| blob | a2008a2571deb65e228a7e8abaa3f7dad0e8ae40 |
1 ## prepare workspace\r
2 cat("\014") # clear console\r
3 setwd("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela")\r
4 rm(list=ls(all=T)) # remove r objects\r
5 ## Get data from ona\r
6 library(devtools)\r
7 update.packages("ona")\r
8 library(ona)\r
9 banana = onaDownload("BCMT_NM2017","seedtracker","megy","megy")\r
10 \r
11 library(dplyr)\r
12 library(tidyr)\r
13 library(stringr)\r
14 library(httr)\r
15 library(jsonlite)\r
16 library(RCurl)\r
17 library(data.table)\r
18 library(gmailr)\r
19 \r
20 ## ORGANIZE DATA\r
21 # FLOWERING DATA\r
22 flowerID = select(banana, "X_submission_time","X_submitted_by",contains("floweringID")) %>%\r
23 gather(flowering, flowerID, ends_with("floweringID"), na.rm = T)\r
24 flowerID$flowering <- NULL\r
25 flower <- as.data.frame(flowerID$flowerID)\r
26 flowerName = select(banana, ends_with("flowerName")) %>%\r
27 gather(flower, accession_name, ends_with("flowerName"), na.rm=T)\r
28 flowerName$flower <- NULL\r
29 datetime = as.data.frame(str_split_fixed(flowerID$X_submission_time, "T", 2))\r
30 flowerIDs = as.data.frame(c(datetime, flowerID, flower, flowerName))\r
31 flowerIDs$X_submission_time <- NULL\r
32 colnames(flowerIDs) = c("submit_date","submit_time","submitted_by","flowerID","flower","accession_name")\r
33 pSex <- select(banana, ends_with("plantSex")) %>%\r
34 gather(psex, sex, ends_with("plantSex"), na.rm = T)\r
35 pSex$psex <- NULL \r
36 floweringDate <- select(banana, ends_with("flowering_date")) %>%\r
37 gather(date, flowering_date, ends_with("flowering_date"), na.rm = T)\r
38 floweringDate$date <- NULL\r
39 flowered <- as.data.frame(c(flowerIDs, floweringDate, pSex))\r
40 fDate = as.Date(flowered$flowering_date)\r
41 fdateLimit = Sys.Date() - 7\r
42 floweringd = filter(flowered, fDate>=fdateLimit)\r
43 flowering <- floweringd[order(floweringd$flowering_date),]\r
44 floweringDF <- write.csv(flowering, file = "flowering.csv", row.names = F)\r
45 all.flowering <- write.csv(flowered, file = "all_flowering.csv", row.names = F)\r
46 \r
47 # FIRST POLLINATION\r
48 FPOLLN = select(banana, "X_submission_time","X_submitted_by",ends_with("_gps_latitude"),ends_with("_gps_longitude"), contains("FirstPollination"))\r
49 parent <- select(FPOLLN,"X_submission_time","X_submitted_by",ends_with("_gps_latitude"),ends_with("_gps_longitude"), ends_with("parent")) %>%\r
50 gather(parents, parentName, ends_with("parent"), na.rm = T)\r
51 parent$parents <- NULL\r
52 First.datetime = as.data.frame(str_split_fixed(parent$X_submission_time, "T", 2))\r
53 parentID = as.data.frame(str_split_fixed(parent$parentName, "/", 2))\r
54 colnames(parentID) <- c("mother", "father")\r
55 femaleID <- as.data.frame(parentID$mother)\r
56 female.acc.name = select(FPOLLN, ends_with("femaleName"))%>%\r
57 gather(female, mother.acc.name, ends_with("femaleName"), na.rm=T)\r
58 female.acc.name$female <- NULL\r
59 male.acc.name = select(FPOLLN, ends_with("maleAccName"))%>%\r
60 gather(male, father.acc.name, ends_with("maleAccName"), na.rm=T)\r
61 male.acc.name$male <- NULL\r
62 \r
63 parents = as.data.frame(c(First.datetime, parent, femaleID, parentID, female.acc.name, male.acc.name))\r
64 parents$X_submission_time <- NULL\r
65 firstDate <- select(FPOLLN, ends_with("firstpollination_date")) %>%\r
66 gather(date, firstpollination_date, ends_with("firstpollination_date"), na.rm = T)\r
67 firstDate$date <- NULL\r
68 cross <- select(FPOLLN, ends_with("crossID")) %>%\r
69 gather(cross, crossnumber, ends_with("crossID"), na.rm = T)\r
70 cross$cross <- NULL\r
71 crossID <- as.data.frame(cross$crossnumber)\r
72 first_pollination <- as.data.frame(c(parents, cross, firstDate, crossID))\r
73 \r
74 colnames(first_pollination) <- c("submission_date","submission_time","submitted_by","latitude","longitude","parentNames","femaleID",\r
75 "mother","father","mother_accessionName","father_accessionName","crossnumber","firstpollination_date","crossID")\r
76 firstpollination = as.data.frame(first_pollination[c(1:8,10,9,11:14)])\r
77 first <- write.csv(firstpollination, file = "firstpollination.csv", row.names = F)\r
78 \r
79 \r
80 # Repeat pollination\r
81 rpt = select(banana, "X_submission_time","X_submitted_by",contains("repeatpollination"))\r
82 \r
83 getCrossID = select(rpt, "X_submission_time","X_submitted_by", ends_with("getCrossID")) %>%\r
84 gather(cross, crossnumber, ends_with("getCrossID"), na.rm = T)\r
85 rptMaleID = select(rpt, ends_with("rptMaleID")) %>%\r
86 gather(rptMale, Male_plotNumber, ends_with("rptMaleID"), na.rm = T)\r
87 rptMale_AccName = select(rpt, ends_with("getMaleAccName")) %>%\r
88 gather(rptMale, Male_accessionName, ends_with("getMaleAccName"), na.rm = T)\r
89 rptPollnDate = select(rpt, ends_with("rptpollination_date")) %>%\r
90 gather(date, repeatPollinationDate, ends_with("rptpollination_date"), na.rm = T)\r
91 \r
92 repeatData <- as.data.frame(c(getCrossID,rptMaleID,rptMale_AccName, rptPollnDate))\r
93 repeatdf = select(repeatData,"X_submission_time","X_submitted_by","crossnumber","Male_plotNumber","Male_accessionName","repeatPollinationDate")\r
94 repeat.df = select(repeatData,"crossnumber","Male_plotNumber","Male_accessionName","repeatPollinationDate")\r
95 repeatdt = data.table(repeat.df)\r
96 repeatDT = as.data.frame(repeatdt[,number := 1:.N, by = crossnumber])\r
97 repeatDTwide = reshape(repeatDT,direction = "wide", idvar = "crossnumber", timevar = "number")\r
98 repeatID = data.frame(repeatDTwide$crossnumber)\r
99 colnames(repeatID) <- "repeatpollinationID"\r
100 repeatDT.wide <- data.frame(c(repeatID, repeatDTwide))\r
101 repeatpollnData <- write.csv(repeatDT.wide, file = "repeatpollination.csv", row.names = F)\r
102 \r
103 # HARVESTING\r
104 harVEST = select(banana, "X_submission_time","X_submitted_by",contains("harvesting"))\r
105 harvestedID = select(harVEST, "X_submission_time","X_submitted_by",ends_with("harvestID")) %>%\r
106 gather(id, crossnumber, ends_with("harvestID"),na.rm = T)\r
107 harvestID <- data.frame(harvestedID$crossnumber)\r
108 harvestdate = select(harVEST, ends_with("harvesting_date")) %>%\r
109 gather(date, harvesting_date, na.rm = T) %>% select(harvesting_date)\r
110 hDate = str_replace(harvestdate$harvesting_date, "-", "/")\r
111 harvestDATE = str_replace(hDate, "-", "/")\r
112 pollinated_date = select(harVEST, ends_with("pollinated_date")) %>%\r
113 gather(date, pollinated_date, na.rm=T) %>% select(pollinated_date) \r
114 pDate = str_replace(pollinated_date$pollinated_date, "-", "/")\r
115 pollinationDATE = str_replace(pDate, "-", "/")\r
116 pollination2Harvest = data.frame(pollinationDATE, harvestDATE)\r
117 pollination2Harvest$days2Maturity <- as.Date(as.character(pollination2Harvest$harvestDATE), format="%Y/%m/%d")-\r
118 as.Date(as.character(pollination2Harvest$pollinationDATE), format="%Y/%m/%d")\r
119 ripeningshed = select(banana, ends_with("taken_ripening_shed")) %>%\r
