refactor: support storing database name instead of active connection

- Add support to store the database file name in the object instead of the
  active connection to the database. This allows to serialize/deserialize
  `CompDb` and `IonDb` classes (and would even support parallel processing). For
  SQLite databases this is now the default. Issue #112.
- Add brackets `()` for all functions in the documentation.

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CompoundDb
 Type: Package
 Title: Creating and Using (Chemical) Compound Annotation Databases
-Version: 1.9.0
+Version: 1.9.1
 Authors@R: c(person(given = "Jan", family = "Stanstrup",
                     email = "[email protected]",
 		    role = c("aut"),

NAMESPACE

@@ -99,6 +99,7 @@ importFrom(DBI,dbDisconnect)
 importFrom(DBI,dbDriver)
 importFrom(DBI,dbExecute)
 importFrom(DBI,dbGetQuery)
+importFrom(DBI,dbIsValid)
 importFrom(DBI,dbListTables)
 importFrom(DBI,dbWriteTable)
 importFrom(IRanges,CharacterList)
@@ -109,6 +110,7 @@ importFrom(MsCoreUtils,rbindFill)
 importFrom(MsCoreUtils,vapply1d)
 importFrom(RSQLite,SQLITE_RO)
 importFrom(RSQLite,SQLITE_RW)
+importFrom(RSQLite,SQLITE_RWC)
 importFrom(RSQLite,dbConnect)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,extractCOLS)
@@ -120,6 +122,7 @@ importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(jsonlite,read_json)
 importFrom(methods,"slot<-")
+importFrom(methods,.hasSlot)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,getMethod)

NEWS.md

@@ -1,3 +1,13 @@
+# CompoundDb version 1.9
+
+## Changes in version 1.9.1
+
+- Allow `CompDb` to store that database name as alternative to an active
+  database connection. This allows to serialize and load an object to/from disk
+  (serializing an active database connection would not be possible) . Each call
+  to extract data from the database will however open (and close) its own
+  connection.
+
 # CompoundDb version 1.7
 
 ## Changes in version 1.7.2

R/CompDb-methods.R

@@ -16,6 +16,8 @@ setMethod("show", "CompDb", function(object) {
     cat("class:", class(object), "\n")
     con <- .dbconn(object)
     if (!is.null(con)) {
+        if (length(.dbname(object)))
+            on.exit(dbDisconnect(con))
         cat(" data source:", .metadata_value(con, "source"), "\n")
         cat(" version:", .metadata_value(con, "source_version"), "\n")
         cat(" organism:", .metadata_value(con, "organism"), "\n")
@@ -124,15 +126,18 @@ setMethod("compounds", "CompDb", function(object,
 #' @rdname CompDb
 setMethod("insertSpectra", signature(object = "CompDb", spectra = "Spectra"),
           function(object, spectra, columns = spectraVariables(spectra), ...) {
-              if (is.null(.dbconn(object)))
+              con <- .dbconn(object)
+              if (is.null(con))
                   stop("Database not initialized")
+              if (length(.dbname(object)))
+                  on.exit(dbDisconnect(con))
               new_sD <- as.data.frame(spectraData(spectra, columns))
               if (!any(colnames(new_sD) == "compound_id"))
                   stop("Column 'compound_id' needs to be provided (as a ",
                        "spectra variable to insert to the database).")
               if (!all(new_sD$compound_id %in%
-                       dbGetQuery(.dbconn(object),
-                                  "select compound_id from ms_compound")[, 1]))
+                       dbGetQuery(
+                           con, "select compound_id from ms_compound")[, 1]))
                   stop("All values of spectra variable 'compound_id' must be",
                        " in 'compound_id' column of the database 'ms_compound'",
                        " table")
@@ -150,20 +155,18 @@ setMethod("insertSpectra", signature(object = "CompDb", spectra = "Spectra"),
               new_sD$mz <- as.list(spectra$mz)
               new_sD$intensity <- as.list(spectra$intensity)
               if (hasMsMsSpectra(object))
-                  .append_msms_spectra(.dbconn(object), new_sD)
+                  .append_msms_spectra(con, new_sD)
               else {
                   if("spectrum_id" %in% colnames(new_sD))
                       warning("'spectrum_id' variable in 'spectra' will be
                               replaced with internal indexes")
                   new_sD$spectrum_id <- seq_len(nrow(new_sD))
-                  .insert_msms_spectra(.dbconn(object), new_sD)
+                  .insert_msms_spectra(con, new_sD)
               }
               object@.properties$tables$msms_spectrum <- colnames(
-                  dbGetQuery(.dbconn(object),
-                             "select * from msms_spectrum limit 1"))
+                  dbGetQuery(con, "select * from msms_spectrum limit 1"))
               object@.properties$tables$msms_spectrum_peak <- colnames(
-                  dbGetQuery(.dbconn(object),
-                             "select * from msms_spectrum_peak limit 1"))
+                  dbGetQuery(con, "select * from msms_spectrum_peak limit 1"))
               object
           })
 
@@ -178,6 +181,8 @@ setMethod("deleteSpectra", signature(object = "CompDb"),
               dbcon <- .dbconn(object)
               if (is.null(dbcon))
                   stop("Database not initialized")
+              if (length(.dbname(object)))
+                  on.exit(dbDisconnect(dbcon))
               if (hasMsMsSpectra(object)) {
                   if(any(!ids %in%
                          dbGetQuery(dbcon, paste0("select spectrum_id ",
@@ -225,6 +230,8 @@ setMethod("insertCompound", "CompDb", function(object, compounds = data.frame(),
         stop("'compounds' is expected to be a data.frame")
     dbcon <- .dbconn(object)
     if (is.null(dbcon)) stop("Database not initialized")
+    if (length(.dbname(object)))
+        on.exit(dbDisconnect(dbcon))
     if (!nrow(compounds)) return(object)
     ref <- data.frame(name = character(), inchi = character(),
                       inchikey = character(), formula = character(),
@@ -269,6 +276,8 @@ setMethod("deleteCompound", "CompDb", function(object, ids = character(),
                                                recursive = FALSE, ...) {
     dbcon <- .dbconn(object)
     if (is.null(dbcon)) stop("Database not initialized")
+    if (length(.dbname(object)))
+        on.exit(dbDisconnect(dbcon))
     if (!length(ids)) return(object)
     id_string <- paste0("'", ids, "'", collapse = ",")
     if (hasMsMsSpectra(object)) {