use httptest

when building vignette to avoid bioc build errors if workbench query times out during build

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: metabolomicsWorkbenchR
 Type: Package
 Title: Metabolomics Workbench in R
-Version: 1.7.0
+Version: 1.7.1
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
@@ -43,6 +43,7 @@ Suggests:
     covr,
     knitr,
     HDF5Array,
+    httptest,
     rmarkdown,
     structToolbox,
     testthat,

vignettes/Introduction_to_metabolomicsWorkbenchR.Rmd

@@ -21,8 +21,10 @@ vignette: >
 ---
 
 ```{r echo = FALSE,include=FALSE}
+suppressPackageStartupMessages(library(grid))
+suppressPackageStartupMessages(library(httptest))
 suppressPackageStartupMessages(library(metabolomicsWorkbenchR))
-library(grid)
+httptest::start_vignette('introduction')
 ```
 
 

vignettes/example_using_structToolbox.Rmd

@@ -23,6 +23,8 @@ vignette: >
 ```{r echo = FALSE,include=FALSE}
 suppressPackageStartupMessages(library(metabolomicsWorkbenchR))
 library(structToolbox)
+library(httptest)
+httptest::start_vignette('structToolbox_example')
 ```
 
 

vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json

@@ -0,0 +1,11 @@
+{
+    "regno": "11",
+    "formula": "C47H75N5O8",
+    "exactmass": "837.561565",
+    "inchi_key": "JLBSVDZUWJLOCF-ZLKQSCCRSA-N",
+    "name": "Dideoxymycobactin",
+    "sys_name": "[(2R)-4-oxo-4-[[(3S)-2-oxoazepan-3-yl]amino]butan-2-yl] (2S)-2-[[(4S)-2-(2-hydroxyphenyl)-4-methyl-5H-1,3-oxazole-4-carbonyl]amino]-6-[[(Z)-icos-2-enoyl]amino]hexanoate",
+    "lm_id": "LMFA00000015",
+    "pubchem_cid": "136029221",
+    "smiles": "CCCCCCCCCCCCCCCCC/C=C\\C(=O)NCCCC[C@H](NC(=O)[C@]1(C)COC(c2ccccc2O)=N1)C(=O)O[C@H](C)CC(=O)N[C@H]1CCCCNC1=O"
+}

vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json

@@ -0,0 +1,99 @@
+{
+    "Row1": {
+        "gene_name": "acetyl-CoA acyltransferase 1",
+        "mgp_id": "MGP000015",
+        "gene_id": "30",
+        "gene_symbol": "ACAA1",
+        "gene_synonyms": "ACAA; THIO; PTHIO;",
+        "alt_names": "3-ketoacyl-CoA thiolase, peroxisomal; acetyl-Coenzyme A acyltransferase 1; beta-ketothiolase; peroxisomal 3-oxoacyl-CoA thiolase; peroxisomal 3-oxoacyl-Coenzyme A thiolase;",
+        "chromosome": "3",
+        "map_location": "3p22.2",
+        "summary": "This gene encodes an enzyme operative in the beta-oxidation system of the peroxisomes. Deficiency of this enzyme leads to pseudo-Zellweger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row2": {
+        "gene_name": "acetyl-CoA carboxylase alpha",
+        "mgp_id": "MGP000016",
+        "gene_id": "31",
+        "gene_symbol": "ACACA",
+        "gene_synonyms": "ACC; ACAC; ACC1; ACCA; ACACAD;",
+        "alt_names": "acetyl-CoA carboxylase 1; ACC-alpha; acetyl-Coenzyme A carboxylase alpha;",
+        "chromosome": "17",
+        "map_location": "17q21",
+        "summary": "Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. There are two ACC forms, alpha and beta, encoded by two different genes. ACC-alpha is highly enriched in lipogenic tissues. The enzyme is under long term control at the transcriptional and translational levels and under short term regulation by the phosphorylation/dephosphorylation of targeted serine residues and by allosteric transformation by citrate or palmitoyl-CoA. Multiple alternatively spliced transcript variants divergent in the 5' sequence and encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row3": {
+        "gene_name": "acetyl-CoA carboxylase beta",
+        "mgp_id": "MGP000017",
+        "gene_id": "32",
+        "gene_symbol": "ACACB",
+        "gene_synonyms": "ACC2; ACCB; HACC275;",
+        "alt_names": "acetyl-CoA carboxylase 2; ACC-beta; acetyl-Coenzyme A carboxylase beta;",
+        "chromosome": "12",
+        "map_location": "12q24.11",
+        "summary": " Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. ACC-beta is thought to control fatty acid oxidation by means of the ability of malonyl-CoA to inhibit carnitine-palmitoyl-CoA transferase I, the rate-limiting step in fatty acid uptake and oxidation by mitochondria. ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. There is evidence for the presence of two ACC-beta isoforms. [provided by RefSeq, Jul 2008]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row4": {
+        "gene_name": "acetyl-CoA acetyltransferase 1",
+        "mgp_id": "MGP000023",
+        "gene_id": "38",
+        "gene_symbol": "ACAT1",
+        "gene_synonyms": "T2; MAT; ACAT; THIL;",
+        "alt_names": "acetyl-CoA acetyltransferase, mitochondrial; acetoacetyl Coenzyme A thiolase; acetoacetyl-CoA thiolase; acetyl-Coenzyme A acetyltransferase 1; mitochondrial acetoacetyl-CoA thiolase;",
+        "chromosome": "11",
+        "map_location": "11q22.3",
+        "summary": "This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA. Defects in this gene are associated with 3-ketothiolase deficiency, an inborn error of isoleucine catabolism characterized by urinary excretion of 2-methyl-3-hydroxybutyric acid, 2-methylacetoacetic acid, tiglylglycine, and butanone. [provided by RefSeq, Feb 2009]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row5": {
+        "gene_name": "acetyl-CoA acetyltransferase 2",
+        "mgp_id": "MGP000024",
+        "gene_id": "39",
+        "gene_symbol": "ACAT2",
+        "alt_names": "acetyl-CoA acetyltransferase, cytosolic; acetoacetyl Coenzyme A thiolase; acetyl-CoA transferase-like protein; cytosolic acetoacetyl-CoA thiolase;",
+        "chromosome": "6",
+        "map_location": "6q25.3",
+        "summary": "The product of this gene is an enzyme involved in lipid metabolism, and it encodes cytosolic acetoacetyl-CoA thiolase. This gene shows complementary overlapping with the 3-prime region of the TCP1 gene in both mouse and human. These genes are encoded on opposite strands of DNA, as well as in opposite transcriptional orientation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row6": {
+        "gene_name": "solute carrier family 33 (acetyl-CoA transporter), member 1",
+        "mgp_id": "MGP003828",
+        "gene_id": "9197",
+        "gene_symbol": "SLC33A1",
+        "gene_synonyms": "AT1; AT-1; ACATN; SPG42; CCHLND;",
+        "alt_names": "acetyl-coenzyme A transporter 1;",
+        "chromosome": "3",
+        "map_location": "3q25.31",
+        "summary": "The protein encoded by this gene is required for the formation of O-acetylated (Ac) gangliosides. The encoded protein is predicted to contain 6 to 10 transmembrane domains, and a leucine zipper motif in transmembrane domain III. Defects in this gene have been reported to cause spastic paraplegia autosomal dominant type 42 (SPG42) in one Chinese family, but not in similar patients of European descent. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    },
+    "Row7": {
+        "gene_name": "acetyl-CoA acyltransferase 2",
+        "mgp_id": "MGP004244",
+        "gene_id": "10449",
+        "gene_symbol": "ACAA2",
+        "gene_synonyms": "DSAEC;",
+        "alt_names": "3-ketoacyl-CoA thiolase, mitochondrial; T1; acetyl-Coenzyme A acyltransferase 2; beta ketothiolase; beta-ketothiolase; mitochondrial 3-oxoacyl-CoA thiolase; mitochondrial 3-oxoacyl-Coenzyme A thiolase;",
+        "chromosome": "18",
+        "map_location": "18q21.1",
+        "summary": "The encoded protein catalyzes the last step of the mitochondrial fatty acid beta-oxidation spiral. Unlike most mitochondrial matrix proteins, it contains a non-cleavable amino-terminal targeting signal. [provided by RefSeq, Jul 2008]",
+        "taxid": "9606",
+        "species": "Human",
+        "species_long": "Homo sapiens"
+    }
+}

vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors.json

@@ -0,0 +1,74 @@
+{
+    "1": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "3"
+    },
+    "2": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:12MO | ROUX_EN_Y": "1"
+    },
+    "3": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:6MO | GASTRIC_BAND": "4"
+    },
+    "4": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "11"
+    },
+    "5": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "7"
+    },
+    "6": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "7"
+    },
+    "7": {
+        "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "12"
+    },
+    "8": {
+        "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "2"
+    },
+    "9": {
+        "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "2"
+    },
+    "10": {
+        "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "4"
+    },
+    "11": {
+        "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "2"
+    },
+    "12": {
+        "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "2"
+    },
+    "13": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "3"
+    },
+    "14": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:12MO | ROUX_EN_Y": "1"
+    },
+    "15": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:6MO | GASTRIC_BAND": "4"
+    },
+    "16": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "11"
+    },
+    "17": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "7"
+    },
+    "18": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "7"
+    },
+    "19": {
+        "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "12"
+    },
+    "20": {
+        "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "2"
+    },
+    "21": {
+        "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "2"
+    },
+    "22": {
+        "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "4"
+    },
+    "23": {
+        "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "2"
+    },
+    "24": {
+        "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "2"
+    }
+}