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comparison make_eml.R @ 2:2af7401f13e0 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
author ecology
date Sat, 23 Dec 2023 20:41:42 +0000
parents 4cd3d9fdb5f3
children
comparison
equal deleted inserted replaced
1:0cfc9b6da2ac 2:2af7401f13e0
1 ##07/06/2023 ##Genthon Tanguy 1 ##07/06/2023 ##Genthon Tanguy
2 ##update 15/11/2023 ##Seguineau Pauline 2 ##update 15/11/2023 ## Seguineau Pauline
3 3
4 ###make_eml 4 ###make_eml
5 5
6 args = commandArgs(trailingOnly=TRUE) 6 args = commandArgs(trailingOnly=TRUE)
7 if(length(args)>0){ 7 if(length(args)>0){
8 title <- args[1] 8 title <- args[1]
9 start <- args[2] 9 start <- args[2]
10 end <-args[3] 10 end <-args[3]
11 data_table <- args[4] 11 data_table <- args[4]
12 data_other <- args[5] 12 data_raster <- args[5]
13 destable <- args[6] 13 data_vector <- args[6]
14 desother <- args[7] 14 data_other <- args[7]
15 quote <- args[8] 15 destable <- args[8]
16 table_url <- args[9] 16 desraster<- args[9]
17 other_url <- args[10] 17 desvector<- args[10]
18 } 18 desother <- args[11]
19 19 quote <- args[12]
20 table_url <- args[13]
21 other_url <- args[14]
22 raster_url <- args[15]
23 vector_url <- args[16]
24 }
25
26 #Load package
27
28 library(EMLassemblyline)
29 sessionInfo()
30
20 31
21 ###Format data### 32 ###Format data###
22
23 if (data_table == ""){ 33 if (data_table == ""){
24 table=NULL 34 table=NULL
25 }else{ 35 }else{
26 table = strsplit(data_table," ") 36 table = strsplit(data_table," ")
27 for (file in table){ 37 for (file in table){
46 quote_table = gsub("none","",quote_table)} 56 quote_table = gsub("none","",quote_table)}
47 tablequote = c(tablequote, quote_table) 57 tablequote = c(tablequote, quote_table)
48 } 58 }
49 59
50 60
61 if (data_raster == ""){
62 raster=NULL
63 }else{
64 raster = strsplit(data_raster," ")
65 for (file in raster){
66 name_raster = gsub("\\.[a-zA-Z]*", "", file)}
67 }
68
69 if (data_vector == ""){
70 vector=NULL
71 }else{
72 vector = strsplit(data_vector," ")
73 for (file in vector){
74 name_vector = gsub("\\.[a-zA-Z]*", "", file)}
75 }
76
51 if (data_other == ""){ 77 if (data_other == ""){
52 other=NULL 78 other=NULL
53 }else{ 79 }else{
54 other = strsplit(data_other," ") 80 other = strsplit(data_other," ")
55 for (file in other){ 81 for (file in other){
61 des_table = name_table 87 des_table = name_table
62 }else{ 88 }else{
63 des_table = strsplit(destable,",")} 89 des_table = strsplit(destable,",")}
64 } 90 }
65 91
92 if (data_raster !=""){
93 if (desraster == ""){
94 des_raster = name_raster
95 }else{
96 des_raster = strsplit(desraster,",")}
97 }
98
99 if (data_vector !=""){
100 if (desvector == ""){
101 des_vector = name_vector
102 }else{
103 des_vector = strsplit(desvector,",")}
104 }
66 105
67 if (data_other !=""){ 106 if (data_other !=""){
68 if (desother == ""){ 107 if (desother == ""){
69 des_other = name_other 108 des_other = name_other
70 }else{ 109 }else{
71 des_other = strsplit(desother,",")} 110 des_other = strsplit(desother,",")}
72 } 111 }
73 112
74
75 if (data_table !=""){ 113 if (data_table !=""){
76 if (table_url == ""){ 114 if (table_url == ""){
77 urltable = "" 115 urltable = ""
78 }else{ 116 }else{
79 table_url = gsub("\\-" ,"", table_url) 117 table_url = gsub("\\-" ,"", table_url)
88 other_url = gsub("\\-" ,"", other_url) 126 other_url = gsub("\\-" ,"", other_url)
89 urlother = strsplit(other_url,",") 127 urlother = strsplit(other_url,",")
90 } 128 }
91 } 129 }
92 130
131 if (data_raster !=""){
132 if (raster_url == ""){
133 urlraster = ""
134 }else{
135 raster_url = gsub("\\-" ,"", raster_url)
136 urlraster = strsplit(raster_url,",")
137 }
138 }
139
140 if (data_vector !=""){
141 if (vector_url == ""){
142 urlvector = ""
143 }else{