120 gather(shed, to_ripeningshed, ends_with("taken_ripening_shed"), na.rm = T)\r
121 harvest.datetime = as.data.frame(str_split_fixed(harvestedID$X_submission_time, "T", 2))\r
122 \r
123 harvested = as.data.frame(c(harvest.datetime,harvestedID, harvestID,harvestdate, pollination2Harvest, ripeningshed))\r
124 harvested$pollinationDATE <- NULL\r
125 harvested$harvestDATE <- NULL\r
126 harvested$X_submission_time <- NULL\r
127 harvestingdf = select(harvested,V1,V2,X_submitted_by, crossnumber,harvestedID.crossnumber, harvesting_date, days2Maturity,to_ripeningshed)\r
128 colnames(harvestingdf) = c("submission_date","submission_time","submitted_by","crossnumber", "harvestID", "harvesting_date","days_to_maturity","to_ripening_shed")\r
129 harvest = write.csv(harvestingdf, file = "harvesting.csv", row.names = F)\r
130 \r
131 # RIPENING\r
132 RIPE = select(banana, "X_submission_time","X_submitted_by",contains("ripening"))\r
133 ripenid = select(RIPE, "X_submission_time","X_submitted_by",ends_with("ripenedID")) %>%\r
134 gather(ids, crossnumber, ends_with("ripenedID"), na.rm = T)\r
135 ripenID <- data.frame(ripenid$crossnumber)\r
136 getHarDate = select(RIPE, ends_with("Harvest_date")) %>%\r
137 gather(date, dateHarvested, ends_with("Harvest_date"), na.rm = T)\r
138 dateHarv = str_replace(getHarDate$dateHarvested, "-", "/")\r
139 dateHarvest = str_replace(dateHarv, "-", "/")\r
140 \r
141 ripendate = select(RIPE, ends_with("ripening_date")) %>% \r
142 gather(date, ripen_date, ends_with("ripening_date"), na.rm = T)\r
143 dateRipe = str_replace(ripendate$ripen_date, "-", "/")\r
144 dateRipened = str_replace(dateRipe, "-", "/")\r
145 Harvest2Ripening = data.frame(dateHarvest, dateRipened)\r
146 Harvest2Ripening$days_harvest_ripening <- as.Date(as.character(Harvest2Ripening$dateRipened), format="%Y/%m/%d")-\r
147 as.Date(as.character(Harvest2Ripening$dateHarvest), format="%Y/%m/%d")\r
148 Harvest2Ripening$dateRipened <- NULL\r
149 Harvest2Ripening$dateHarvest <- NULL\r
150 ripen.datetime = as.data.frame(str_split_fixed(ripenid$X_submission_time, "T", 2))\r
151 ripened = as.data.frame(c(ripen.datetime, ripenid, ripenID,ripendate, Harvest2Ripening))\r
152 ripened$X_submission_time <- NULL\r
153 ripeningdf = select(ripened, V1,V2,X_submitted_by,crossnumber, ripenid.crossnumber, ripen_date, days_harvest_ripening)\r
154 colnames(ripeningdf) = c("submission_date","submission_time","submitted_by","crossnumber", "ripenID","ripen_date","days_harvest_ripening")\r
155 \r
156 ripening = write.csv(ripeningdf, file = "ripening.csv", row.names = F) \r
157 \r
158 # EXTRACTION\r
159 EXTRACTION = select(banana, "X_submission_time", "X_submitted_by", contains("seedExtraction"))\r
160 extractid = select(EXTRACTION, "X_submission_time", "X_submitted_by", ends_with("extractionID")) %>%\r
161 gather(extract, crossnumber,ends_with("extractionID"), na.rm = T)\r
162 extractID <- data.frame(extractid$crossnumber)\r
163 total = select(banana, ends_with("totalSeedsExtracted")) %>% \r
164 gather(total, number_seeds, ends_with("totalSeedsExtracted"), na.rm = T)\r
165 extractdate = select(EXTRACTION, ends_with("extraction_date")) %>% \r
166 gather(date, seed_extraction_date, ends_with("extraction_date"),na.rm = T)\r
167 dateExtract = str_replace(extractdate$seed_extraction_date, "-", "/")\r
168 dateExtrd = str_replace(dateExtract, "-", "/")\r
169 \r
170 DateRipen = select(EXTRACTION, ends_with("ripened_date"))%>%\r
171 gather(date, DateRipen, ends_with("ripened_date"), na.rm=T)\r
172 dateRip = str_replace(DateRipen$DateRipen, "-", "/")\r
173 dateRip = str_replace(dateRip, "-", "/")\r
174 ripen2Extract = data.frame(dateExtrd, dateRip)\r
175 ripen2Extract$days_ripening_extraction <- as.Date(as.character(ripen2Extract$dateExtrd), format="%Y/%m/%d")-\r
176 as.Date(as.character(ripen2Extract$dateRip), format="%Y/%m/%d")\r
177 ripen2Extract$dateExtrd <- NULL\r
178 ripen2Extract$dateRip <- NULL\r
179 extr.datetime = as.data.frame(str_split_fixed(extractid$X_submission_time, "T", 2))\r
180 extracted = as.data.frame(c(extr.datetime,extractid, extractID,extractdate, total, ripen2Extract))\r
181 extracted$X_submission_time <- NULL\r
182 extractiondf = select(extracted, V1, V2,X_submitted_by,crossnumber,extractid.crossnumber, seed_extraction_date, number_seeds, days_ripening_extraction)\r
183 colnames(extractiondf) = c("submission_date","submission_time","submitted_by", "crossnumber", "extractID","seed_extraction_date", "number_seeds", \r
184 "days_ripening_extraction")\r
185 extractd = write.csv(extractiondf, file = "extraction.csv", row.names = F)\r
186 \r
187 \r
188 ## STOLEN\r
189 # mother\r
190 statuses = select(banana, "X_submission_time","X_submitted_by",contains("plantstatus"))\r
191 stolen.type = select(statuses, ends_with("plant_status")) %>%\r
192 gather(type, status, ends_with("plant_status"), na.rm = T) %>%\r
193 filter(status=="bunch_stolen")\r
194 mother.stolenID = select(statuses, "X_submission_time","X_submitted_by",ends_with("stolen_statusID"))%>%\r
195 gather(mother.status, motherID, ends_with("stolen_statusID"), na.rm = T)\r
196 mother.stolen.ID <- data.frame(mother.stolenID$motherID)\r
197 stolendate = select(statuses, ends_with("stolen_date")) %>%\r
198 gather(date, stolen_date, ends_with("stolen_date"), na.rm = T)\r
199 \r
200 stolen.status.datetime = as.data.frame(str_split_fixed(mother.stolenID$X_submission_time, "T", 2))\r
201 mother.stolen.status = as.data.frame(c(stolen.status.datetime, mother.stolenID, mother.stolen.ID, stolendate, stolen.type))\r
202 mother.stolen.status$X_submission_time <- NULL\r
203 mother.stolendf = select(mother.stolen.status, V1,V2,X_submitted_by, motherID, mother.stolenID.motherID, stolen_date, status)\r
204 colnames(mother.stolendf) = c("submission_date","submission_time","submitted_by","ID", "statusID","date", "status")\r
205 \r
206 # stolen cross\r
207 cross.stolenID = select(statuses, "X_submission_time","X_submitted_by",ends_with("stolenBunch_statusID"))%>%\r
208 gather(cross.status, crossID, ends_with("stolenBunch_statusID"), na.rm = T)\r
209 cross.stolen.ID <- data.frame(cross.stolenID$crossID)\r
210 if(dim(mother.stolendf)[1]>0 & dim(cross.stolenID)[1]>0){\r
211 cross.status.datetime = as.data.frame(str_split_fixed(cross.stolenID$X_submission_time, "T", 2))\r
212 cross.stolen.status = as.data.frame(c(cross.status.datetime, cross.stolenID, cross.stolen.ID, stolendate, stolen.type))\r
213 cross.stolen.status$X_submission_time <- NULL\r
214 cross.stolendf = select(cross.stolen.status, V1,V2,X_submitted_by, crossID, cross.stolenID.crossID, stolen_date, status)\r
215 colnames(cross.stolendf) = c("submission_date","submission_time","submitted_by","ID", "statusID","date", "status")\r
216 stolendf = rbind(mother.stolendf, cross.stolendf)\r
217 } else {\r
218 stolendf = mother.stolendf\r
219 }\r
220 \r
221 ########################################################\r
222 \r
223 # Fallen mother\r
