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Build # 383

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Pull #39

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Pull Request Pull Request #39: v0.2.1

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/R/pipeline_interface.R

#' Get outputs from pipeline defined in an output schema
#' 
#' Extracts the output file templates defined for a given pipeline
#'
#' @param pipeline an object of \code{\link[pepr]{Config-class}} 
#' @param parent a path to parent folder to use
#' @param projectContext logical indicating whether a only project-level 
#' pifaces should be considered. Otherwise, only sample-level ones are. 
#'
#' @return named list of output path templates, 
#' like: \code{'aligned_{sample.genome}/{sample.sample_name}_sort.bam'}
.getOutputs = function(pipeline, 
    parent, projectContext = FALSE) {
    if (!OUTPUT_SCHEMA_SECTION %in% 
        names(pipeline)) 
        return(invisible(NULL))
    outputSchema = readSchema(pipeline[[OUTPUT_SCHEMA_SECTION]], 
        parent)
    sect = "properties"
    if (!projectContext) 
        sect = SCHEMA_SAMPLE_OUTS
    if (!pepr::.checkSection(outputSchema, 
        sect)) {
        pipName = ifelse(is.null(pipeline[[PIP_NAME_KEY]]), 
            "provided", pipeline[[PIP_NAME_KEY]])
        warning("There is no '", 
            paste(sect, collapse = ":"), 
            "' section in the ", 
            pipName, " pipeline output schema.")
        return(invisible(NULL))
    }
    outputs = outputSchema[[sect]]
    if ("samples" %in% names(outputs)) 
        outputs[["samples"]] = NULL
    x = lapply(outputs, function(x) {
        return(x[["path"]])
    })
    if (is.null(unlist(lapply(x, 
        is.null)))) 
        return(invisible(NULL))
    x
}

#' Populates and returns output files for a given sample
#'
#' Returns the pipeline outputs which are defined in the pipeline interface
#' indicated in the \code{\link[pepr]{Project-class}}
#'
#' @param project \code{\link[pepr]{Project-class}} object
#' @param ... other arguemnts
#' 
#' @return a list of output file paths. The order of the first level of the
#' list corresponds to the order of the pipeline interface files, second level 
#' is a named list of file paths populated by the samples
#'
#' @export
#' @examples
#' projectConfig = system.file('extdata',
#' 'example_peps-master',
#' 'example_piface',
#' 'project_config.yaml',
#' package = 'BiocProject')
#' p = Project(file = projectConfig)
#' getOutputsBySample(p)
#' getOutputsBySample(p, 'sample1')
setGeneric("getOutputsBySample", 
    function(project, ...) standardGeneric("getOutputsBySample"), 
    signature = "project")

#' @describeIn getOutputsBySample Populates and returns output files
#'  for a given sample
#' @param sampleNames names of the samples 
#' @importFrom yaml yaml.load_file
setMethod("getOutputsBySample", 
    c(project = "Project"), function(project, 
        sampleNames = NULL) {
        pifacesBySample = pipelineInterfacesBySample(project = project)
        defSampleNames = names(pifacesBySample)
        if (!is.null(sampleNames)) 
            defSampleNames = intersect(sampleNames, 
                defSampleNames)
        if (length(defSampleNames) < 
            1) 
            stop("No samples matched by: ", 
                paste0(sampleNames, 
                  collapse = ","))
        ret = list()
        for (sampleName in defSampleNames) {
            sampleRet = list()
            pifaceSources = pifacesBySample[[sampleName]]
            for (pifaceSource in pifaceSources) {
                piface = yaml::yaml.load_file(pifaceSource)
                if (!.checkPifaceType(piface, 
                  "sample")) 
                  return(invisible(NULL))
                outputs = .getOutputs(piface, 
                  parent = dirname(pifaceSource))
                sampleRet[[pifaceSource]] = .populateTemplates(project, 
                  outputs, sampleName)
            }
            ret[[sampleName]] = sampleRet
        }
        ret
    })

#' Populates and returns output files for a
#'  given \code{\link[pepr]{Project-class}}
#'
#' Returns the pipeline outputs which are defined in the pipeline interface
#' indicated in the \code{\link[pepr]{Project-class}}
#'
#' @param project \code{\link[pepr]{Project-class}} object
#'
#' @return a list of output file paths. The order of the first level of the
#' list corresponds to the order of the pipeline interface files, second level 
#' is a named list of file paths populated 
#' by the \code{\link[pepr]{Project-class}}
#'
#' @export
#' @examples
#' projectConfig = system.file('extdata',
#' 'example_peps-master',
#' 'example_piface',
#' 'project_config.yaml',
#' package = 'BiocProject')
#' p = Project(file = projectConfig)
#' getProjectOutputs(p)
setGeneric("getProjectOutputs", 
    function(project) standardGeneric("getProjectOutputs"), 
    signature = "project")