144 vector_url = gsub("\\-" ,"", vector_url)
145 urlvector = strsplit(vector_url,",")
146 }
147 }
148
149
150
93 ###Make EML### 151 ###Make EML###
94 152
95 if (!is.null(table) && !is.null(other)){ 153 if (!is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
96 154
97 EMLassemblyline::make_eml( 155 EMLassemblyline::make_eml(
98 path="output_template", 156 path="output_template",
99 data.path="data_files", 157 data.path="data_files",
100 eml.path=".", 158 eml.path=".",
101 dataset.title = title, 159 dataset.title = title,
102 temporal.coverage = c(start,end), 160 temporal.coverage = c(start,end),
103 data.table=table[[1]], 161 data.table=table[[1]],
104 data.table.name = name_table, 162 data.table.name = name_table,
105 data.table.description = des_table[[1]], 163 data.table.description = des_table[[1]],
106 data.table.quote.character = tablequote, 164 data.table.quote.character = tablequote,
107 data.table.url = urltable[[1]], 165 data.table.url = urltable[[1]],
108 other.entity=other[[1]], 166 spatial.raster=raster[[1]],
109 other.entity.name = name_other, 167 spatial.raster.name = name_raster,
110 other.entity.description = des_other[[1]], 168 spatial.raster.description = des_raster[[1]],
111 other.entity.url= urlother[[1]] 169 spatial.raster.url = urlraster[[1]],
170 spatial.vector=vector[[1]],
171 spatial.vector.name = name_vector,
172 spatial.vector.description = des_vector[[1]],
173 spatial.vector.url = urlvector[[1]],
174 other.entity=other[[1]],
175 other.entity.name = name_other,
176 other.entity.description = des_other[[1]],
177 other.entity.url= urlother[[1]])
178
179 }else if (is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
180
181 EMLassemblyline::make_eml(
182 path="output_template",
183 data.path="data_files",
184 eml.path=".",
185 dataset.title = title,
186 temporal.coverage = c(start,end))
187
188 }else if (!is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
189
190 EMLassemblyline::make_eml(
191 path="output_template",
192 data.path="data_files",
193 eml.path=".",
194 dataset.title = title,
195 temporal.coverage = c(start,end),
196 data.table=table[[1]],
197 data.table.name = name_table,
198 data.table.description = des_table[[1]],
199 data.table.quote.character = tablequote,
200 data.table.url = urltable[[1]]
112 ) 201 )
113 202
114 }else if (is.null(table) && is.null(other)){ 203 }else if (!is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
204
205 EMLassemblyline::make_eml(
206 path="output_template",
207 data.path="data_files",
208 eml.path=".",
209 dataset.title = title,
210 temporal.coverage = c(start,end),
211 data.table=table[[1]],
212 data.table.name = name_table,
213 data.table.description = des_table[[1]],
214 data.table.quote.character = tablequote,
215 data.table.url = urltable[[1]],
216 spatial.raster=raster[[1]],
217 spatial.raster.name = name_raster,
218 spatial.raster.description = des_raster[[1]],
219 spatial.raster.url = urlraster[[1]])
220
221 }else if (!is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
115 222
116 EMLassemblyline::make_eml( 223 EMLassemblyline::make_eml(
117 path="output_template", 224 path="output_template",
118 data.path="data_files", 225 data.path="data_files",
119 eml.path=".", 226 eml.path=".",
120 dataset.title = title, 227 dataset.title = title,
121 temporal.coverage = c(start,end)) 228 temporal.coverage = c(start,end),
122 229 data.table=table[[1]],
123 }else if (!is.null(table) && is.null(other)){ 230 data.table.name = name_table,
124 231 data.table.description = des_table[[1]],
125 EMLassemblyline::make_eml( 232 data.table.quote.character = tablequote,
126 path="output_template", 233 data.table.url = urltable[[1]],
127 data.path="data_files", 234 spatial.raster=raster[[1]],