224 fallen.type = select(statuses, ends_with("plant_status")) %>%\r
225 gather(type, status, ends_with("plant_status"), na.rm = T) %>%\r
226 filter(status=="fallen")\r
227 mother.fallenID = select(statuses, "X_submission_time","X_submitted_by",ends_with("fallen_statusID"))%>%\r
228 gather(mother.status, motherID, ends_with("fallen_statusID"), na.rm = T)\r
229 mother.fallen.ID <- data.frame(mother.fallenID$motherID)\r
230 fallendate = select(statuses, ends_with("fallen_date")) %>%\r
231 gather(date, fallen_date, ends_with("fallen_date"), na.rm = T)\r
232 \r
233 fallen.status.datetime = as.data.frame(str_split_fixed(mother.fallenID$X_submission_time, "T", 2))\r
234 mother.fallen.status = as.data.frame(c(fallen.status.datetime, mother.fallenID, mother.fallen.ID, fallendate, fallen.type))\r
235 mother.fallen.status$X_submission_time <- NULL\r
236 mother.fallendf = select(mother.fallen.status, V1,V2,X_submitted_by, motherID, mother.fallenID.motherID, fallen_date, status)\r
237 colnames(mother.fallendf) = c("submission_date","submission_time","submitted_by","ID", "statusID","date", "status")\r
238 \r
239 # fallen cross\r
240 cross.fallenID = select(statuses, "X_submission_time","X_submitted_by",ends_with("fallenBunch_statusID"))%>%\r
241 gather(cross.status, crossID, ends_with("fallenBunch_statusID"), na.rm = T)\r
242 cross.fallen.ID <- data.frame(cross.fallenID$crossID)\r
243 if(dim(mother.fallendf)[1]>0 & dim(cross.fallenID)[1]>0){\r
244 cross.status.datetime = as.data.frame(str_split_fixed(cross.fallenID$X_submission_time, "T", 2))\r
245 cross.fallen.status = as.data.frame(c(cross.status.datetime, cross.fallenID, cross.fallen.ID, fallendate, fallen.type))\r
246 cross.fallen.status$X_submission_time <- NULL\r
247 cross.fallendf = select(cross.fallen.status, V1,V2,X_submitted_by, crossID, cross.fallenID.crossID, fallen_date, status)\r
248 colnames(cross.fallendf) = c("submission_date","submission_time","submitted_by","ID", "statusID","date", "status")\r
249 fallendf = rbind(mother.fallendf, cross.fallendf)\r
250 } else {\r
251 fallendf = mother.fallendf\r
252 }\r
253 \r
254 # Other statuses\r
255 target = c("has_disease","died","unusual","okay")\r
256 othertype = select(statuses, ends_with("plant_status")) %>%\r
257 gather(type, status, ends_with("plant_status"), na.rm = T) %>%\r
258 filter(status %in% target)\r
259 otherID = select(statuses, "X_submission_time","X_submitted_by",ends_with("plant_statusID"))%>%\r
260 gather(status, ID, ends_with("plant_statusID"), na.rm = T)\r
261 other.ID <- data.frame(otherID$ID)\r
262 other.date = select(statuses, ends_with("status_Date")) %>%\r
263 gather(sdate, date, ends_with("status_Date"), na.rm = T)\r
264 \r
265 otherstatus.datetime = as.data.frame(str_split_fixed(otherID$X_submission_time, "T", 2))\r
266 otherstatus = as.data.frame(c(otherstatus.datetime, other.date, otherID, other.ID, other.date, othertype))\r
267 otherstatus$X_submission_time <- NULL\r
268 otherdf = select(otherstatus, V1,V2,X_submitted_by, ID, otherID.ID, date, status.1)\r
269 colnames(otherdf) = c("submission_date","submission_time","submitted_by","ID", "statusID","date", "status")\r
270 \r
271 statusDF = rbind(stolendf, fallendf, otherdf)\r
272 \r
273 ## LAB\r
274 # RESCUE\r
275 good = select(banana, ends_with("goodSeeds")) %>%\r
276 gather(good, good_seeds,ends_with("goodSeeds"), na.rm = T)\r
277 bad = select(banana, ends_with("badSeeds")) %>%\r
278 gather(bad, bad_seeds, ends_with("badSeeds"),na.rm = T)\r
279 RESCUED = select(banana, "X_submission_time","X_submitted_by",contains("embryoRescue"))\r
280 rescueid = select(RESCUED, "X_submission_time","X_submitted_by",ends_with("embryorescueID"))%>%\r
281 gather(id, crossnumber,ends_with("embryorescueID"), na.rm = T)\r
282 rescueID <- data.frame(rescueid$crossnumber)\r
283 rescueseeds = select(RESCUED, ends_with("embryorescue_seeds")) %>%\r
284 gather(seeds, number_rescued, ends_with("embryorescue_seeds"),na.rm = T)\r
285 rescuedate = select(RESCUED, ends_with("embryorescue_date"))%>%\r
286 gather(id, rescue_date,ends_with("embryorescue_date"), na.rm = T)\r
287 date_Resc = str_replace(rescuedate$rescue_date, "-", "/")\r
288 dateResc = str_replace(date_Resc, "-", "/")\r
289 \r
290 dateEXTRD = select(RESCUED, ends_with("extracted_date")) %>%\r
291 gather(date, extract_date, ends_with("extracted_date"), na.rm = T)\r
292 date_EXTRD = str_replace(dateEXTRD$extract_date, "-", "/")\r
293 dateEXTRD = str_replace(date_EXTRD, "-", "/")\r
294 Extract2Rescue = data.frame(dateEXTRD, dateResc)\r
295 Extract2Rescue$days_extraction_rescue <- as.Date(as.character(Extract2Rescue$dateResc), format="%Y/%m/%d")-\r
296 as.Date(as.character(Extract2Rescue$dateEXTRD), format="%Y/%m/%d")\r
297 Extract2Rescue$dateEXTRD <- NULL\r
298 Extract2Rescue$dateResc <-NULL\r
299 resc.datetime = as.data.frame(str_split_fixed(rescueid$X_submission_time, "T", 2))\r
300 rescued = as.data.frame(c(resc.datetime,rescueid,rescueID,good, bad, rescuedate, rescueseeds, Extract2Rescue))\r
301 rescued$X_submission_time <- NULL\r
302 rescuingdf = select(rescued, V1, V2,X_submitted_by,crossnumber, rescueid.crossnumber, good_seeds, bad_seeds, number_rescued, rescue_date, days_extraction_rescue)\r
303 colnames(rescuingdf) = c("submission_date","submission_time","submitted_by","crossnumber", "rescueID","good_seeds","badseeds","number_rescued", "rescue_date", "days_extraction_rescue")\r
304 rescueed = write.csv(rescuingdf, file = "rescued.csv", row.names = F)\r
305 \r
306 # 2 WEEKS GERMINATION\r
307 week2Germination = select(banana,"X_submission_time","X_submitted_by", contains("embryo_germinatn_after_2wks") )\r
308 twowksID = select(week2Germination, "X_submission_time","X_submitted_by",ends_with("germinating_2wksID")) %>%\r
309 gather(germinating, crossnumber, ends_with("germinating_2wksID"), na.rm = T)\r
310 week2ID <- data.frame(twowksID$crossnumber)\r
311 active2wks = select(week2Germination, ends_with("actively_2wks")) %>%\r
312 gather(active, actively_germination_after_two_weeks, ends_with("actively_2wks"),na.rm = T)\r
313 twowksDate = select(week2Germination, ends_with("2wks_date")) %>% \r
314 gather(date, germination_after_2weeks_date, ends_with("2wks_date"),na.rm = T)\r
315 date2wk = str_replace(twowksDate$germination_after_2weeks_date, "-", "/")\r
316 date2wks = str_replace(date2wk, "-", "/")\r
317 rescDate = select(week2Germination, ends_with("rescued_date")) %>%\r
318 gather(date, rescuedDate, ends_with("rescued_date"), na.rm = T)\r
319 dateERescue = str_replace(rescDate$rescuedDate, "-", "/")\r
320 dateERescued = str_replace(dateERescue, "-", "/")\r
321 \r
322 Rescue_2wks = data.frame(date2wks, dateERescued)\r
323 Rescue_2wks$days_rescue_2wksGermination <- as.Date(as.character(Rescue_2wks$date2wks), format="%Y/%m/%d")-\r
324 as.Date(as.character(Rescue_2wks$dateERescued), format="%Y/%m/%d")\r
325 Rescue_2wks$date2wks <- NULL\r
326 Rescue_2wks$dateERescued <- NULL\r