#' @describeIn getProjectOutputs Populates and returns output files for 
#' a given \code{\link[pepr]{Project-class}}
setMethod("getProjectOutputs", 
    c(project = "Project"), function(project) {
        pifaceSources = gatherPipelineInterfaces(project, 
            projectLevel = TRUE)
        ret = list()
        for (pifaceSource in pifaceSources) {
            piface = yaml::yaml.load_file(pifaceSource)
            if (!.checkPifaceType(piface, 
                "project")) 
                return(invisible(NULL))
            outputs = .getOutputs(piface, 
                parent = dirname(pifaceSource), 
                projectContext = TRUE)
            ret[[pifaceSource]] = .populateTemplates(project, 
                outputs, projectContext = TRUE)
        }
        ret
    })

#' Collect all pipeline interfaces
#' 
#' Collects all relevant pipeline interfaces 
#' for this \code{\link[pepr]{Project-class}}
#'
#' @param project \code{\link[pepr]{Project-class}} object
#' @param ... other arguments 
#'
#' @return a list of pipeline interface file paths.
#'
#' @export
#' @examples
#' projectConfig = system.file('extdata',
#' 'example_peps-master',
#' 'example_piface',
#' 'project_config.yaml',
#' package = 'BiocProject')
#' p = Project(file = projectConfig)
#' gatherPipelineInterfaces(p)
#' gatherPipelineInterfaces(p, TRUE)
setGeneric("gatherPipelineInterfaces", 
    function(project, ...) standardGeneric("gatherPipelineInterfaces"), 
    signature = "project")

#' @describeIn gatherPipelineInterfaces Collect all pipeline interfaces
#' @param projectLevel logical indicating whether a only project-level pifaces 
#' should be considered. Otherwise, only sample-level ones are.
#' @importFrom stats setNames
setMethod("gatherPipelineInterfaces", 
    c(project = "Project"), function(project, 
        projectLevel = FALSE) {
        if (!projectLevel) {
            return(.gatherSamplePipelineInterfaces(project))
        } else {
            pik = PIP_IFACE_NAME
            if (!is.null(config(project)[[LOOPER_SECTION]][[PIP_IFACE_KEY]])) 
                pik = config(project)[[LOOPER_SECTION]][[PIP_IFACE_KEY]]
            if (!is.null(config(project)[[LOOPER_SECTION]][[pik]])) 
                return(setNames(vapply(unlist(
                    config(project)[[LOOPER_SECTION]][[pik]]), 
                  function(x) {
                    pepr::.makeAbsPath(x, 
                      parent = dirname(project@file))
                  }, character(1)), 
                  NULL))
            warning("No project pipeline interfaces defined")
            return(invisible(NULL))
        }
    })

setGeneric(".gatherSamplePipelineInterfaces", 
    function(project) standardGeneric(".gatherSamplePipelineInterfaces"), 
    signature = "project")

#' @describeIn gatherPipelineInterfaces extracts pipeline outputs 
#' for a given pipeline
#' @importFrom pryr partial
setMethod(".gatherSamplePipelineInterfaces", 
    c(project = "Project"), function(project) {
        t = pepr::sampleTable(project)
        .mkAbs = pryr::partial(.mkPathsAbs, 
            parent = dirname(project@file))
        if (PIP_IFACE_NAME %in% 
            colnames(t)) 
            return(setNames(vapply(unique(unlist(t[, 
                PIP_IFACE_NAME])), 
                .mkAbs, character(1)), 
                NULL))
        return(invisible(NULL))
    })

#' Get pipeline interfaces by sample
#' 
#' Collects all relevant pipeline interfaces for this 
#' \code{\link[pepr]{Project-class}} and provides a sample to interfaces mapping
#'
#' @param project \code{\link[pepr]{Project-class}} object
#'
#' @return a list of pipeline interface file paths keyed by sample names
#'
#' @export
#' @examples
#' projectConfig = system.file('extdata',
#' 'example_peps-master',
#' 'example_piface',
#' 'project_config.yaml',
#' package = 'BiocProject')
#' p = Project(file = projectConfig)
#' pipelineInterfacesBySample(p)
setGeneric("pipelineInterfacesBySample", 
    function(project) standardGeneric("pipelineInterfacesBySample"), 
    signature = "project")