128 eml.path=".", 235 spatial.raster.name = name_raster,
129 dataset.title = title, 236 spatial.raster.description = des_raster[[1]],
130 temporal.coverage = c(start,end), 237 spatial.raster.url = urlraster[[1]],
131 data.table=table[[1]], 238 spatial.vector=vector[[1]],
132 data.table.name = name_table, 239 spatial.vector.name = name_vector,
133 data.table.description = des_table[[1]], 240 spatial.vector.description = des_vector[[1]],
134 data.table.quote.character = tablequote, 241 spatial.vector.url = urlvector[[1]])
135 data.table.url = urltable[[1]]) 242
136 243 }else if (is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
137 244
138 }else if (is.null(table) && !is.null(other)){ 245 EMLassemblyline::make_eml(
139 246 path="output_template",
140 EMLassemblyline::make_eml( 247 data.path="data_files",
141 path="output_template", 248 eml.path=".",
142 data.path="data_files", 249 dataset.title = title,
143 eml.path=".", 250 temporal.coverage = c(start,end),
144 dataset.title = title, 251 spatial.raster=raster[[1]],
145 temporal.coverage = c(start,end), 252 spatial.raster.name = name_raster,
253 spatial.raster.description = des_raster[[1]],
254 spatial.raster.url = urlraster[[1]])
255
256 }else if (is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
257
258 EMLassemblyline::make_eml(
259 path="output_template",
260 data.path="data_files",
261 eml.path=".",
262 dataset.title = title,
263 temporal.coverage = c(start,end),
264 spatial.raster=raster[[1]],
265 spatial.raster.name = name_raster,
266 spatial.raster.description = des_raster[[1]],
267 spatial.raster.url = urlraster[[1]],
268 spatial.vector=vector[[1]],
269 spatial.vector.name = name_vector,
270 spatial.vector.description = des_vector[[1]],
271 spatial.vector.url = urlvector[[1]])
272
273 }else if (is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
274
275 EMLassemblyline::make_eml(
276 path="output_template",
277 data.path="data_files",
278 eml.path=".",
279 dataset.title = title,
280 temporal.coverage = c(start,end),
281 spatial.raster=raster[[1]],
282 spatial.raster.name = name_raster,
283 spatial.raster.description = des_raster[[1]],
284 spatial.raster.url = urlraster[[1]],
285 spatial.vector=vector[[1]],
286 spatial.vector.name = name_vector,
287 spatial.vector.description = des_vector[[1]],
288 spatial.vector.url = urlvector[[1]],
289 other.entity=other[[1]],
290 other.entity.name = name_other,
291 other.entity.description = des_other[[1]],
292 other.entity.url= urlother[[1]])
293
294 }else if (is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
295
296 EMLassemblyline::make_eml(
297 path="output_template",
298 data.path="data_files",
299 eml.path=".",
300 dataset.title = title,
301 temporal.coverage = c(start,end),
302 spatial.vector=vector[[1]],
303 spatial.vector.name = name_vector,
304 spatial.vector.description = des_vector[[1]],
305 spatial.vector.url = urlvector[[1]])
306
307 }else if (is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
308
309 EMLassemblyline::make_eml(
310 path="output_template",
311 data.path="data_files",
312 eml.path=".",
313 dataset.title = title,
314 temporal.coverage = c(start,end),
315 spatial.vector=vector[[1]],
316 spatial.vector.name = name_vector,
317 spatial.vector.description = des_vector[[1]],
318 spatial.vector.url = urlvector[[1]],
319 other.entity=other[[1]],
320 other.entity.name = name_other,
321 other.entity.description = des_other[[1]],
322 other.entity.url= urlother[[1]])
323
324 }else if (is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
325
326 EMLassemblyline::make_eml(
327 path="output_template",
328 data.path="data_files",
329 eml.path=".",
330 dataset.title = title,
331 temporal.coverage = c(start,end),
332 other.entity=other[[1]],
333 other.entity.name = name_other,