327 two.datetime = as.data.frame(str_split_fixed(twowksID$X_submission_time, "T", 2))\r
328 germination2weeks = as.data.frame(c(two.datetime,twowksID, week2ID, twowksDate, active2wks, Rescue_2wks))\r
329 germination2weeks$X_submission_time <- NULL\r
330 germination2weeksdf = select(germination2weeks, V1,V2,X_submitted_by,crossnumber,twowksID.crossnumber, germination_after_2weeks_date, actively_germination_after_two_weeks, days_rescue_2wksGermination)\r
331 colnames(germination2weeksdf) = c("submission_date","submission_time","submitted_by","crossnumber", "week2ID","germination_after_2weeks_date", \r
332 "actively_germination_after_two_weeks","days_rescue_2weeksGermination")\r
333 germ2wks = write.csv(germination2weeksdf, file = "germinating2weeks.csv", row.names = F)\r
334 \r
335 # 6 weeks GERMINATION\r
336 week6 = select(banana,"X_submission_time","X_submitted_by",contains("embryo_germinatn_after_6weeks"))\r
337 week6ID = select(week6, "X_submission_time","X_submitted_by", ends_with("germinating_6weeksID"))%>%\r
338 gather(germinating, crossnumber, ends_with("germinating_6weeksID"),na.rm = T)\r
339 week6.ID <- data.frame(week6ID$crossnumber)\r
340 active6weeks = select(week6, ends_with("actively_6weeks")) %>%\r
341 gather(active, actively_germination_after_6weeks, ends_with("actively_6weeks"),na.rm = T)\r
342 \r
343 week6Date = select(week6, ends_with("germinating_6weeks_date")) %>%\r
344 gather(date, germination_after_6weeks_date, ends_with("germinating_6weeks_date"),na.rm = T)\r
345 date6weeks = str_replace(week6Date$germination_after_6weeks_date, "-", "/")\r
346 date.6weeks = str_replace(date6weeks, "-", "/")\r
347 germ2wks_date = select(week6, ends_with("germinated_2wksdate")) %>%\r
348 gather(date, germ2wksdate, ends_with("germinated_2wksdate"), na.rm = T)\r
349 germ2wkDate = str_replace(germ2wks_date$germ2wksdate, "-","/")\r
350 germinated2wksDate = str_replace(germ2wkDate,"-","/")\r
351 Germination_2wks_6weeks = data.frame(germinated2wksDate, date.6weeks)\r
352 Germination_2wks_6weeks$days_2weeks_6weeks_Germination <- as.Date(as.character(Germination_2wks_6weeks$date.6weeks), format="%Y/%m/%d")-\r
353 as.Date(as.character(Germination_2wks_6weeks$germinated2wksDate), format="%Y/%m/%d")\r
354 Germination_2wks_6weeks$germinated2wksDate <- NULL\r
355 Germination_2wks_6weeks$dateOneM <- NULL\r
356 week6.datetime = as.data.frame(str_split_fixed(week6ID$X_submission_time, "T", 2))\r
357 germination6weeks = as.data.frame(c(week6.datetime,week6ID, week6.ID, week6Date, active6weeks, Germination_2wks_6weeks))\r
358 germination6weeks$X_submission_time <- NULL\r
359 germination6weeksdf = select(germination6weeks,V1, V2,X_submitted_by,crossnumber,week6ID.crossnumber, germination_after_6weeks_date, actively_germination_after_6weeks, days_2weeks_6weeks_Germination)\r
360 colnames(germination6weeksdf) = c("submission_date","submission_time","submitted_by","crossnumber", "week6ID","germination_after_6weeks_date",\r
361 "actively_germination_after_6weeks", "days_2weeksGermination_6weeksGermination")\r
362 germ6weeks = write.csv(germination6weeksdf, file = "germinating6weeks.csv", row.names = F)\r
363 \r
364 # SUBCULTURE\r
365 SUBCT = select(banana, "X_submission_time","X_submitted_by", contains("subculturing"))\r
366 subcultureid = select(SUBCT, "X_submission_time","X_submitted_by", ends_with("subcultureID"))%>%\r
367 gather(ids, crossnumber, ends_with("subcultureID"), na.rm = T)\r
368 subcultureID <- data.frame(subcultureid$crossnumber)\r
369 subcdate = select(SUBCT, ends_with("subculture_date")) %>%\r
370 gather(date, subculture_date, ends_with("subculture_date"),na.rm = T)\r
371 subDate = str_replace(subcdate$subculture_date, "-","/")\r
372 subdDate = str_replace(subDate,"-","/")\r
373 week6Gdate = select(SUBCT, ends_with("germinated_6weeksdate")) %>%\r
374 gather(date, week6germDate, ends_with("germinated_6weeksdate"), na.rm = T)\r
375 week6Date = str_replace(week6Gdate$week6germDate, "-","/")\r
376 week6.Date = str_replace(week6Date,"-","/")\r
377 week6Germ_subculture = data.frame(subdDate, week6.Date)\r
378 week6Germ_subculture$days_6weeks_Germination_subculture <- as.Date(as.character(week6Germ_subculture$subdDate), format="%Y/%m/%d")-\r
379 as.Date(as.character(week6Germ_subculture$week6.Date), format="%Y/%m/%d")\r
380 week6Germ_subculture$subdDate <- NULL\r
381 week6Germ_subculture$monthDate <- NULL\r
382 subcultures = select(SUBCT, ends_with("multiplicationNumber")) %>% \r
383 gather(date, subcultures,ends_with("multiplicationNumber"), na.rm = T)\r
384 sub.datetime = as.data.frame(str_split_fixed(subcultureid$X_submission_time, "T", 2))\r
385 subculturin = as.data.frame(c(sub.datetime, subcultureid, subcultureID, subcdate, subcultures, week6Germ_subculture))\r
386 subculturin$X_submission_time <- NULL\r
387 subculturingdf = select(subculturin, V1, V2, X_submitted_by,crossnumber, subcultureid.crossnumber, subculture_date, subcultures, days_6weeks_Germination_subculture)\r
388 colnames(subculturingdf) = c("submision_date","submission_time","submitted_by","crossnumber","subcultureID", "subculture_date","subcultures", "days_6weeks_Germination_subculture")\r
389 #multiplication = select(subculture, ends_with("multiplicationID"))\r
390 subdata = write.csv(subculturingdf, file = "subculture.csv", row.names = F)\r
391 \r
392 ## SUBPLANTS\r
393 if (is.na(SUBCT$Laboratory.subculturing.subcultureID)){\r
394 crossnumber = NA\r
395 plantletID = NA\r
396 subculture = NA\r
397 subculture_date = NA\r
398 subIDs = cbind(crossnumber,plantletID, subculture, subculture_date)\r
399 colnames(subIDs) = c("crossnumber","plantletID", "subculture","subculture_date")\r
400 }else{\r
401 subplants = select(SUBCT,ends_with("subculture_date"), ends_with("multiplicationID"))%>%\r
402 gather(plantlets, subplants, ends_with("multiplicationID"), na.rm=T)\r
403 subplants$plantlets <- NULL\r
404 subplants$Laboratory.subculturing.subculture_date <- NULL\r
405 subID = data.frame(str_sub(subplants$subplants, 1, str_length(subplants$subplants)-4))\r
406 subIDplants = data.frame(c(subID, subplants))\r
407 subIDp = subIDplants[,c(1,2,5)]\r
408 colnames(subIDp) = c("crossnumber","subculture_date", "subculture")\r
409 subIDp$plantletID <- subIDp$subculture \r
410 subIDs= subIDp[,c(1,4,3,2)]\r
411 }\r
412 subplants = write.csv(subIDs, file = "subplants.csv", row.names = F)\r
413 \r
414 # ROOTING\r
415 ROOT = select(banana,"X_submission_time","X_submitted_by",contains("rooting"))\r
416 rootid = select(ROOT, "X_submission_time","X_submitted_by", ends_with("rootingID")) %>% \r
417 gather(id, plantletID, ends_with("rootingID"),na.rm = T)\r
418 rootID <- data.frame(rootid$plantletID)\r
419 root.datetime = as.data.frame(str_split_fixed(rootid$X_submission_time, "T", 2))\r
420 \r
421 rootdate = select(ROOT, ends_with("rooting_date")) %>%\r
422 gather(date, date_rooting, ends_with("rooting_date"),na.rm = T)\r
