2,
    rmarkdown,
    knitr,
    BiocStyle,
    mzR
License: Artistic-2.0
LazyData: false
VignetteBuilder: knitr
BugReports: https://github.com/RforMassSpectrometry/SpectraQL/issues
URL: https://github.com/RforMassSpectrometry/SpectraQL
biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.2

bioc-issue-bot · 2024-09-03T19:28:56Z

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bioc-issue-bot · 2024-09-04T13:05:38Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR, 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 build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.0.tar.gz

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Remember: if you submitted your package after July 7th, 2020,
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git@git.bioconductor.org:packages/SpectraQL to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep · 2024-09-04T13:19:05Z

we are investigating an SSL issue on our builder; this is likely on our end to fix.

bioc-issue-bot · 2024-09-05T08:38:00Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9eb4fc63017ce73555df13b2050f887e4fa9fb5b

bioc-issue-bot · 2024-09-05T08:42:07Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/SpectraQL to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-09-05T10:07:50Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 8240f07b562e9b26a452d8b34078c63f4230f069

bioc-issue-bot · 2024-09-05T10:11:06Z

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Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
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Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): SpectraQL_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/SpectraQL to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-09-11T18:25:27Z

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

jianhong · 2024-09-26T13:16:40Z

Package 'SpectraQL' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. It is in pretty good shape. I am looking for a bone in an egg now. Please try to answer the comments line by line when you are ready for a second review.
Code: Note: please consider; Important: must be addressed.

R code

NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.
- In file R/massql-parser.R:
  - at line 171 found ' for (i in seq_len(l)) {'
To avoid the * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions in BioCheck,
could you please change the word error to other word in
- R/massql-parser.R (line 63, column 14)
NOTE: Functional programming: code repetition.
- repetition in .filter, .what, and .where
  - in .filter
    - line 1:{
    - line 2: res <- sub(".?filter[[:space:]](.?)[[:space:]](where.*|$)",
    - line 3: "\1", x, ignore.case = TRUE)
    - line 4: res[res == x] <- NA_character_
    - line 5: res <- unlist(strsplit(res, split = "[[:space:]](and|AND)[[:space:]]"))
    - line 6: res[nchar(res) > 0 & !is.na(res)]
  - in .what
    - line 1:{
    - line 2: res <- sub(".?query[[:space:]](.?)[[:space:]](where.|filter.|$)",
    - line 3: "\1", x, ignore.case = TRUE)
    - line 4: res[res == x] <- NA_character_
    - line 5: res
  - in .where
    - line 1:{
    - line 2: res <- sub(".?where[[:space:]](.?)[[:space:]](filter.*|$)",
    - line 3: "\1", x, ignore.case = TRUE)
    - line 4: res[res == x] <- NA_character_
    - line 5: res <- unlist(strsplit(res, split = "[[:space:]](and|AND)[[:space:]]"))
    - line 6: res[nchar(res) > 0 & !is.na(res)]
- repetition in .translate_condition_ms2nl, .translate_condition_ms2prec, .translate_condition_peak_mz, and .translate_filter_mz_value
  - in .translate_condition_ms2nl
    - line 1: function (...)
    - line 2: {
    - line 3: parms <- list(...)[[1L]]
    - line 4: nl <- numeric(0)
    - line 5: ppm <- 0
    - line 6: tolerance <- 0
    - line 7: if (any(names(parms) == "MS2NL"))
    - line 8: nl <- as.numeric(.parse_or(parms["MS2NL"]))
    - line 9: if (anyNA(nl))
    - line 10: stop("Non-numeric value/s for 'MS2NL'")
    - line 11: if (any(names(parms) == "TOLERANCEMZ"))
    - line 12: tolerance <- as.numeric(parms["TOLERANCEMZ"])
    - line 13: if (is.na(tolerance))
    - line 14: stop("Non-numeric value for 'TOLERANCEMZ'")
    - line 15: if (any(names(parms) == "TOLERANCEPPM"))
    - line 16: ppm <- as.numeric(parms["TOLERANCEPPM"])
    - line 17: if (is.na(ppm))
    - line 18: stop("Non-numeric value for 'TOLERANCEPPM'")
    - line 19: if (length(nl)) {
  - in .translate_condition_ms2prec
    - line 1: function (...)
    - line 2: {
    - line 3: parms <- list(...)[[1L]]
    - line 4: pmz <- numeric()
    - line 5: ppm <- 0
    - line 6: tolerance <- 0
    - line 7: if (any(names(parms) == "MS2PREC"))
    - line 8: pmz <- as.numeric(.parse_or(parms["MS2PREC"]))
    - line 9: if (anyNA(pmz))
    - line 10: stop("Missing or non-numeric value(s) for 'MS2PREC'")
    - line 11: if (any(names(parms) == "TOLERANCEMZ"))
    - line 12: tolerance <- as.numeric(parms["TOLERANCEMZ"])
    - line 13: if (is.na(tolerance))
    - line 14: stop("Non-numeric value for 'TOLERANCEMZ'")
    - line 15: if (any(names(parms) == "TOLERANCEPPM"))
    - line 16: ppm <- as.numeric(parms["TOLERANCEPPM"])
    - line 17: if (is.na(ppm))
    - line 18: stop("Non-numeric value for 'TOLERANCEPPM'")
    - line 19: if (length(pmz)) {
    - line 20: ProcessingStep(filterPrecursorMzValues, ARGS = list(mz = pmz,
  - in .translate_condition_peak_mz
    - line 1: function (..., msLevel = 2L, value = "MS2PROD")
    - line 2: {
    - line 3: parms <- list(...)[[1L]]
    - line 4: pmz <- numeric(0)
    - line 5: ppm <- 0
    - line 6: tolerance <- 0
    - line 7: if (any(names(parms) == value))
    - line 8: pmz <- as.numeric(.parse_or(parms[value]))
    - line 9: if (anyNA(pmz))
    - line 10: stop("Missing or non-numeric value(s) for '", value,
    - line 11: "'")
    - line 12: if (any(names(parms) == "TOLERANCEMZ"))
    - line 13: tolerance <- as.numeric(parms["TOLERANCEMZ"])
    - line 14: if (is.na(tolerance))
    - line 15: stop("Non-numeric value for 'TOLERANCEMZ'")
    - line 16: if (any(names(parms) == "TOLERANCEPPM"))
    - line 17: ppm <- as.numeric(parms["TOLERANCEPPM"])
    - line 18: if (is.na(ppm))
    - line 19: stop("Non-numeric value for 'TOLERANCEPPM'")
    - line 20: if (length(pmz)) {
  - in .translate_filter_mz_value
    - line 1: function (..., msLevel = 2L, value = "MS2MZ")
    - line 2: {
    - line 3: parms <- list(...)[[1L]]
    - line 4: mz <- numeric(0)
    - line 5: ppm <- 0
    - line 6: tolerance <- 0
    - line 7: if (any(names(parms) == value))
    - line 8: mz <- as.numeric(.parse_or(parms[value]))
    - line 9: if (anyNA(mz))
    - line 10: stop("Missing or non-numeric value(s) for '", value,
    - line 11: "'")
    - line 12: if (any(names(parms) == "TOLERANCEMZ"))
    - line 13: tolerance <- as.numeric(parms["TOLERANCEMZ"])
    - line 14: if (is.na(tolerance))
    - line 15: stop("Non-numeric value for 'TOLERANCEMZ'")
    - line 16: if (any(names(parms) == "TOLERANCEPPM"))
    - line 17: ppm <- as.numeric(parms["TOLERANCEPPM"])
    - line 18: if (is.na(ppm))
    - line 19: stop("Non-numeric value for 'TOLERANCEPPM'")
    - line 20: if (length(mz))
    - line 21: ProcessingStep(filterMzValues, ARGS = list(mz = mz,