334 other.entity.description = des_other[[1]],
335 other.entity.url= urlother[[1]])
336
337 }else if (!is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
338
339 EMLassemblyline::make_eml(
340 path="output_template",
341 data.path="data_files",
342 eml.path=".",
343 dataset.title = title,
344 temporal.coverage = c(start,end),
345 data.table=table[[1]],
346 data.table.name = name_table,
347 data.table.description = des_table[[1]],
348 data.table.quote.character = tablequote,
349 data.table.url = urltable[[1]],
350 spatial.vector=vector[[1]],
351 spatial.vector.name = name_vector,
352 spatial.vector.description = des_vector[[1]],
353 spatial.vector.url = urlvector[[1]])
354
355 }else if (!is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
356
357 EMLassemblyline::make_eml(
358 path="output_template",
359 data.path="data_files",
360 eml.path=".",
361 dataset.title = title,
362 temporal.coverage = c(start,end),
363 data.table=table[[1]],
364 data.table.name = name_table,
365 data.table.description = des_table[[1]],
366 data.table.quote.character = tablequote,
367 data.table.url = urltable[[1]],
368 other.entity=other[[1]],
369 other.entity.name = name_other,
370 other.entity.description = des_other[[1]],
371 other.entity.url= urlother[[1]])
372
373 }else if (is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
374
375 EMLassemblyline::make_eml(
376 path="output_template",
377 data.path="data_files",
378 eml.path=".",
379 dataset.title = title,
380 temporal.coverage = c(start,end),
381 spatial.raster=raster[[1]],
382 spatial.raster.name = name_raster,
383 spatial.raster.description = des_raster[[1]],
384 spatial.raster.url = urlraster[[1]],
385 other.entity=other[[1]],
386 other.entity.name = name_other,
387 other.entity.description = des_other[[1]],
388 other.entity.url= urlother[[1]])
389
390 }else if (!is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
391
392 EMLassemblyline::make_eml(
393 path="output_template",
394 data.path="data_files",
395 eml.path=".",
396 dataset.title = title,
397 temporal.coverage = c(start,end),
398 data.table=table[[1]],
399 data.table.name = name_table,
400 data.table.description = des_table[[1]],
401 data.table.quote.character = tablequote,
402 data.table.url = urltable[[1]],
403 spatial.vector=vector[[1]],
404 spatial.vector.name = name_vector,
405 spatial.vector.description = des_vector[[1]],
406 spatial.vector.url = urlvector[[1]],
407 other.entity=other[[1]],
408 other.entity.name = name_other,
409 other.entity.description = des_other[[1]],
410 other.entity.url= urlother[[1]])
411
412 }else if (!is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
413
414 EMLassemblyline::make_eml(
415 path="output_template",
416 data.path="data_files",
417 eml.path=".",
418 dataset.title = title,
419 temporal.coverage = c(start,end),
420 data.table=table[[1]],
421 data.table.name = name_table,
422 data.table.description = des_table[[1]],
423 data.table.quote.character = tablequote,
424 data.table.url = urltable[[1]],
425 spatial.raster=raster[[1]],
426 spatial.raster.name = name_raster,
427 spatial.raster.description = des_raster[[1]],
428 spatial.raster.url = urlraster[[1]],
146 other.entity=other[[1]], 429 other.entity=other[[1]],
147 other.entity.name = name_other, 430 other.entity.name = name_other,
148 other.entity.description = des_other[[1]], 431 other.entity.description = des_other[[1]],
149 other.entity.url= urlother[[1]])} 432 other.entity.url= urlother[[1]])}
150 433
151 434 issues()
152
153 old.names <- list.files(path=".", pattern=".xml") 435 old.names <- list.files(path=".", pattern=".xml")
154 print(old.names)
155 file.rename(from=old.names, to="eml.xml") 436 file.rename(from=old.names, to="eml.xml")
156 437
157 438
158 439
159 440