423 rootDate = str_replace(rootdate$date_rooting, "-","/")\r
424 rDate = str_replace(rootDate,"-","/")\r
425 \r
426 sub_date = select(ROOT, ends_with("getSubDate"))%>%\r
427 gather(date, date_subcultured, ends_with("getSubDate"), na.rm = T)\r
428 subDate = str_replace(sub_date$date_subcultured, "-","/")\r
429 sub.date = str_replace(subDate,"-","/")\r
430 \r
431 subculture_rooting = data.frame(rDate, sub.date)\r
432 subculture_rooting$days_subculture_rooting <- as.Date(as.character(subculture_rooting$rDate), format="%Y/%m/%d")-\r
433 as.Date(as.character(subculture_rooting$sub.date), format="%Y/%m/%d")\r
434 subculture_rooting$rDate <- NULL\r
435 subculture_rooting$sub.date <- NULL\r
436 \r
437 rootin = as.data.frame(c(root.datetime,rootid, rootID, rootdate, subculture_rooting))\r
438 rootin$X_submission_time <- NULL\r
439 rootingdf = select(rootin, V1, V2,X_submitted_by,plantletID, rootid.plantletID, date_rooting, days_subculture_rooting )\r
440 colnames(rootingdf) = c("submission_date","submission_time","submitted_by","plantletID","rootID", "date_rooting", "days_subculture_rooting")\r
441 rooted = write.csv(rootingdf, file = "rooting.csv", row.names = F)\r
442 \r
443 \r
444 # SCREEN HOUSE\r
445 HOUSE = select(banana, "X_submission_time","X_submitted_by", contains("screenhouse"))\r
446 transferscrnhseid = select(HOUSE,"X_submission_time","X_submitted_by", ends_with("screenhseID")) %>%\r
447 gather(id, plantletID,ends_with("screenhseID"), na.rm = T)\r
448 transferscrnhseID <- data.frame(transferscrnhseid$plantletID)\r
449 transferdate = select(HOUSE, ends_with("screenhse_transfer_date")) %>% \r
450 gather(date, date_of_transfer_to_screenhse,ends_with("screenhse_transfer_date"), na.rm = T)\r
451 \r
452 dateHSE = str_replace(transferdate$date_of_transfer_to_screenhse, "-", "/")\r
453 dateHSED = str_replace(dateHSE, "-", "/")\r
454 rootedDate = select(HOUSE, ends_with("rooted_date")) %>%\r
455 gather(date, rootdate, ends_with("rooted_date"), na.rm = T)\r
456 dateRTD = str_replace(rootedDate$rootdate, "-", "/")\r
457 dateROOTED = str_replace(dateRTD, "-", "/")\r
458 rooting2Screenhse = data.frame(dateROOTED, dateHSED)\r
459 rooting2Screenhse$days_rooting_screenhse <- as.Date(as.character(rooting2Screenhse$dateHSED), format="%Y/%m/%d")-\r
460 as.Date(as.character(rooting2Screenhse$dateROOTED), format="%Y/%m/%d")\r
461 rooting2Screenhse$dateROOTED <- NULL\r
462 rooting2Screenhse$dateHSED <- NULL\r
463 trans.datetime = as.data.frame(str_split_fixed(transferscrnhseid$X_submission_time, "T", 2))\r
464 transferscreenhse = as.data.frame(c(trans.datetime,transferscrnhseid, transferscrnhseID, transferdate, rooting2Screenhse))\r
465 transferscreenhse$X_submission_time <- NULL\r
466 screenhsedf = select(transferscreenhse, V1, V2,X_submitted_by,plantletID,transferscrnhseid.plantletID, date_of_transfer_to_screenhse,days_rooting_screenhse) #transfer to screenhsedf\r
467 colnames(screenhsedf) = c("submission_date","submission_time","submitted_by","plantletID", "transferscrnhseID","screenhse_transfer_date","days_rooting_screenhse")\r
468 screenhse = write.csv(screenhsedf, file = "screenhouse.csv", row.names = F)\r
469 \r
470 # Hardening\r
471 HARD = select(banana, "X_submission_time","X_submitted_by", contains("hardening"))\r
472 hardenedid = select(HARD,"X_submission_time","X_submitted_by", ends_with("hardeningID")) %>%\r
473 gather(id, plantletID, ends_with("hardeningID"),na.rm = T)\r
474 hardenID <- data.frame(hardenedid$plantletID)\r
475 hardeneddate = select(HARD, ends_with("hardening_date")) %>% \r
476 gather(date, hardening_date,ends_with("hardening_date"), na.rm = T)\r
477 dateHARD = str_replace(hardeneddate$hardening_date, "-", "/")\r
478 dateHARDENED = str_replace(dateHARD, "-", "/")\r
479 \r
480 screenhseDATE = select(HARD, ends_with("screenhsed_date")) %>%\r
481 gather(date, screendate, ends_with("screenhsed_date"), na.rm = T)\r
482 dateSHSE = str_replace(screenhseDATE$screendate, "-", "/")\r
483 dateSHSED = str_replace(dateSHSE, "-", "/")\r
484 screenhse2Hardening = data.frame(dateHARDENED, dateSHSED)\r
485 screenhse2Hardening$days_scrnhse_hardening <- as.Date(as.character(screenhse2Hardening$dateHARDENED), format="%Y/%m/%d")-\r
486 as.Date(as.character(screenhse2Hardening$dateSHSED), format="%Y/%m/%d")\r
487 screenhse2Hardening$dateHARDENED <- NULL\r
488 screenhse2Hardening$dateSHSED <- NULL\r
489 harden.datetime = as.data.frame(str_split_fixed(hardenedid$X_submission_time, "T", 2))\r
490 hardening = as.data.frame(c(harden.datetime,hardenedid,hardenID, hardeneddate, screenhse2Hardening))\r
491 hardening$X_submission_time <- NULL\r
492 hardeningdf = select(hardening, V1, V2, X_submitted_by, plantletID, hardenedid.plantletID,hardening_date, days_scrnhse_hardening) ## hardening\r
493 colnames(hardeningdf) = c("submission_date","submission_time","submitted_by","plantletID","hardenID", "hardening_date", "days_scrnhse_hardening")\r
494 hardenned = write.csv(hardeningdf, file = "hardening.csv", row.names = F)\r
495 \r
496 # Open field\r
497 OPEN = select(banana,"X_submission_time","X_submitted_by", contains("transplant_openfield"))\r
498 openfield_ID = select(OPEN, "X_submission_time","X_submitted_by",ends_with("openfieldID")) %>%\r
499 gather(id, plantletID,ends_with("openfieldID"), na.rm = T)\r
500 openfieldID <- data.frame(openfield_ID$plantletID)\r
501 opendate = select(OPEN, ends_with("transplanting_date")) %>%\r
502 gather(date, date_of_transfer_to_openfield, ends_with("transplanting_date"),na.rm = T)\r
503 dateOPEN = str_replace(opendate$date_of_transfer_to_openfield, "-", "/")\r
504 dateOPENFD = str_replace(dateOPEN, "-", "/")\r
505 \r
506 dateHardd = select(OPEN, ends_with("hardened_date"))%>%\r
507 gather(date, hard_date, ends_with("hardened_date"), na.rm = T)\r
508 dateHarder = str_replace(dateHardd$hard_date, "-","/")\r
509 dateHD = str_replace(dateHarder, "-","/")\r
510 harden2OField = data.frame(dateOPENFD, dateHD)\r
511 harden2OField$days_hardening_openfield <- as.Date(as.character(harden2OField$dateOPENFD), format="%Y/%m/%d")-\r
512 as.Date(as.character(harden2OField$dateHD), format="%Y/%m/%d")\r
513 harden2OField$dateOPENFD <- NULL\r
514 harden2OField$dateHD <- NULL\r
515 open.datetime = as.data.frame(str_split_fixed(openfield_ID$X_submission_time, "T", 2))\r
516 openfieldtransfer = as.data.frame(c(open.datetime,openfield_ID,openfieldID, opendate, harden2OField))\r
517 openfieldtransfer$X_submission_time <- NULL\r
518 openfieldtransferdf = select(openfieldtransfer,V1, V2, X_submitted_by, plantletID,openfield_ID.plantletID,date_of_transfer_to_openfield, days_hardening_openfield) #to open field\r
519 colnames(openfieldtransferdf) = c("submission_date","submission_time","submitted_by","plantletID", "openfieldID","date_of_transfer_to_openfield",\r
520 "days_hardening_openfield")\r
521 openfd = write.csv(openfieldtransferdf, file = "openfield.csv", row.names = F)\r
522 \r
523 # Screenhouse status\r
