Testing new functions locally

man/string_parsing.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parsers.R
+\name{string_parsing}
+\alias{string_parsing}
+\title{Main parsing function}
+\usage{
+string_parsing(.data)
+}
+\arguments{
+\item{.data}{dataframe with parsed metadata}
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+This function will parse the data from the Image name and will return the metadata there contained
+The metadata will be then associated to the count file as well
+}

renv.lock

@@ -133,6 +133,30 @@
       ],
       "Hash": "c39fbec8a30d23e721980b8afb31984c"
     },
+    "bit": {
+      "Package": "bit",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "d242abec29412ce988848d0294b208fd"
+    },
+    "bit64": {
+      "Package": "bit64",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bit",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+    },
     "boot": {
       "Package": "boot",
       "Version": "1.3-28",
@@ -241,6 +265,16 @@
       ],
       "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
     },
+    "clipr": {
+      "Package": "clipr",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
+    },
     "colorspace": {
       "Package": "colorspace",
       "Version": "2.1-0",
@@ -577,6 +611,20 @@
       ],
       "Hash": "06230136b2d2b9ba5805e1963fa6e890"
     },
+    "hms": {
+      "Package": "hms",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "lifecycle",
+        "methods",
+        "pkgconfig",
+        "rlang",
+        "vctrs"
+      ],
+      "Hash": "b59377caa7ed00fa41808342002138f9"
+    },
     "isoband": {
       "Package": "isoband",
       "Version": "0.2.7",
@@ -872,6 +920,16 @@
       "Repository": "CRAN",
       "Hash": "a555924add98c99d2f411e37e7d25e9f"
     },
+    "prettyunits": {
+      "Package": "prettyunits",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
+    },
     "processx": {
       "Package": "processx",
       "Version": "3.8.3",
@@ -885,6 +943,20 @@
       ],
       "Hash": "82d48b1aec56084d9438dbf98087a7e9"
     },
+    "progress": {
+      "Package": "progress",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "crayon",
+        "hms",
+        "prettyunits"
+      ],
+      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
+    },
     "ps": {
       "Package": "ps",
       "Version": "1.7.6",
@@ -929,6 +1001,29 @@
       ],
       "Hash": "1bbc97f7d637ab3917c514a69047b2c1"
     },
+    "readr": {
+      "Package": "readr",
+      "Version": "2.1.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "clipr",
+        "cpp11",
+        "crayon",
+        "hms",
+        "lifecycle",
+        "methods",
+        "rlang",
+        "tibble",
+        "tzdb",
+        "utils",
+        "vroom"
+      ],
+      "Hash": "9de96463d2117f6ac49980577939dfb3"
+    },
     "rematch2": {
       "Package": "rematch2",
       "Version": "2.1.2",
@@ -1172,6 +1267,17 @@
       ],
       "Hash": "79540e5fcd9e0435af547d885f184fd5"
     },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+    },
     "utf8": {
       "Package": "utf8",
       "Version": "1.2.4",
@@ -1206,6 +1312,32 @@
       ],
       "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
     },
+    "vroom": {
+      "Package": "vroom",
+      "Version": "1.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bit64",
+        "cli",
+        "cpp11",
+        "crayon",
+        "glue",
+        "hms",
+        "lifecycle",
+        "methods",
+        "progress",
+        "rlang",
+        "stats",
+        "tibble",
+        "tidyselect",
+        "tzdb",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "390f9315bc0025be03012054103d227c"
+    },
     "waldo": {
       "Package": "waldo",
       "Version": "0.5.2",

tests/testthat/test_cases.R

@@ -45,4 +45,22 @@ test_that("Check that the config.txt is made and can be read", {
   expect_true(exists("list_of_relabeling"))
 })
 
-# WIP add for the regex in preprocessing
+# WIP add for the regex in processing the data
+# test_that("Check that parsig does work", {
+#
+#   Image1 <- "B516_Ascites_2023-11-25_DOC2020-12-14_CarboplatinPaclitaxel_100_uM_10_nM_Ecad_cCasp3_(series 01).tif"
+#   Image2 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
+#   Image3 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
+#   Image4 <- "B38_Eye_2023.11.10_DOC2023.10.05_GentamicinePaclitaxel_100_uM_10_nM_EpCAM_Ecad_cCasp3_(series 01).tif"
+#
+#   # make a dataframe of those images examples
+#   dt <- data.frame(
+#     Image = c(Image1, Image2, Image3, Image4),
+#     Example = c("Protocol", "Fake", "Fake", "Fake")
+#   )
+#
+#   # run parser
+#   dt1 <- DRUGSENS:::string_parsing(dt)
+#
+#   expect_true(exists("list_of_relabeling"))
+# })