Documentation

Note: Vignette installation section should be formatted as source code.
- rmd file vignettes/SpectraQL.Rmd

jorainer · 2024-09-27T09:06:21Z

Thanks for your review @jianhong ! Below I address your points - I will add each point as a separate comment to avoid having a single very long comment.

[ ] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.

I had a look at the mentioned for loop at line 171, but could not come up with a (safe) and more efficient way using *apply. I'm accessing two different variables mini and maxi within that loop, so I would anyway to loop over an index - and doing that using e.g. lapply (lapply(seq_len(l), function ... would IMHO not be more efficient - and also less readable. So, if you agree, I would like to keep the for loop in that particular case. Note that I usually use vapply whenever possible.

jorainer · 2024-09-27T09:10:57Z

[ ] To avoid the * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions in BioCheck,

Thanks for the comment. It indeed would look ugly. I changed the wording from Syntax error to Wrong syntax.

jorainer · 2024-09-27T09:42:00Z

code repetition:

repetition in .filter, .what, and .where

Thanks, that's a great suggestion! I've moved the respective code into a new .parse_query function (that is called by .what, .where etc.

The changes are in this commit: rformassspectrometry/SpectraQL@cf1dd9a

jorainer · 2024-09-27T10:19:34Z

code repetition:

repetition in .translate_condition_ms2nl, .translate_condition_ms2prec, .translate_condition_peak_mz, and .translate_filter_mz_value

Thanks for spotting this! I've created two new helper functions to reduce the repeated code.

The changes are in this commit: rformassspectrometry/SpectraQL@49f4b1e

jorainer · 2024-09-27T10:24:40Z

Note: Vignette installation section should be formatted as source code.

Also done.

Changes are in this commit: rformassspectrometry/SpectraQL@f4bbe03

bioc-issue-bot · 2024-09-27T10:32:21Z

Received a valid push on git.bioconductor.org; starting a build for commit id: f4bbe03f7eeb3db99545542940496c9cc53e1f5a

jorainer · 2024-09-27T10:33:20Z

Changes have now all been pushed to BioC too. Thanks again for the review @jianhong ! Looking forward to the second round of review.

bioc-issue-bot · 2024-09-27T10:35:22Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): SpectraQL_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/SpectraQL to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-10-01T12:17:27Z

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bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Aug 21, 2024

jorainer mentioned this issue Aug 21, 2024

Submit to Bioconductor rformassspectrometry/SpectraQL#20

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SpectraQL package to support MassQL on Bioconductor's mass spectrometry objects #3525

SpectraQL package to support MassQL on Bioconductor's mass spectrometry objects #3525

jorainer commented Aug 21, 2024

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SpectraQL package to support MassQL on Bioconductor's mass spectrometry objects #3525

SpectraQL package to support MassQL on Bioconductor's mass spectrometry objects #3525

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Package 'SpectraQL' Review

R code

Documentation

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