#' @describeIn pipelineInterfacesBySample Get pipeline interfaces by sample
setMethod("pipelineInterfacesBySample", 
    c(project = "Project"), function(project) {
        t = pepr::sampleTable(project)
        if (PIP_IFACE_NAME %in% 
            colnames(t)) {
            .mkAbs = pryr::partial(.mkPathsAbs, 
                parent = dirname(project@file))
            pifaces = t[, PIP_IFACE_NAME]
            names(pifaces) = unlist(t[, 
                "sample_name"])
            return(lapply(pifaces, 
                .mkAbs))
        }
        return(invisible(NULL))
    })


#' Populate list of path templates
#'
#' @param project an object of \code{\link[pepr]{Config-class}} 
#' @param templList list of strings, 
#' like: 'aligned_{sample.genome}/{sample.sample_name}_sort.bam'
#' @param sampleName string, name of the protocol to select the samples
#' @param projectContext logical indicating whether project context 
#' should be applied. Default: sample
#'
#' @return list of strings
.populateTemplates = function(project, 
    templList, sampleName = NULL, 
    projectContext = FALSE) {
    if (!projectContext && is.null(sampleName)) 
        stop("Must specify the sample to populate templates for")
    expandedTemplList = lapply(templList, 
        pepr::.expandPath)
    lapply(expandedTemplList, .populateString, 
        project, sampleName, projectContext)
}