524 sstatus = select(banana, "X_submission_time","X_submitted_by", contains("screenhse_status"))\r
525 sstatusDate = select(sstatus, ends_with("scrnhsestatus_Date"))%>%\r
526 gather(sdate,date, ends_with("scrnhsestatus_Date"), na.rm = T)\r
527 sstatusDate$sdate <-NULL\r
528 sstatusID = select(sstatus, "X_submission_time","X_submitted_by", ends_with("scrnhse_statusID"))%>%\r
529 gather(ssID, statusID, ends_with("scrnhse_statusID"), na.rm = T)\r
530 sstatusID$ssID <- NULL\r
531 sstatusID$sstatus_datetime = as.data.frame(str_split_fixed(sstatusID$X_submission_time, "T", 2))\r
532 sstatusID$X_submission_time <- NULL\r
533 s.status = select(sstatus, ends_with("scrnhseStatus"))%>%\r
534 gather(sstatus, status, ends_with("scrnhseStatus"), na.rm = T)\r
535 s.status$sstatus <- NULL\r
536 scrnhse.status = data.frame(c(sstatusID, sstatusDate, s.status))\r
537 scrnhse.status$ID = scrnhse.status$statusID\r
538 colnames(scrnhse.status) = c("submitted_by", "statusID", "submission_date","submission_time","date","status","ID")\r
539 select(scrnhse.status, "submission_date","submission_time","submitted_by","ID","statusID","date","status")\r
540 \r
541 merged_status = rbind(statusDF, scrnhse.status)\r
542 merged.status = write.csv(merged_status, file = "status.csv", row.names = F)\r
543 \r
544 # Contamination\r
545 ContaminID <- select(banana, "X_submission_time","X_submitted_by",ends_with("econtaminationID")) %>%\r
546 gather(contamination, crossnumber, ends_with("econtaminationID"), na.rm = T)\r
547 contaminationID <- data.frame(ContaminID$crossnumber)\r
548 ContaminDate <- select(banana, ends_with("contamination_date")) %>%\r
549 gather(date, contamination_date, ends_with("contamination_date"), na.rm = T)\r
550 contam.datetime = as.data.frame(str_split_fixed(ContaminID$X_submission_time, "T", 2))\r
551 contaminated = select(banana, ends_with("contaminated")) %>%\r
552 gather(contamination, contaminated, ends_with("contaminated"), na.rm=T)\r
553 \r
554 contamination <- as.data.frame(c(contam.datetime,ContaminID, contaminationID, ContaminDate, contaminated)) %>%\r
555 select(V1,V2,"X_submitted_by", crossnumber,ContaminID.crossnumber, contamination_date, contaminated)\r
556 colnames(contamination) <- c("submission_date","submission_time","submitted_by","crossnumber","contaminationID","contamination_date","contamination")\r
557 contamination$time <- NULL\r
558 contamin <- write.csv(contamination, file = "contamination.csv", row.names = F)\r
559 \r
560 ## ALL DATA\r
561 allbanana = list(firstpollination, repeatDT.wide, harvestingdf[,4:8], ripeningdf[,4:7], extractiondf[,4:8], rescuingdf[,4:10], germination2weeksdf[,4:8],\r
562 germination6weeksdf[,4:8], subculturingdf[,4:8]) \r
563 bananadat = Reduce(function(x,y) merge(x,y, all = T, by= "crossnumber"), allbanana)\r
564 bananadf = select(bananadat, crossnumber, everything())\r
565 bananadata = bananadf\r
566 bananadata1 = write.csv(bananadata, file = "bananadata.csv", row.names = F)\r
567 \r
568 ## PLANTLETS\r
569 allplantlets = list(subIDs, rootingdf[,4:7], screenhsedf[,4:7], hardeningdf[,4:7], openfieldtransferdf[,4:7])\r
570 merge_plantlets = Reduce(function(x,y) merge(x,y, all=T, by = "plantletID"), allplantlets)\r
571 plantsDF = select(merge_plantlets, crossnumber, plantletID, everything())\r
572 plantletsdf = write.csv(plantsDF, file = "plantlets.csv", row.names = F)\r
573 \r
574 ## EMAIL NOTIFICATIONS\r
575 today = Sys.Date()\r
576 # 1. status reported today\r
577 pStatus = statusDF\r
578 filter.status = filter(pStatus, status!='okay')\r
579 sdate = as.Date(filter.status$date)\r
580 filter.status.date = filter(filter.status, sdate==today)\r
581 \r
582 if (dim(filter.status.date)[1]!=0){\r
583 write.csv(filter.status.date, file = "statusReport.csv", row.names = F)\r
584 mime() %>%\r
585 to("karanjamargaret@gmail.com") %>%\r
586 from("megykah@gmail.com") %>%\r
587 text_body("Please see the list of accession that have been reported to have a problem today. Bests, Margaret") -> first_part\r
588 \r
589 first_part %>%\r
590 subject("Banana pipeline today status report") %>%\r
591 attach_file("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\statusReport.csv") -> file_attachment\r
592 \r
593 send_message(file_attachment)\r
594 }\r
595 \r
596 # Datasets \r
597 dataset <- c(bananadata, firstpollination, harvestingdf, ripeningdf, extractiondf, rescuingdf, germination2weeksdf,\r
598 germination6weeksdf, subculturingdf, rootingdf, screenhsedf, hardeningdf, openfieldtransferdf)\r
599 \r
600 ## POST MEDIA FILES TO ONA\r
601 # Get tokens\r
602 raw.result <- GET("https://api.ona.io/api/v1/user.json", authenticate(user = "seedtracker",password = "Seedtracking101"))\r
603 raw.result.char<-rawToChar(raw.result$content)\r
604 raw.result.json<-fromJSON(raw.result.char)\r
605 TOKEN_KEY <- raw.result.json$temp_token\r
606 \r
607 # DELETE CSV FILES\r
608 # flowering\r
609 meta_flowerid <- readChar("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_flowerid.txt", 10)\r
610 hdr=c(Authorization=paste("Temptoken ",TOKEN_KEY))\r
611 DELETE(paste("https://api.ona.io/api/v1/metadata/",meta_flowerid),add_headers(Authorization=paste("Temptoken ",TOKEN_KEY)))\r
612 \r
613 # bananadata\r
614 meta_bananaid <- readChar("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_bananaid.txt", 10)\r
615 hdr=c(Authorization=paste("Temptoken ",TOKEN_KEY))\r
616 DELETE(paste("https://api.ona.io/api/v1/metadata/",meta_bananaid),add_headers(Authorization=paste("Temptoken ",TOKEN_KEY)))\r
617 \r
618 # Status\r
619 meta_statusID <- readChar("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_statusID.txt", 10)\r
620 hdr=c(Authorization=paste("Temptoken ",TOKEN_KEY))\r
621 DELETE(paste("https://api.ona.io/api/v1/metadata/",meta_statusID),add_headers(Authorization=paste("Temptoken ",TOKEN_KEY)))\r
622 \r
623 # Contamination\r
624 meta_contaminationID <- readChar("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_contaminationID.txt", 10)\r
625 hdr=c(Authorization=paste("Temptoken ",TOKEN_KEY))\r
626 DELETE(paste("https://api.ona.io/api/v1/metadata/",meta_contaminationID),add_headers(Authorization=paste("Temptoken ",TOKEN_KEY)))\r
627 \r
628 # Plantlets\r
629 meta_plantletsID = readChar("D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_plantletsID.txt", 10)\r
630 hdr=c(Authorization=paste("Temptoken ",TOKEN_KEY))\r
631 DELETE(paste("https://api.ona.io/api/v1/metadata/",meta_plantletsID),add_headers(Authorization=paste("Temptoken ",TOKEN_KEY)))\r
632 \r
633 ## UPLOAD FLOWERING DATA\r
634 header=c(Authorization=paste("Temptoken ", TOKEN_KEY), `Content-Type` = 'multipart/form-data')\r
635 post.flower.results <- postForm("https://api.ona.io/api/v1/metadata.json",\r
636 data_value='flowering.csv',data_type='media',xform=237289,\r
637 data_file=fileUpload(filename = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\flowering.csv",contentType = 'text/csv'),\r
638 .opts=list(httpheader=header), verbose = TRUE)\r
639 # upload bananadata\r
640 header=c(Authorization=paste("Temptoken ", TOKEN_KEY), `Content-Type` = 'multipart/form-data')\r
641 post.banana.results <- postForm("https://api.ona.io/api/v1/metadata.json",\r
642 data_value='bananadata.csv',data_type='media',xform=237289,\r
643 data_file=fileUpload(filename = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\bananadata.csv",contentType = 'text/csv'),\r
644 .opts=list(httpheader=header), verbose = TRUE)\r
645 # status upload\r
646 header=c(Authorization=paste("Temptoken ", TOKEN_KEY), `Content-Type` = 'multipart/form-data')\r
647 post.status.results <- postForm("https://api.ona.io/api/v1/metadata.json",\r
648 data_value='status.csv',data_type='media',xform=237289,\r
649 data_file=fileUpload(filename = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\status.csv",contentType = 'text/csv'),\r
650 .opts=list(httpheader=header), verbose = TRUE)\r
651 \r
652 # contamination upload\r
653 header=c(Authorization=paste("Temptoken ", TOKEN_KEY), `Content-Type` = 'multipart/form-data')\r
654 post.contamination.results <- postForm("https://api.ona.io/api/v1/metadata.json",\r
655 data_value='contamination.csv',data_type='media',xform=237289,\r
656 data_file=fileUpload(filename = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\contamination.csv",contentType = 'text/csv'),\r
657 .opts=list(httpheader=header), verbose = TRUE)\r
658 \r
659 # Plantlets upload\r
660 header=c(Authorization=paste("Temptoken ", TOKEN_KEY), `Content-Type` = 'multipart/form-data')\r
661 post.plantlets.results <- postForm("https://api.ona.io/api/v1/metadata.json",\r
662 data_value='plantlets.csv',data_type='media',xform=237289,\r
663 data_file=fileUpload(filename = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\plantlets.csv",contentType = 'text/csv'),\r
664 .opts=list(httpheader=header), verbose = TRUE)\r
665 D:\github\ODK_bananaCrossingTool\Nelson Mandela\r
666 \r
667 ## get ID\r
668 # flowerID\r
669 flower.raw.result.json<-fromJSON(post.flower.results)\r
670 metadata_flowerid <- flower.raw.result.json$id\r
671 meta_flower <- cat(metadata_flowerid, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_flowerid.txt")\r
672 \r
673 # Bananadata ID\r
674 banana.raw.result.json<-fromJSON(post.banana.results)\r
675 metadata_bananaid <- banana.raw.result.json$id\r
676 meta_flower <- cat(metadata_bananaid, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_bananaid.txt")\r
677 \r
678 # get status ID\r
679 status.raw.result.json<-fromJSON(post.status.results)\r
680 metadata_statusid <- status.raw.result.json$id\r
681 meta_status <- cat(metadata_statusid, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_statusID.txt")\r
682 \r
683 # get contamination ID\r
684 contamination.raw.result.json<-fromJSON(post.contamination.results)\r
685 metadata_contaminationid <- contamination.raw.result.json$id\r
686 meta_contamination <- cat(metadata_contaminationid, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_contaminationID.txt")\r
687 \r
688 # get subplantlets ID\r
689 plantlets.raw.result.json<-fromJSON(post.plantlets.results)\r
690 metadata_plantletsid <- plantlets.raw.result.json$id\r
691 meta_plantlets <- cat(metadata_plantletsid, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\metadata_plantletsID.txt")\r
692 \r
693 ## DATA EXPLORER\r
694 # organize shiny app data\r
695 library(dplyr)\r
696 library(tidyr)\r
697 nFlower = strrep(c("Arusha","flowering"),1)\r
698 if (dim(flowered)[1]!=0){\r
699 flower = data.frame(c(nFlower, flowered))\r
700 flowered <- select(flower, "X.Arusha.","X.flowering.","accession_name", "submit_date", "submitted_by")\r
701 colnames(flowered) <- c("location","activity","accession","date","contributor")\r
702 } else {\r
703 flowered <- data.frame(0)\r
704 }\r
705 \r
706 # F.Polln\r
707 nFirst = strrep(c("Arusha","firstpollination"), 1)\r
708 if(dim(firstpollination)[1]!=0) {\r
709 first = data.frame(c(nFirst, firstpollination))\r
710 first_pollinationed = select(first,"X.Arusha.","X.firstpollination.", "crossnumber", "submission_date", "submitted_by")\r
711 colnames(first_pollinationed) = c("location","activity","accession","date","contributor")\r
712 } else {\r
713 first_pollinationed <- data.frame(0)\r
714 }\r
715 \r
716 # Repeat Polln\r
717 nRepeat = strrep(c("Arusha","repeatpollination"), 1)\r
718 if(dim(repeatdf)[1]!=0) {\r
719 repeatP = data.frame(c(nRepeat, repeatdf))\r
720 repeat_pollinationed = select(repeatP,"X.Arusha.","X.repeatpollination.", "crossnumber", "repeatPollinationDate","X_submitted_by")\r
721 colnames(repeat_pollinationed) = c("location","activity","accession","date","contributor")\r
722 } else {\r
723 repeat_pollinationed <- data.frame(0)\r
724 }\r
725 \r
726 # Harvest\r
727 nHarvest = strrep(c("Arusha","harvested"), 1)\r
728 if(dim(harvestingdf)[1]!=0){\r
729 Harvest = data.frame(c(nHarvest,harvestingdf))\r
730 harvestdf = select(Harvest,"X.Arusha.", "X.harvested.", "crossnumber", "harvesting_date", "submitted_by")\r
731 colnames(harvestdf) = c("location","activity","accession","date","contributor")\r
732 }else {\r
733 harvestdf <- data.frame(0)\r
734 }\r
735 \r
736 # Ripening\r
737 nRipen = strrep(c("Arusha","ripened"), 1)\r
738 if(dim(ripeningdf)[1]!=0){\r
739 ripenD = data.frame(c(nRipen,ripeningdf))\r
740 ripendf = select(ripenD,"X.Arusha.", "X.ripened.", "crossnumber", "ripen_date", "submitted_by")\r
741 colnames(ripendf) = c("location","activity","accession","date","contributor")\r
742 }else {\r
743 ripendf <- data.frame(0)\r
744 }\r
745 \r
746 # Extracted\r
747 nExtr = strrep(c("Arusha","extracted"), 1)\r
748 if(dim(extractiondf)[1]!=0){\r
749 Extr = as.data.frame(c(nExtr,extractiondf))\r
750 extracted <- select(Extr,"X.Arusha.", "X.extracted.", "crossnumber", "seed_extraction_date", "submitted_by")\r
751 colnames(extracted) <- c("location","activity","accession","date","contributor")\r
752 }else {\r
753 extracted <- data.frame(0)\r
754 }\r
755 # Rescue\r
756 nRescue = strrep(c("Arusha","embryrescued"), 1)\r
757 if(dim(rescuingdf)[1]!=0){\r
758 Rescue = as.data.frame(c(nRescue,rescuingdf))\r
759 rescued <- select(Rescue,"X.Arusha.", "X.embryrescued.", "crossnumber", "rescue_date", "submitted_by")\r
760 colnames(rescued) <- c("location","activity","accession","date","contributor")\r
761 }else {\r
762 rescued <- data.frame(0)\r
763 }\r
764 # Germinated after 2wks\r
765 n2Wks = strrep(c("Arusha","germinated after 2 weeks"), 1)\r
766 if(dim(germination2weeksdf)[1]!=0){\r
767 G2wk = as.data.frame(c(n2Wks,germination2weeksdf))\r
768 germinated_2weeks <- select(G2wk, "X.Arusha.","X.germinated.after.2.weeks.", "crossnumber", "germination_after_2weeks_date", "submitted_by")\r
769 colnames(germinated_2weeks) <- c("location","activity","accession","date","contributor")\r
770 }else {\r
771 germinated_2weeks <- data.frame(0)\r
772 }\r
773 \r
774 # Germinated after 6weeks\r