1	#' Get outputs from pipeline defined in an output schema
2	#'
3	#' Extracts the output file templates defined for a given pipeline
4	#'
5	#' @param pipeline an object of \code{\link[pepr]{Config-class}}
6	#' @param parent a path to parent folder to use
7	#' @param projectContext logical indicating whether a only project-level
8	#' pifaces should be considered. Otherwise, only sample-level ones are.
9	#'
10	#' @return named list of output path templates,
11	#' like: \code{'aligned_{sample.genome}/{sample.sample_name}_sort.bam'}
12	.getOutputs = function(pipeline,
13	parent, projectContext = FALSE) {
14	if (!OUTPUT_SCHEMA_SECTION %in%	20✔
15	names(pipeline))	20✔
16	return(invisible(NULL))	×
17	outputSchema = readSchema(pipeline[[OUTPUT_SCHEMA_SECTION]],	20✔
18	parent)	20✔
19	sect = "properties"	20✔
20	if (!projectContext)	20✔
21	sect = SCHEMA_SAMPLE_OUTS	18✔
22	if (!pepr::.checkSection(outputSchema,	20✔
23	sect)) {	20✔
24	pipName = ifelse(is.null(pipeline[[PIP_NAME_KEY]]),	×
25	"provided", pipeline[[PIP_NAME_KEY]])	×
26	warning("There is no '",	×
27	paste(sect, collapse = ":"),	×
28	"' section in the ",	×
29	pipName, " pipeline output schema.")	×
30	return(invisible(NULL))	×
31	}
32	outputs = outputSchema[[sect]]	20✔
33	if ("samples" %in% names(outputs))	20✔
34	outputs[["samples"]] = NULL	2✔
35	x = lapply(outputs, function(x) {	20✔
36	return(x[["path"]])	40✔
37	})
38	if (is.null(unlist(lapply(x,	20✔
39	is.null))))	20✔
40	return(invisible(NULL))	×
41	x	20✔
42	}
43
44	#' Populates and returns output files for a given sample
45	#'
46	#' Returns the pipeline outputs which are defined in the pipeline interface
47	#' indicated in the \code{\link[pepr]{Project-class}}
48	#'
49	#' @param project \code{\link[pepr]{Project-class}} object
50	#' @param ... other arguemnts
51	#'
52	#' @return a list of output file paths. The order of the first level of the
53	#' list corresponds to the order of the pipeline interface files, second level
54	#' is a named list of file paths populated by the samples
55	#'
56	#' @export
57	#' @examples
58	#' projectConfig = system.file('extdata',
59	#' 'example_peps-master',
60	#' 'example_piface',
61	#' 'project_config.yaml',
62	#' package = 'BiocProject')
63	#' p = Project(file = projectConfig)
64	#' getOutputsBySample(p)
65	#' getOutputsBySample(p, 'sample1')
66	setGeneric("getOutputsBySample",
67	function(project, ...) standardGeneric("getOutputsBySample"),	6✔
68	signature = "project")
69
70	#' @describeIn getOutputsBySample Populates and returns output files
71	#' for a given sample
72	#' @param sampleNames names of the samples
73	#' @importFrom yaml yaml.load_file
74	setMethod("getOutputsBySample",
75	c(project = "Project"), function(project,
76	sampleNames = NULL) {
77	pifacesBySample = pipelineInterfacesBySample(project = project)	5✔
78	defSampleNames = names(pifacesBySample)	5✔
79	if (!is.null(sampleNames))	5✔
80	defSampleNames = intersect(sampleNames,	3✔
81	defSampleNames)	3✔
82	if (length(defSampleNames) <	5✔
83	1)	5✔
84	stop("No samples matched by: ",	×
85	paste0(sampleNames,	×
86	collapse = ","))	×
87	ret = list()	5✔
88	for (sampleName in defSampleNames) {	5✔
89	sampleRet = list()	9✔
90	pifaceSources = pifacesBySample[[sampleName]]	9✔
91	for (pifaceSource in pifaceSources) {	9✔
92	piface = yaml::yaml.load_file(pifaceSource)	18✔
93	if (!.checkPifaceType(piface,	18✔
94	"sample"))	18✔
95	return(invisible(NULL))	×
96	outputs = .getOutputs(piface,	18✔
97	parent = dirname(pifaceSource))	18✔
98	sampleRet[[pifaceSource]] = .populateTemplates(project,	18✔
99	outputs, sampleName)	18✔
100	}
101	ret[[sampleName]] = sampleRet	9✔
102	}
103	ret	5✔
104	})
105
106	#' Populates and returns output files for a
107	#' given \code{\link[pepr]{Project-class}}
108	#'
109	#' Returns the pipeline outputs which are defined in the pipeline interface
110	#' indicated in the \code{\link[pepr]{Project-class}}
111	#'
112	#' @param project \code{\link[pepr]{Project-class}} object
113	#'
114	#' @return a list of output file paths. The order of the first level of the
115	#' list corresponds to the order of the pipeline interface files, second level
116	#' is a named list of file paths populated
117	#' by the \code{\link[pepr]{Project-class}}
118	#'
119	#' @export
120	#' @examples
121	#' projectConfig = system.file('extdata',
122	#' 'example_peps-master',
123	#' 'example_piface',
124	#' 'project_config.yaml',
125	#' package = 'BiocProject')
126	#' p = Project(file = projectConfig)
127	#' getProjectOutputs(p)
128	setGeneric("getProjectOutputs",
129	function(project) standardGeneric("getProjectOutputs"),	1✔
130	signature = "project")
131
132	#' @describeIn getProjectOutputs Populates and returns output files for
133	#' a given \code{\link[pepr]{Project-class}}
134	setMethod("getProjectOutputs",
135	c(project = "Project"), function(project) {
136	pifaceSources = gatherPipelineInterfaces(project,	1✔
137	projectLevel = TRUE)	1✔
138	ret = list()	1✔
139	for (pifaceSource in pifaceSources) {	1✔
140	piface = yaml::yaml.load_file(pifaceSource)	2✔
141	if (!.checkPifaceType(piface,	2✔