775 n6weeks = strrep(c("Arusha","germinated after 6 weeks"), 1)\r
776 if(dim(germination6weeksdf)[1]!=0){\r
777 G6weeks = as.data.frame(c(n6weeks,germination6weeksdf))\r
778 germinated_6weeks <- select(G6weeks,"X.Arusha.", "X.germinated.after.6.weeks.", "crossnumber", "germination_after_6weeks_date", "submitted_by")\r
779 colnames(germinated_6weeks) <- c("location","activity","accession","date","contributor")\r
780 }else {\r
781 germinated_6weeks <- data.frame(0)\r
782 }\r
783 # Subculture\r
784 nSub = strrep(c("Arusha","subcultured"), 1)\r
785 if(dim(subculturingdf)[1]!=0){\r
786 Sub = as.data.frame(c(nSub,subculturingdf))\r
787 subculturing <- select(Sub, "X.Arusha.","X.subcultured.", "crossnumber", "subculture_date", "submitted_by")\r
788 colnames(subculturing) <- c("location","activity","accession","date","contributor")\r
789 }else {\r
790 subculturing <- data.frame(0)\r
791 }\r
792 # Rooted\r
793 nRoot = strrep(c("Arusha","rooted"), 1)\r
794 if(dim(rootingdf)[1]!=0){\r
795 Root = as.data.frame(c(nRoot,rootingdf))\r
796 rooted <- select(Root, "X.Arusha.","X.rooted.", "plantletID", "date_rooting", "submitted_by")\r
797 colnames(rooted) <- c("location","activity","accession","date","contributor")\r
798 }else {\r
799 rooted <- data.frame(0)\r
800 }\r
801 # Screenhse\r
802 n.Shse = strrep(c("Arusha","screenhouse"), 1)\r
803 if(dim(screenhsedf)[1]!=0){\r
804 S.hse = as.data.frame(c(n.Shse,screenhsedf))\r
805 screen_housed <- select(S.hse,"X.Arusha.", "X.screenhouse.", "plantletID", "screenhse_transfer_date", "submitted_by")\r
806 colnames(screen_housed) <- c("location","activity","accession","date","contributor")\r
807 }else {\r
808 screen_housed <- data.frame(0)\r
809 }\r
810 # Hardened\r
811 nHard = strrep(c("Arusha","hardened"), 1)\r
812 if(dim(hardeningdf)[1]!=0){\r
813 Hard = as.data.frame(c(nHard,hardeningdf))\r
814 hardened <- select(Hard,"X.Arusha.", "X.hardened.", "plantletID", "hardening_date", "submitted_by")\r
815 colnames(hardened) <- c("location","activity","accession","date","contributor")\r
816 }else {\r
817 hardened <- data.frame(0)\r
818 }\r
819 \r
820 # Openfield\r
821 nOpn = strrep(c("Arusha","openfield"), 1)\r
822 if(dim(openfieldtransferdf)[1]!=0){\r
823 opn = as.data.frame(c(nOpn,openfieldtransferdf))\r
824 open_field <- select(opn, "X.Arusha.","X.openfield.", "plantletID", "date_of_transfer_to_openfield", "submitted_by")\r
825 colnames(open_field) <- c("location","activity","accession","date","contributor")\r
826 } else {\r
827 open_field <- data.frame(0)\r
828 }\r
829 # Status\r
830 nStatus = strrep(c("Arusha","status"), 1)\r
831 if(dim(statusDF)[1]!=0){\r
832 sta = as.data.frame(c(nStatus,statusDF))\r
833 statusD <- select(sta, "X.Arusha.","X.status.", "statusID", "date", "submitted_by")\r
834 colnames(statusD) <- c("location","activity","accession","date","contributor")\r
835 } else {\r
836 statusD <- data.frame(0)\r
837 }\r
838 \r
839 mylist <- list(flowered,first_pollinationed,repeat_pollinationed, harvestdf,ripendf, extracted,rescued,germinated_2weeks,germinated_6weeks,\r
840 subculturing,rooted,screen_housed,hardened,open_field, statusD)\r
841 r <- mylist[[1]]\r
842 for (i in 2:length(mylist)) {\r
843 r <- merge(r, mylist[[i]], all=TRUE)\r
844 }\r
845 cleantable = r\r
846 cleanTable = write.csv(r, file = "D:\\github\\ODK_bananaCrossingTool\\Nelson Mandela\\cleantable.csv", row.names = F)\r
847 \r
848 # NUMBER OF ACCESSION IN DIFFERENT STAGES OF PROJECT\r
849 all_crosses <- bananadata %>% select("crossnumber","repeatPollinationDate.1","harvesting_date", "ripen_date","seed_extraction_date","rescue_date","germination_after_2weeks_date",\r
850 "germination_after_6weeks_date","subculture_date")\r
851 nrows<-dim(all_crosses)[1]\r
852 firstpollination=0\r
853 repeatpollination=0\r
854 harvested=0\r
855 ripening=0\r
856 seedextraction=0\r
857 embryorescue=0\r
858 germinatingafter2weeks=0\r
859 germinatingafter1month=0\r
860 \r
861 # LOOP\r
862 for(i in 1:nrows){\r
863 if (is.na(all_crosses$repeatPollinationDate.1[i])){\r
864 firstpollination<-firstpollination+1\r
865 }\r
866 else{\r
867 if(is.na(all_crosses$harvesting_date[i]) & all_crosses$repeatPollinationDate.1[i]!="NULL") {\r
868 repeatpollination<-repeatpollination+1\r
869 }\r
870 else{\r
871 if(is.na(all_crosses$ripen_date[i]) & all_crosses$harvesting_date[i]!="NULL"){\r
872 harvested <- harvested+1\r
873 }\r
874 else{\r
875 if(is.na(all_crosses$seed_extraction_date[i]) & all_crosses$ripen_date[i]!="NULL"){\r
876 ripening <- ripening+1\r
877 }\r
878 else{\r
879 if(is.na(all_crosses$rescue_date[i]) & all_crosses$seed_extraction_date[i]!="NULL"){\r
880 seedextraction = seedextraction+1\r
881 }\r
882 else{\r
883 if(is.na(all_crosses$germination_after_2weeks_date[i]) & all_crosses$rescue_date[i]!="NULL"){\r
884 embryorescue = embryorescue+1\r
885 }\r
886 else{\r
887 if(is.na(all_crosses$germination_after_6weeks_date[i]) & all_crosses$germination_after_2weeks_date[i]!="NULL"){\r
888 germinatingafter2weeks = germinatingafter2weeks+1\r
889 }\r
890 else{\r
891 if(is.na(all_crosses$subculture_date[i]) & all_crosses$germination_after_6weeks_date[i]!="NULL"){\r
892 germinatingafter1month = germinatingafter1month+1\r
893 }\r
894 }\r
895 }\r
896 }\r
897 }\r
898 }\r
899 }\r
900 }\r
901 }\r
902 # Planlets\r
903 all_plantlets = plantsDF %>% select("crossnumber","plantletID","subculture_date","date_rooting","screenhse_transfer_date", \r
904 "hardening_date","date_of_transfer_to_openfield")\r
905 nplants = dim(all_plantlets)[1]\r
906 subculture=0\r
907 rooting=0\r
908 screenhouse=0\r
909 hardening=0\r
910 openfield=0\r
911 \r
912 # LOOP\r
913 for(i in 1:nplants){\r
914 if (is.na(all_plantlets$date_rooting[i])){\r
915 subcultures=subcultures+1\r
916 }\r
917 else{\r
918 if(is.na(all_plantlets$screenhse_transfer_date[i]) & all_plantlets$date_rooting[i]!="NULL") {\r
919 rooting=rooting+1\r
920 }\r
921 else{\r
922 if(is.na(all_plantlets$hardening_date[i]) & all_plantlets$screenhse_transfer_date[i]!="NULL"){\r
923 screenhouse=screenhouse+1\r
924 }\r
925 else{\r
926 if(is.na(all_plantlets$date_of_transfer_to_openfield[i]) & all_plantlets$hardening_date[i]!="NULL"){\r
927 hardening = hardening+1\r
928 }\r
929 else{\r
930 if(all_plantlets$date_of_transfer_to_openfield[i]!="NULL"){\r
931 openfield = openfield+1\r
932 }\r
933 }\r
934 }\r
935 }\r
936 }\r
937 }\r
938 \r
939 \r
940 # Table out\r
941 in_activity = c("firstpollination","repeatpollination","harvested","ripening","seedextraction","embryorescue",\r
942 "germinatingafter2weeks","germinatingafter1month","subculture","rooting","screenhouse","hardening","openfield")\r
943 number = c(firstpollination,repeatpollination,harvested,ripening,seedextraction,embryorescue,\r
944 germinatingafter2weeks,germinatingafter1month,subculture,rooting,screenhouse,hardening,openfield)\r
945 nTable = as.data.frame(cbind(in_activity, number))\r
946 n.Table = write.csv(nTable, file="nTable.csv", row.names = F)\r