142	"project"))	2✔
143	return(invisible(NULL))	×
144	outputs = .getOutputs(piface,	2✔
145	parent = dirname(pifaceSource),	2✔
146	projectContext = TRUE)	2✔
147	ret[[pifaceSource]] = .populateTemplates(project,	2✔
148	outputs, projectContext = TRUE)	2✔
149	}
150	ret	1✔
151	})
152
153	#' Collect all pipeline interfaces
154	#'
155	#' Collects all relevant pipeline interfaces
156	#' for this \code{\link[pepr]{Project-class}}
157	#'
158	#' @param project \code{\link[pepr]{Project-class}} object
159	#' @param ... other arguments
160	#'
161	#' @return a list of pipeline interface file paths.
162	#'
163	#' @export
164	#' @examples
165	#' projectConfig = system.file('extdata',
166	#' 'example_peps-master',
167	#' 'example_piface',
168	#' 'project_config.yaml',
169	#' package = 'BiocProject')
170	#' p = Project(file = projectConfig)
171	#' gatherPipelineInterfaces(p)
172	#' gatherPipelineInterfaces(p, TRUE)
173	setGeneric("gatherPipelineInterfaces",
174	function(project, ...) standardGeneric("gatherPipelineInterfaces"),	9✔
175	signature = "project")
176
177	#' @describeIn gatherPipelineInterfaces Collect all pipeline interfaces
178	#' @param projectLevel logical indicating whether a only project-level pifaces
179	#' should be considered. Otherwise, only sample-level ones are.
180	#' @importFrom stats setNames
181	setMethod("gatherPipelineInterfaces",
182	c(project = "Project"), function(project,
183	projectLevel = FALSE) {
184	if (!projectLevel) {	9✔
185	return(.gatherSamplePipelineInterfaces(project))	6✔
186	} else {
187	pik = PIP_IFACE_NAME	3✔
188	if (!is.null(config(project)[[LOOPER_SECTION]][[PIP_IFACE_KEY]]))	3✔
189	pik = config(project)[[LOOPER_SECTION]][[PIP_IFACE_KEY]]	×
190	if (!is.null(config(project)[[LOOPER_SECTION]][[pik]]))	3✔
191	return(setNames(vapply(unlist(	2✔
192	config(project)[[LOOPER_SECTION]][[pik]]),	2✔
193	function(x) {	2✔
194	pepr::.makeAbsPath(x,	4✔
195	parent = dirname(project@file))	4✔
196	}, character(1)),	2✔
197	NULL))	2✔
198	warning("No project pipeline interfaces defined")	1✔
199	return(invisible(NULL))	1✔
200	}
201	})
202
203	setGeneric(".gatherSamplePipelineInterfaces",
204	function(project) standardGeneric(".gatherSamplePipelineInterfaces"),	6✔
205	signature = "project")
206
207	#' @describeIn gatherPipelineInterfaces extracts pipeline outputs
208	#' for a given pipeline
209	#' @importFrom pryr partial
210	setMethod(".gatherSamplePipelineInterfaces",
211	c(project = "Project"), function(project) {
212	t = pepr::sampleTable(project)	6✔
213	.mkAbs = pryr::partial(.mkPathsAbs,	6✔
214	parent = dirname(project@file))	6✔
215	if (PIP_IFACE_NAME %in%	6✔
216	colnames(t))	6✔
217	return(setNames(vapply(unique(unlist(t[,	4✔
218	PIP_IFACE_NAME])),	4✔
219	.mkAbs, character(1)),	4✔
220	NULL))	4✔
221	return(invisible(NULL))	2✔
222	})
223
224	#' Get pipeline interfaces by sample
225	#'
226	#' Collects all relevant pipeline interfaces for this
227	#' \code{\link[pepr]{Project-class}} and provides a sample to interfaces mapping
228	#'
229	#' @param project \code{\link[pepr]{Project-class}} object
230	#'
231	#' @return a list of pipeline interface file paths keyed by sample names
232	#'
233	#' @export
234	#' @examples
235	#' projectConfig = system.file('extdata',
236	#' 'example_peps-master',
237	#' 'example_piface',
238	#' 'project_config.yaml',
239	#' package = 'BiocProject')
240	#' p = Project(file = projectConfig)
241	#' pipelineInterfacesBySample(p)
242	setGeneric("pipelineInterfacesBySample",
243	function(project) standardGeneric("pipelineInterfacesBySample"),	5✔
244	signature = "project")
245
246	#' @describeIn pipelineInterfacesBySample Get pipeline interfaces by sample
247	setMethod("pipelineInterfacesBySample",
248	c(project = "Project"), function(project) {
249	t = pepr::sampleTable(project)	5✔
250	if (PIP_IFACE_NAME %in%	5✔
251	colnames(t)) {	5✔
252	.mkAbs = pryr::partial(.mkPathsAbs,	5✔
253	parent = dirname(project@file))	5✔
254	pifaces = t[, PIP_IFACE_NAME]	5✔
255	names(pifaces) = unlist(t[,	5✔
256	"sample_name"])	5✔
257	return(lapply(pifaces,	5✔
258	.mkAbs))	5✔
259	}
260	return(invisible(NULL))	×
261	})
262
263
264	#' Populate list of path templates
265	#'
266	#' @param project an object of \code{\link[pepr]{Config-class}}
267	#' @param templList list of strings,
268	#' like: 'aligned_{sample.genome}/{sample.sample_name}_sort.bam'
269	#' @param sampleName string, name of the protocol to select the samples
270	#' @param projectContext logical indicating whether project context
271	#' should be applied. Default: sample
272	#'
273	#' @return list of strings
274	.populateTemplates = function(project,
275	templList, sampleName = NULL,
276	projectContext = FALSE) {
277	if (!projectContext && is.null(sampleName))	20✔
278	stop("Must specify the sample to populate templates for")	×
279	expandedTemplList = lapply(templList,	20✔
280	pepr::.expandPath)	20✔
281	lapply(expandedTemplList, .populateString,	20✔
282	project, sampleName, projectContext)	20✔
283	}

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Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous