1# =========================================================================== 2# 3# PUBLIC DOMAIN NOTICE 4# National Center for Biotechnology Information 5# 6# This software/database is a "United States Government Work" under the 7# terms of the United States Copyright Act. It was written as part of 8# the author's official duties as a United States Government employee and 9# thus cannot be copyrighted. This software/database is freely available 10# to the public for use. The National Library of Medicine and the U.S. 11# Government have not placed any restriction on its use or reproduction. 12# 13# Although all reasonable efforts have been taken to ensure the accuracy 14# and reliability of the software and data, the NLM and the U.S. 15# Government do not and cannot warrant the performance or results that 16# may be obtained by using this software or data. The NLM and the U.S. 17# Government disclaim all warranties, express or implied, including 18# warranties of performance, merchantability or fitness for any particular 19# purpose. 20# 21# Please cite the author in any work or product based on this material. 22# 23# =========================================================================== 24 25default: runtests 26runtests: std announce urls_and_accs out_dir_and_file s-option truncated kart resume quality 27slowtests: announce vdbcache wgs lots_wgs hs37d5 ncbi1GB 28 29TOP ?= $(abspath ../..) 30MODULE = test/prefetch 31include $(TOP)/build/Makefile.env 32 33CWD = $(shell pwd) 34PUBLIC=/repository/user/main/public 35CGI=https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi 36SDL=https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve 37LARGE=fasp://aspera@demo.asperasoft.com:aspera-test-dir-large/100MB 38SRA=https://sra-download.ncbi.nlm.nih.gov 39SRAF=fasp://dbtest@sra-download.ncbi.nlm.nih.gov 40#SRAF=fasp://dbtest@srafiles31-1.st-va.ncbi.nlm.nih.gov 41KMER=$(SRA)/traces/nannot01/kmer/000/390/GCA_000390265.1_R 42KMERF=$(SRAF):data/sracloud/traces/nannot01/kmer/000/390/GCA_000390265.1_R 43REFSEQ=$(SRA)/traces/refseq/KC702174.1 44REFSEQF=$(SRAF):data/sracloud/traces/refseq/KC702174.1 45SRAC=SRR053325 46SRR=$(SRA)/sos2/sra-pub-run-15/$(SRAC)/$(SRAC).4 47SRR=$(shell NCBI_SETTINGS=/ ${BINDIR}/srapath ${SRAC}) 48INT=https://sra-download-internal.ncbi.nlm.nih.gov 49DDB=https://sra-downloadb.be-md.ncbi.nlm.nih.gov 50#SRR=$(DDB)/sos/sra-pub-run-5/$(SRAC)/$(SRAC).3 51SRAI=fasp://dbtest@sra-download-internal.ncbi.nlm.nih.gov 52SRRF=$(SRAF):data/sracloud/traces/sra57/SRR/000052/$(SRAC) 53SRRF=$(SRAI):data/sracloud/traces/sra57/SRR/000052/$(SRAC) 54WGS=$(SRA)/traces/wgs03/WGS/AF/VF/AFVF01.1 55WGSF=$(SRAF):data/sracloud/traces/wgs03/WGS/AF/VF/AFVF01.1 56 57DIRTOTEST ?= $(BINDIR) 58SRR=$(shell SRATOOLS_FORCE_INSTALL=1 ${DIRTOTEST}/srapath ${SRAC}) 59B=$(DIRTOTEST) 60 61HTTP_URL=https://test.ncbi.nlm.nih.gov/home/about/contact.shtml 62HTTPFILE=contact.shtml 63 64INT_TOOLS = \ 65 66EXT_TOOLS = \ 67 test-quality 68 69ALL_TOOLS = \ 70 $(INT_TOOLS) \ 71 $(EXT_TOOLS) 72 73#------------------------------------------------------------------------------- 74# outer targets 75# 76all std: vers-includes 77 @ $(MAKE_CMD) $(TARGDIR)/$@ 78 79$(ALL_TOOLS): vers-includes 80 @ $(MAKE_CMD) $(BINDIR)/$@ 81 82.PHONY: all std $(ALL_TOOLS) 83 84#------------------------------------------------------------------------------- 85# all 86# 87$(TARGDIR)/all: \ 88 $(addprefix $(BINDIR)/,$(ALL_TOOLS)) 89 90.PHONY: $(TARGDIR)/all 91 92#------------------------------------------------------------------------------- 93# std 94# 95$(TARGDIR)/std: \ 96 $(addprefix $(BINDIR)/,$(EXT_TOOLS)) 97 98.PHONY: $(TARGDIR)/std 99 100#------------------------------------------------------------------------------- 101# vers-includes 102# 103$(TARGDIR)/vers-includes: $(addsuffix .vers.h,$(EXT_TOOLS)) 104 105.PHONY: $(TARGDIR)/vers-includes 106 107#------------------------------------------------------------------------------- 108# clean 109# 110clean: stdclean 111 112.PHONY: clean 113 114#------------------------------------------------------------------------------- 115# TOOL_SRC 116# 117TOOL_SRC = \ 118 test-quality \ 119 120TOOL_OBJ = \ 121 $(addsuffix .$(OBJX),$(TOOL_SRC)) 122 123TOOL_LIB = \ 124 -lkapp \ 125 -sncbi-vdb \ 126 -lm 127 128$(BINDIR)/test-quality: $(TOOL_OBJ) 129 $(LP) --exe --vers $(SRCDIR) -o $@ $^ -L$(VDB_LIBDIR) -L$(VDB_LIBDIR)/../ilib $(TOOL_LIB) 130 131announce: 132 @echo Testing $(DIRTOTEST) 133 134################################################################################ 135urls_and_accs: 136 @mkdir -p tmp tmp2 137 @rm -fr tmp/* tmp2/* 138 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 139 140 @echo prefetch URL-1 when there is no kfg 141 @rm -f wiki 142 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 143 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki 144 @rm wiki 145 146 @echo prefetch URL-2/2 when there is no kfg 147 @rm -f index.html 148 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 149 $(DIRTOTEST)/prefetch https://github.com/ncbi/ >/dev/null 150 @rm index.html 151 152 @echo prefetch URL-2/1 when there is no kfg 153 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 154 if ping -c1 intranet > /dev/null ; then \ 155 $(DIRTOTEST)/prefetch http://intranet/ >/dev/null ; rm index.html ; \ 156 fi 157 158 @echo prefetch URL-2/3 when there is no kfg 159 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 160 if ping -c1 intranet > /dev/null ; then \ 161 $(DIRTOTEST)/prefetch $(HTTP_URL) > /dev/null; \ 162 fi 163 164 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 165 @echo '$(PUBLIC)/apps/file/volumes/flat = "files"' >> tmp/t.kfg 166 @echo '$(PUBLIC)/root = "$(CWD)/tmp"' >> tmp/t.kfg 167 168 @if ls `pwd`/tmp2/$(HTTPFILE) 2> /dev/null ; \ 169 then echo $(HTTPFILE) found ; exit 1 ; fi 170 @echo HTTP download when user repository is configured 171 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 172 if ping -c1 intranet > /dev/null ; then \ 173 $(DIRTOTEST)/prefetch $(HTTP_URL) > /dev/null ; fi 174 @if ping -c1 intranet > /dev/null ; \ 175 then ls `pwd`/tmp2/$(HTTPFILE) > /dev/null ; fi 176 177 @echo Running prefetch second time finds previous download 178 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 179 if ping -c1 intranet > /dev/null ; then \ 180 $(DIRTOTEST)/prefetch $(HTTP_URL) \ 181 | grep "found local" > /dev/null ; fi 182 183 @rm -f $(HTTPFILE) 184 185 @if ls `pwd`/tmp2/index.html 2> /dev/null ; \ 186 then echo index.shtml found ; exit 1; fi 187 @echo HTTP download when user repository is configured 188 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 189 if ping -c1 intranet > /dev/null ; then \ 190 $(DIRTOTEST)/prefetch http://intranet/ > /dev/null ; fi 191 @if ping -c1 intranet>/dev/null; then ls `pwd`/tmp2/index.html > /dev/null;fi 192 193 @echo Running prefetch second time finds previous download 194 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 195 if ping -c1 intranet > /dev/null ; then \ 196 $(DIRTOTEST)/prefetch http://intranet/ | grep "found local" >/dev/null;fi 197 @rm -f `pwd`/tmp2/index.html 198 199 @echo URL download when user repository is configured 200 @if ls `pwd`/tmp2/wiki 2> /dev/null ; then echo wiki found ; exit 1; fi 201 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 202 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki > /dev/null 203 @ls `pwd`/tmp2/wiki > /dev/null 204 205 @echo Running prefetch second time finds previous download 206 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 207 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki \ 208 | grep "found local" > /dev/null 209 210 @echo URL/ download when user repository is configured 211 @if ls `pwd`/tmp2/index.html 2> /dev/null ; \ 212 then echo index.html found ; exit 1; fi 213 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 214 $(DIRTOTEST)/prefetch https://github.com/ncbi/ > /dev/null 215 @ls `pwd`/tmp2/index.html > /dev/null 216 217 @echo Running prefetch second time finds previous download 218 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 219 $(DIRTOTEST)/prefetch https://github.com/ncbi/|grep "found local">/dev/null 220 @rm `pwd`/tmp2/index.html 221 222 @ if echo $(SRR) | grep -vq /sdlr/sdlr.fcgi?jwt= ; \ 223 then \ 224 echo prefetch $(SRR) when there is no kfg && \ 225 NCBI_VDB_RELIABLE=y NCBI_SETTINGS=/ VDB_CONFIG=`pwd`/tmp \ 226 $(DIRTOTEST)/prefetch $(SRR) > /dev/null && \ 227 rm -r $(SRAC) ; \ 228 else \ 229 echo prefetch test when CE is required is skipped ; \ 230 fi 231 232 @echo '$(PUBLIC)/apps/sra/volumes/sraFlat = "sra"' >> tmp/t.kfg 233 @rm -f `pwd`/tmp/sra/$(SRAC).sra 234 @ if echo $(SRR) | grep -vq /sdlr/sdlr.fcgi?jwt= ; \ 235 then \ 236 echo SRR download when user repository is configured && \ 237 NCBI_SETTINGS=/ NCBI_VDB_RELIABLE=y VDB_CONFIG=`pwd`/tmp \ 238 ENV_VAR_LOG_HTTP_RETRY=1 $(DIRTOTEST)/prefetch $(SRR) > /dev/null && \ 239 ls `pwd`/tmp/sra/$(SRAC).sra > /dev/null && \ 240 \ 241 echo Running prefetch second time finds previous download && \ 242 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 243 $(DIRTOTEST)/prefetch $(SRR) | grep "found local" > /dev/null ; \ 244 else \ 245 echo prefetch test when CE is required is skipped ; \ 246 fi 247 248 @echo prefetch $(REFSEQ) when there is no kfg 249 @rm -f KC702174.1 250 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 251 $(DIRTOTEST)/prefetch $(REFSEQ) > /dev/null 252 @rm KC702174.1* 253 254 @echo '$(PUBLIC)/apps/refseq/volumes/refseq = "refseq"' >> tmp/t.kfg 255 @echo REFSEQ HTTP download when user repository is configured 256 @if ls `pwd`/tmp/refseq/KC702174.1 2> /dev/null ; \ 257 then echo KC702174.1 found ; exit 1; fi 258 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 259 $(DIRTOTEST)/prefetch $(REFSEQ) > /dev/null 260 @ls `pwd`/tmp/refseq/KC702174.1 > /dev/null 261 262 @echo Running prefetch second time finds previous download 263 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 264 $(DIRTOTEST)/prefetch $(REFSEQ) | grep "found local" > /dev/null 265 266 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 267 if $(DIRTOTEST)/prefetch $(KMER) > /dev/null 2>&1 ; \ 268 then echo "prefetch $(KMER) when there is no kfg should fail"; exit 1; \ 269 fi 270 271 @echo '$(PUBLIC)/apps/nakmer/volumes/nakmerFlat = "nannot"' >> tmp/t.kfg 272 @echo NANNOT download when user repository is configured 273 @if ls `pwd`/tmp/nannot/GCA_000390265.1_R 2> /dev/null ; \ 274 then echo GCA_000390265.1_R found ; exit 1 ; fi 275 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 276 $(DIRTOTEST)/prefetch $(KMER) > /dev/null 277 @ls `pwd`/tmp/nannot/GCA_000390265.1_R > /dev/null 278 279 @echo Running prefetch second time finds previous download 280 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 281 $(DIRTOTEST)/prefetch $(KMER) | grep "found local" > /dev/null 282 283 @echo "prefetch $(WGS) when there is no kfg" 284 @NCBI_SETTINGS=/ VDB_CONFIG=`pwd`/tmp \ 285 $(DIRTOTEST)/prefetch $(WGS) > /dev/null 2>&1 286 @rm AFVF01.1 287 288 @echo '$(PUBLIC)/apps/wgs/volumes/wgsFlat = "wgs"' >> tmp/t.kfg 289 @echo 290 @echo WGS HTTP download when user repository is configured 291 @if ls `pwd`/tmp/wgs/AFVF01.1 2> /dev/null ; \ 292 then echo AFVF01.1 found ; exit 1; fi 293 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 294 $(DIRTOTEST)/prefetch $(WGS) > /dev/null 295 @ls `pwd`/tmp/wgs/AFVF01.1 > /dev/null 296 @rm `pwd`/tmp/wgs/AFVF01.1 297 @echo 298 299 @rm -f `pwd`/tmp/refseq/KC702174.1 300 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 301 echo REFSEQ FASP download when user repository is configured ; \ 302 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 303 $(DIRTOTEST)/prefetch $(REFSEQF) > /dev/null && \ 304 ls `pwd`/tmp/refseq/KC702174.1 > /dev/null ; \ 305 else echo download of $(REFSEQF) when ascp is not found is disabled ; \ 306 fi 307 308 @rm `pwd`/tmp/nannot/GCA_000390265.1_R 309 @echo NANNOT FASP download when user repository is configured 310 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 311 echo NANNOT FASP download when user repository is configured ; \ 312 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 313 $(DIRTOTEST)/prefetch $(KMERF) > /dev/null ; \ 314 ls `pwd`/tmp/nannot/GCA_000390265.1_R > /dev/null ; \ 315 else echo download of $(KMERF) when ascp is not found is disabled ; \ 316 fi 317 318 @if ls `pwd`/tmp/wgs/AFVF01.1 2> /dev/null ; \ 319 then echo AFVF01.1 found ; exit 1; fi 320 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then echo ; \ 321 echo WGS FASP download when user repository is configured ; \ 322 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 323 $(DIRTOTEST)/prefetch $(WGSF) > /dev/null ; \ 324 ls `pwd`/tmp/wgs/AFVF01.1 > /dev/null ; \ 325 rm `pwd`/tmp/wgs/AFVF01.1 ; \ 326 else echo download of $(WGSF) when ascp is not found is disabled ; \ 327 fi 328 @echo 329 330 @rm -f `pwd`/tmp/sra/$(SRAC).sra 331 332 @echo 'repository/remote/main/CGI/resolver-cgi = "$(CGI)"' >> tmp/t.kfg 333 @echo SRR accession download 334 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 335 $(DIRTOTEST)/prefetch $(SRAC) > /dev/null 336 @ls `pwd`/tmp/sra/$(SRAC).sra > /dev/null 337 338 @echo prefetch run with refseqs 339 @rm -fr `pwd`/SRR619505 340 @rm -fv `pwd`/tmp/sra/SRR619505.sra 341 @rm -fv `pwd`/tmp/refseq/NC_000005.8 342 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 343 $(DIRTOTEST)/prefetch SRR619505 > /dev/null 344 @ls `pwd`/tmp/sra/SRR619505.sra > /dev/null 345 @ls `pwd`/tmp/refseq/NC_000005.8 > /dev/null 346 347 @echo REFSEQ accession download 348 @rm -f `pwd`/tmp/refseq/KC702174.1 349 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 350 $(DIRTOTEST)/prefetch KC702174.1 > /dev/null 351 @ls `pwd`/tmp/refseq/KC702174.1 > /dev/null 352 353 @echo NANNOT accession download 354 @rm -f `pwd`/tmp/nannot/GCA_000390265.1_R 355 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 356 $(DIRTOTEST)/prefetch GCA_000390265.1_R > /dev/null 357 @ls `pwd`/tmp/nannot/GCA_000390265.1_R > /dev/null 358 359 @echo WGS accession download 360 @rm -f `pwd`/tmp/wgs/AFVF01 361 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 362 $(DIRTOTEST)/prefetch AFVF01 > /dev/null 363 @ls `pwd`/tmp/wgs/AFVF01 > /dev/null 364 @rm `pwd`/tmp/wgs/AFVF01 365 366 @if ls `pwd`/tmp2/100MB 2> /dev/null ; \ 367 then echo 100MB found ; exit 1; fi 368 @ echo FASP download: asperasoft/100MB: turned off 369 370 @if ascp -h > /dev/null ; \ 371 then \ 372 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 373 else \ 374 if $(DIRTOTEST)/prefetch $(LARGE) 2> /dev/null ; \ 375 then \ 376 echo "prefetch <FASP URL> when ascp is not found should fail" ; \ 377 exit 1; \ 378 fi ; \ 379 fi 380 381 @rm -f `pwd`/tmp2/100MB 382 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 383 if $(DIRTOTEST)/prefetch fasp://anonftp@ftp.ncbi.nlm.nih.gov:100MB \ 384 > /dev/null 2>&1; \ 385 then echo "prefetch <FASP> when FASP source is not found should fail"; \ 386 exit 1 ; \ 387 fi 388 389 @rm -r tmp* 390 391vdbcache: 392 @ echo vdbcache download 393 394 @ rm -frv tmp 395 396 @ mkdir -p tmp 397 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 398 399 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 400 cd tmp && $(DIRTOTEST)/prefetch SRR6667190 > /dev/null 401 @ ls `pwd`/tmp/SRR6667190/SRR6667190.sra > /dev/null 402 @ ls `pwd`/tmp/SRR6667190/SRR6667190.sra.vdbcache > /dev/null 403 404 @ rm -r tmp 405 406################################################################################ 407 408ncbi1GB: 409 @mkdir -p tmp 410 411 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 412 413 @if ls `pwd`/tmp/1GB 2> /dev/null; \ 414 then echo 1GB found ; exit 1; fi 415 416 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 417 echo FASP download: ncbi/1GB ; \ 418 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && cd tmp && \ 419 $(DIRTOTEST)/prefetch fasp://anonftp@ftp.ncbi.nlm.nih.gov:1GB>/dev/null&&\ 420 ls `pwd`/1GB > /dev/null ; \ 421 fi 422 423 @rm -r tmp 424 425################################################################################ 426 427out_dir_and_file: 428 @ mkdir -p tmp tmp2 429 @ rm -fr tmp*/* 430 @ echo version 1.0 > tmp/k 431 @ echo '0||SRR053325||' >> tmp/k 432 @ echo '$$end' >> tmp/k 433 434 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 435 @ echo 'repository/remote/main/CGI/resolver-cgi = "$(CGI)"' >> tmp/t.kfg 436 @ echo '$(PUBLIC)/apps/sra/volumes/sraFlat = "sra"' >> tmp/t.kfg 437 @ echo '$(PUBLIC)/root = "$(CWD)/tmp"' >> tmp/t.kfg 438 @ echo '/repository/site/disabled = "true"' >> tmp/t.kfg 439 440 @ echo PREFETCH ACCESSION TO OUT-FILE 441 @ rm -f `pwd`/tmp-file* 442 @ NCBI_SETTINGS=/ NCBI_VDB_RELIABLE=y VDB_CONFIG=`pwd`/tmp \ 443 $(DIRTOTEST)/prefetch $(SRAC) -o tmp-file -v > /dev/null 444 @ ls `pwd`/tmp-file > /dev/null 445 @ rm `pwd`/tmp-file 446 447 @ echo PREFETCH ACCESSION TO OUT-FILE INSIDE OF DIR 448 @ if ls `pwd`/tmp3/dir/file 2> /dev/null ; \ 449 then echo file found ; exit 1 ; fi 450 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 451 $(DIRTOTEST)/prefetch $(SRAC) -O / -o tmp3/dir/file -v > /dev/null 452 @ ls `pwd`/tmp3/dir/file > /dev/null 453 454 @ if echo $(SRR) | grep -vq /sdlr/sdlr.fcgi?jwt= ; \ 455 then \ 456 echo PREFETCH SRR HTTP URL TO OUT-FILE && \ 457 rm -f `pwd`/tmp3/dir/file && \ 458 NCBI_SETTINGS=/ NCBI_VDB_RELIABLE=y VDB_CONFIG=`pwd`/tmp \ 459 $(DIRTOTEST)/prefetch $(SRR) -O / -o tmp3/dir/file > /dev/null && \ 460 ls `pwd`/tmp3/dir/file > /dev/null ; \ 461 else \ 462 echo prefetch test when CE is required is skipped ; \ 463 fi 464 465 @ echo PREFETCH SRR FASP URL TO OUT-FILE IS DISABLED 466# @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 467 echo PREFETCH SRR FASP URL TO OUT-FILE ; \ 468 rm -f `pwd`/tmp3/dir/file ; \ 469 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 470 $(DIRTOTEST)/prefetch $(SRRF) -O / -o tmp3/dir/file > /dev/null ; \ 471 ls `pwd`/tmp3/dir/file > /dev/null ; \ 472 else echo download of SRR FASP URL when ascp is not found is disabled ; \ 473 fi 474# @ echo 475# @ echo 476 477 @ echo PREFETCH HTTP DIRECTORY URL TO OUT-FILE 478 @ rm -f `pwd`/tmp3/dir/file 479 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 480 $(DIRTOTEST)/prefetch https://github.com/ncbi/ -O / -o tmp3/dir/file \ 481 > /dev/null 482 @ ls `pwd`/tmp3/dir/file > /dev/null 483# @ echo 484 485 @ echo PREFETCH HTTP FILE URL TO OUT-FILE 486 @ rm -f `pwd`/tmp3/dir/file 487 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 488 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki -O / \ 489 -o tmp3/dir/file > /dev/null 490 @ ls `pwd`/tmp3/dir/file > /dev/null 491# @ echo 492 493 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 494 echo PREFETCH FASP URL TO OUT-FILE ; \ 495 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 496 rm -f `pwd`/tmp3/dir/file ; \ 497 $(DIRTOTEST)/prefetch $(REFSEQF) -O / -o tmp3/dir/file > /dev/null ; \ 498 ls `pwd`/tmp3/dir/file > /dev/null ; \ 499 else echo download of SRR FASP URL when ascp is not found is disabled ; \ 500 fi 501 502 @ if [ "$(BUILD)" = "dbg" ]; then \ 503 echo PREFETCH TEXT-KART was disabled: need to have a public example of protected run or add support of public accessions; \ 504 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 505 echo $(DIRTOTEST)/prefetch --text-kart tmp/k > /dev/null ; \ 506 echo ls `pwd`/tmp/sra/SRR053325.sra > /dev/null ; \ 507 fi 508 509 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 510 if $(DIRTOTEST)/prefetch SRR045450 $(SRAC) -o tmp/o 2> /dev/null ; \ 511 then echo unexpected success when downloading multiple items to file ; \ 512 exit 1 ; \ 513 fi ; 514 515 @ echo PREFETCH MULTIPLE ITEMS 516 @ rm -fr `pwd`/SRR0* `pwd`/tmp/sra 517 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 518 $(DIRTOTEST)/prefetch SRR045450 $(SRAC) > /dev/null 519 @ ls `pwd`/tmp/sra/SRR045450.sra `pwd`/tmp/sra/$(SRAC).sra > /dev/null 520 521 @ if echo $(SRR) | grep -vq /sdlr/sdlr.fcgi?jwt= ; \ 522 then \ 523 echo PREFETCH SRR HTTP URL && \ 524 rm `pwd`/tmp/sra/$(SRAC).sra && \ 525 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 526 $(DIRTOTEST)/prefetch $(SRR) > /dev/null && \ 527 ls `pwd`/tmp/sra/$(SRAC).sra > /dev/null ; \ 528 else \ 529 echo prefetch test when CE is required is skipped ; \ 530 fi 531 532 @ echo PREFETCH SRR FASP URL IS DISABLED 533# @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 534 echo PREFETCH SRR FASP URL ; \ 535 rm `pwd`/tmp/sra/$(SRAC).sra ; \ 536 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 537 $(DIRTOTEST)/prefetch $(SRRF) > /dev/null ; \ 538 ls `pwd`/tmp/sra/$(SRAC).sra > /dev/null ; \ 539 else echo download of SRR FASP URL when ascp is not found is disabled ; \ 540 fi 541 542 @ echo PREFETCH HTTP DIRECTORY URL 543 @ if ls `pwd`/tmp2/index.html 2> /dev/null ; then exit 1; fi 544 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 545 $(DIRTOTEST)/prefetch https://github.com/ncbi/ > /dev/null 546 @ ls `pwd`/tmp2/index.html > /dev/null 547 @ rm `pwd`/tmp2/index.html 548 549 @ echo PREFETCH HTTP FILE URL 550 @ if ls `pwd`/tmp2/wiki 2> /dev/null ; \ 551 then echo wiki found ; exit 1 ; fi 552 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 553 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki > /dev/null 554 @ ls `pwd`/tmp2/wiki > /dev/null 555 556 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 557 echo PREFETCH FASP URL ; \ 558 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; cd tmp2 ; \ 559 if ls `pwd`/KC702174.1 2> /dev/null ; then exit 1; fi ; \ 560 $(DIRTOTEST)/prefetch $(REFSEQF) > /dev/null && \ 561 ls `pwd`/KC702174.1 > /dev/null ; \ 562 else echo download of FASP URL when ascp is not found is disabled ; \ 563 fi 564 565 @ echo PREFETCH ACCESSION TO OUT-DIR 566 @ rm -f `pwd`/tmp3/dir/$(SRAC).sra 567 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 568 $(DIRTOTEST)/prefetch $(SRAC) -O tmp3/dir > /dev/null 569 @ ls `pwd`/tmp3/dir/$(SRAC).sra > /dev/null 570 571 @ if echo $(SRR) | grep -vq /sdlr/sdlr.fcgi?jwt= ; \ 572 then \ 573 echo PREFETCH SRR HTTP URL TO OUT-DIR && \ 574 rm -f `pwd`/tmp3/dir/$(SRAC).sra && \ 575 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 576 $(DIRTOTEST)/prefetch $(SRR) -O tmp3/dir > /dev/null && \ 577 ls `pwd`/tmp3/dir/$(SRAC).sra > /dev/null ; \ 578 else \ 579 echo prefetch test when CE is required is skipped ; \ 580 fi 581 582 @ echo PREFETCH SRR FASP URL TO OUT-DIR IS DISABLED 583# @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 584 echo PREFETCH SRR FASP URL TO OUT-DIR ; \ 585 rm -f `pwd`/tmp3/dir/$(SRAC).sra ; \ 586 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 587 $(DIRTOTEST)/prefetch $(SRRF) -O tmp3/dir > /dev/null ; \ 588 ls `pwd`/tmp3/dir/$(SRAC).sra > /dev/null ; \ 589 else echo download of SRR FASP URL when ascp is not found is disabled ; \ 590 fi 591# @ echo 592 593 @ echo PREFETCH HTTP DIRECTORY URL TO OUT-DIR 594 @ rm -f index.html 595 @ if ls `pwd`/tmp3/dir/index.html 2> /dev/null ; \ 596 then echo index.html found ; exit 1 ; fi 597 @export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 598 $(DIRTOTEST)/prefetch https://github.com/ncbi/ -O tmp3/dir > /dev/null 599 @ ls `pwd`/tmp3/dir/index.html > /dev/null 600# @ echo 601 602 @ echo PREFETCH HTTP FILE URL TO OUT-DIR 603 @ rm -f wiki 604 @ if ls `pwd`/tmp3/dir/wiki 2> /dev/null ; \ 605 then echo wiki found ; exit 1 ; fi 606 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 607 $(DIRTOTEST)/prefetch https://github.com/ncbi/ngs/wiki -O tmp3/dir \ 608 > /dev/null 609 @ ls `pwd`/tmp3/dir/wiki > /dev/null 610# @ echo 611 612 @ if [ "${HAVE_NCBI_ASCP}" = "1" ] ; then \ 613 echo PREFETCH FASP URL TO OUT-DIR ; \ 614 export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 615 if ls `pwd`/tmp3/dir/KC702174.1 2> /dev/null ; then \ 616 echo 100MB found ; exit 1 ; fi ; \ 617 $(DIRTOTEST)/prefetch $(REFSEQF) -O tmp3/dir > /dev/null && \ 618 ls `pwd`/tmp3/dir/KC702174.1 > /dev/null ; \ 619 else echo download of SRR FASP URL when ascp is not found is disabled ; \ 620 fi 621# @ echo 622 623 @ rm -r tmp* 624 625s-option: 626 @ mkdir -p tmp 627 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 628 @ echo 'repository/remote/main/CGI/resolver-cgi = "$(CGI)"' >> tmp/t.kfg 629 @ echo '$(PUBLIC)/apps/sra/volumes/sraFlat = "sra"' >> tmp/t.kfg 630 @ echo '$(PUBLIC)/root = "$(CWD)/tmp"' >> tmp/t.kfg 631 632 @ echo Downloading KART was disabled: need to have a public example of protected run or add support of public accessions 633 @ rm -f tmp/sra/SRR0* 634 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 635 # $(DIRTOTEST)/prefetch kart.krt > /dev/null 636 637 @ echo Downloading KART: ORDER BY SIZE / SHORT OPTION disabled, too 638 @ rm -f tmp/sra/* 639 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 640 # $(DIRTOTEST)/prefetch kart.krt -os > /dev/null 641 642 @ echo Downloading KART: ORDER BY KART / SHORT OPTION disabled, too 643 @ rm -f tmp/sra/* 644 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 645 # $(DIRTOTEST)/prefetch kart.krt -ok > /dev/null 646 647 @ echo Downloading KART: ORDER BY SIZE / LONG OPTION disabled, too 648 @ rm -f tmp/sra/* 649 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 650 # $(DIRTOTEST)/prefetch kart.krt --order s > /dev/null 651 652 @ echo Downloading KART: ORDER BY KART / LONG OPTION disabled, too 653 @ rm -f tmp/sra/* 654 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 655 # $(DIRTOTEST)/prefetch kart.krt --order k > /dev/null 656 657 @ echo Downloading ACCESSION 658 @ rm -f tmp/sra/$(SRAC).sra 659 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 660 $(DIRTOTEST)/prefetch $(SRAC) > /dev/null 661 662 @ echo Downloading ACCESSION TO FILE: SHORT OPTION 663 @ rm -f tmp/1 664 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 665 $(DIRTOTEST)/prefetch $(SRAC) -otmp/1 > /dev/null 666# @ echo 667 668 @ echo Downloading ACCESSION TO FILE: LONG OPTION 669 @ rm -f tmp/2 670 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 671 $(DIRTOTEST)/prefetch $(SRAC) --output-file tmp/2 > /dev/null 672 673 @ echo Downloading ACCESSIONS 674 @ rm -f tmp/sra/* 675 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 676 $(DIRTOTEST)/prefetch $(SRAC) SRR045450 > /dev/null 677 678 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 679 if $(DIRTOTEST)/prefetch SRR045450 $(SRAC) -o tmp/o 2> /dev/null ; \ 680 then echo unexpected success when downloading multiple items to file ; \ 681 exit 1 ; \ 682 fi ; 683 684 @ export VDB_CONFIG=`pwd`/tmp; export NCBI_SETTINGS=/ ; \ 685 if $(DIRTOTEST)/prefetch SRR045450 $(SRAC) -output-file tmp/o \ 686 2> /dev/null ; \ 687 then echo unexpected success when downloading multiple items to file ; \ 688 exit 1 ; \ 689 fi ; 690 691 @ echo version 1.0 > tmp/k 692 @ echo '0||SRR045450||' >> tmp/k 693 @ echo '0||SRR053325||' >> tmp/k 694 @ echo '$$end' >> tmp/k 695 696 @ if [ "$(BUILD)" = "dbg" ]; then \ 697 echo Downloading TEXT KART is disabled, as well ; \ 698 if [ "$(BUILD)" = "dg" ]; then \ 699 echo Downloading TEXT KART && \ 700 rm -f tmp/sra/* && \ 701 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 702 $(DIRTOTEST)/prefetch --text-kart tmp/k > /dev/null && \ 703 \ 704 echo Downloading TEXT KART: ORDER BY SIZE / SHORT OPTION && \ 705 rm -f tmp/sra/* && \ 706 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 707 $(DIRTOTEST)/prefetch --text-kart tmp/k -os > /dev/null 2>&1 && \ 708 \ 709 echo Downloading TEXT KART: ORDER BY KART / SHORT OPTION && \ 710 rm -f tmp/sra/* && \ 711 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 712 $(DIRTOTEST)/prefetch --text-kart tmp/k -ok > /dev/null 2>&1 && \ 713 \ 714 echo Downloading TEXT KART: ORDER BY SIZE / LONG OPTION && \ 715 rm -f tmp/sra/* && \ 716 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 717 $(DIRTOTEST)/prefetch --text-kart tmp/k --order s > /dev/null && \ 718 \ 719 echo Downloading TEXT KART: ORDER BY KART / LONG OPTION && \ 720 rm -f tmp/sra/* && \ 721 export VDB_CONFIG=`pwd`/tmp && export NCBI_SETTINGS=/ && \ 722 $(DIRTOTEST)/prefetch --text-kart tmp/k --order k > /dev/null ; \ 723 fi \ 724 fi 725 726 @ rm -r tmp* 727 728truncated: 729 @ echo prefetch correctly re-downloads incomplete files 730 731#setup 732 @ mkdir -p tmp/sra 733 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 734 @ echo 'repository/remote/main/CGI/resolver-cgi = "$(CGI)"' >> tmp/t.kfg 735 @ echo '$(PUBLIC)/apps/sra/volumes/sraFlat = "sra"' >> tmp/t.kfg 736 @ echo '$(PUBLIC)/root = "$(CWD)/tmp"' >> tmp/t.kfg 737# @ ls -l tmp @ cat tmp/t.kfg 738# @ VDB_CONFIG=`pwd`/tmp NCBI_SETTINGS=/ $(DIRTOTEST)/vdb-config -on 739# @ VDB_CONFIG=`pwd`/tmp NCBI_SETTINGS=/ $(DIRTOTEST)/srapath $(SRAC) 740# echo 669 perl check-size.pl 4 echo 671 741 742# create truncated run 743 @ echo '123' > tmp/sra/$(SRAC).sra 744 @ if perl check-size.pl 4 > /dev/null; \ 745 then echo "run should be truncated for this test"; exit 1; \ 746 fi 747 748# prefetch should detect truncated run and redownload it 749 @ VDB_CONFIG=`pwd`/tmp NCBI_SETTINGS=/ $(DIRTOTEST)/prefetch $(SRAC) >tmp/out 750 @ if grep ": 1) '$(SRAC)' is found locally" tmp/out ; \ 751 then echo "prefetch incorrectly stopped on truncated run"; exit 1; \ 752 fi 753# @ wc tmp/sra/$(SRAC).sra @ wc -c tmp/sra/$(SRAC).sra 754 755# run should be complete 756 @ perl check-size.pl 4 757 758# the second run of prefetch should find local file 759 @ VDB_CONFIG=`pwd`/tmp NCBI_SETTINGS=/ $(DIRTOTEST)/prefetch $(SRAC) >tmp/out 760 @ grep -q ": 1) '$(SRAC)' is found locally" tmp/out 761 @ perl check-size.pl 4 762 763#cleanup 764 @ rm -r tmp 765 766kart: ########################################################################## 767 @rm -frv tmp/* 768 @mkdir -p tmp 769 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 770 @echo 'repository/remote/main/SDL.2/resolver-cgi = "$(SDL)"' >> tmp/t.kfg 771 772 @echo "Downloading --cart <kart> ordered by default (size)" 773 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 774 NCBI_SETTINGS=/ VDB_CONFIG=. \ 775 perl ../check-prefetch-out.pl 0 0 \ 776 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc --cart ../data/3-dbGaP-0.krt -Cn" 777 @cd tmp && rm SRR1219879/SRR1219879_dbGaP-0.sra* 778 @cd tmp && rm SRR1219880/SRR1219880_dbGaP-0.sra* 779 @cd tmp && rm SRR1257493/SRR1257493_dbGaP-0.sra* 780 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 781 782 @echo "Downloading kart ordered by default (size)" 783 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 784 NCBI_SETTINGS=/ VDB_CONFIG=. \ 785 perl ../check-prefetch-out.pl 0 0 \ 786 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -Cn" 787 @cd tmp && rm SRR1219879/SRR1219879_dbGaP-0.sra* 788 @cd tmp && rm SRR1219880/SRR1219880_dbGaP-0.sra* 789 @cd tmp && rm SRR1257493/SRR1257493_dbGaP-0.sra* 790 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 791 792 @echo "Downloading kart ordered by size" 793 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 794 NCBI_SETTINGS=/ VDB_CONFIG=. \ 795 perl ../check-prefetch-out.pl 0 0 \ 796 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -os -Cn" 797 @cd tmp && rm SRR1219879/SRR1219879_dbGaP-0.sra* 798 @cd tmp && rm SRR1219880/SRR1219880_dbGaP-0.sra* 799 @cd tmp && rm SRR1257493/SRR1257493_dbGaP-0.sra* 800 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 801 802 @echo "Downloading kart ordered by kart" 803 @cd tmp && printf "ding 'SRR1257493'\nding 'SRR1219880'\nding 'SRR1219879'"|\ 804 NCBI_SETTINGS=/ VDB_CONFIG=. \ 805 perl ../check-prefetch-out.pl 0 0 \ 806 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -ok -Cn" 807 @rm tmp/SRR1219879/SRR1219879_dbGaP-0.sra* 808 @rm tmp/SRR1219880/SRR1219880_dbGaP-0.sra* 809 @rm tmp/SRR1257493/SRR1257493_dbGaP-0.sra* 810 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 811 812 @rm -frv tmp/sra 813 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/t.kfg 814 @echo 'repository/remote/main/SDL.2/resolver-cgi = "$(SDL)"' >> tmp/t.kfg 815 @echo '$(PUBLIC)/apps/sra/volumes/sraFlat = "sra"' >> tmp/t.kfg 816 @echo '$(PUBLIC)/root = "$(CWD)/tmp"' >> tmp/t.kfg 817 818 @echo "Downloading kart ordered by default (size) to user repo" 819 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 820 NCBI_SETTINGS=/ VDB_CONFIG=. \ 821 perl ../check-prefetch-out.pl 0 0 \ 822 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -Cn" 823 @rm tmp/sra/SRR1219879_dbGaP-0.sra* 824 @rm tmp/sra/SRR1219880_dbGaP-0.sra* 825 @rm tmp/sra/SRR1257493_dbGaP-0.sra* 826 @rmdir tmp/sra 827 828 @echo "Downloading kart ordered by size to user repo" 829 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 830 NCBI_SETTINGS=/ VDB_CONFIG=. \ 831 perl ../check-prefetch-out.pl 0 0 \ 832 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -os -Cn" 833 @rm tmp/sra/SRR1219879_dbGaP-0.sra* 834 @rm tmp/sra/SRR1219880_dbGaP-0.sra* 835 @rm tmp/sra/SRR1257493_dbGaP-0.sra* 836 @rmdir tmp/sra 837 838 @echo "Downloading kart ordered by kart to user repo" 839 @cd tmp && printf "ding 'SRR1257493'\nding 'SRR1219880'\nding 'SRR1219879'"|\ 840 NCBI_SETTINGS=/ VDB_CONFIG=. \ 841 perl ../check-prefetch-out.pl 0 0 \ 842 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -ok -Cn" 843 @rm tmp/sra/SRR1219879_dbGaP-0.sra* 844 @rm tmp/sra/SRR1219880_dbGaP-0.sra* 845 @rm tmp/sra/SRR1257493_dbGaP-0.sra* 846 @rmdir tmp/sra 847 848 @echo '/tools/prefetch/download_to_cache = "false"' >> tmp/t.kfg 849 @echo "Downloading kart ordered by default (size) ignoring user repo" 850 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 851 NCBI_SETTINGS=/ VDB_CONFIG=. \ 852 perl ../check-prefetch-out.pl 0 0 \ 853 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -Cn" 854 @cd tmp && rm SRR1219879/SRR1219879_dbGaP-0.sra* 855 @cd tmp && rm SRR1219880/SRR1219880_dbGaP-0.sra* 856 @cd tmp && rm SRR1257493/SRR1257493_dbGaP-0.sra* 857 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 858 859 @echo "Downloading kart ordered by size ignoring user repo" 860 @cd tmp && printf "ding 'SRR1219879'\nding 'SRR1219880'\nding 'SRR1257493'"|\ 861 NCBI_SETTINGS=/ VDB_CONFIG=. \ 862 perl ../check-prefetch-out.pl 0 0 \ 863 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -os -Cn" 864 @cd tmp && rm SRR1219879/SRR1219879_dbGaP-0.sra* 865 @cd tmp && rm SRR1219880/SRR1219880_dbGaP-0.sra* 866 @cd tmp && rm SRR1257493/SRR1257493_dbGaP-0.sra* 867 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 868 869 @echo "Downloading kart ordered by kart ignoring user repo" 870 @cd tmp && printf "ding 'SRR1257493'\nding 'SRR1219880'\nding 'SRR1219879'"|\ 871 NCBI_SETTINGS=/ VDB_CONFIG=. \ 872 perl ../check-prefetch-out.pl 0 0 \ 873 "$(DIRTOTEST)/prefetch --ngc ../data/prj_phs710EA_test.ngc ../data/3-dbGaP-0.krt -ok -Cn" 874 @rm tmp/SRR1219879/SRR1219879_dbGaP-0.sra* 875 @rm tmp/SRR1219880/SRR1219880_dbGaP-0.sra* 876 @rm tmp/SRR1257493/SRR1257493_dbGaP-0.sra* 877 @cd tmp && rmdir SRR1219879 SRR1219880 SRR1257493 878 879 @rm -r tmp 880 881wgs: 882 @echo Verifying prefetch of runs with WGS references... 883 884 @rm -fr tmp 885 @mkdir tmp 886 887 @#pwd 888 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/k 889 890 @cd tmp && NCBI_SETTINGS=k $B/prefetch SRR619505 -fy > /dev/null 891 @ls tmp/SRR619505/SRR619505.sra tmp/SRR619505/NC_000005.8 > /dev/null 892 @rm -r tmp/S* 893 894 @echo '/repository/site/disabled = "true"' >> tmp/k 895 @echo '/repository/remote/main/SDL.2/resolver-cgi = "https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve"' >> tmp/k 896 @echo '/repository/user/main/public/apps/refseq/volumes/refseq = "refseq"' \ 897 >> tmp/k 898 @echo '/repository/user/main/public/apps/wgs/volumes/wgsFlat = "wgs"' >> tmp/k 899 @printf '/repository/user/main/public/root = "%s/tmp"\n' `pwd` >> tmp/k 900 @#cat tmp/k 901 902 @cd tmp && NCBI_SETTINGS=/ VDB_CONFIG=k $B/prefetch SRR619505 -fy > /dev/null 903 @ls tmp/SRR619505/SRR619505.sra tmp/refseq/NC_000005.8 > /dev/null 904 @rm -r tmp/[rS]* 905 906#TODO: TO ADD AD for AAAB01 cd tmp && prefetch SRR353827 -fy -+VFS 907 908 @cd tmp && NCBI_SETTINGS=/ VDB_CONFIG=k $B/prefetch SRR353827 -fy > /dev/null 909 @cd tmp && NCBI_SETTINGS=/ VDB_CONFIG=k $B/align-info SRR353827 \ 910 | grep -v 'false,remote::https:' > /dev/null 911 @ls tmp/SRR353827/SRR353827.sra tmp/wgs/AAAB01 > /dev/null 912 @rm -r tmp/[wS]* 913 @rm -r tmp 914 915lots_wgs: 916 @echo Verifying prefetch of run with with a lot of WGS references... 917 @rm -fr tmp 918 @mkdir tmp 919 920 @#pwd 921 @echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/k 922 @echo '/repository/site/disabled = "true"' >> tmp/k 923 @echo '/repository/remote/main/SDL.2/resolver-cgi = "https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve"' >> tmp/k 924 @echo '/repository/user/main/public/apps/refseq/volumes/refseq = "refseq"' \ 925 >> tmp/k 926 @echo '/repository/user/main/public/apps/wgs/volumes/wgsFlat = "wgs"' >> tmp/k 927 @printf '/repository/user/main/public/root = "%s/tmp"\n' `pwd` >> tmp/k 928 @#cat tmp/k 929 930 @echo ' ... prefetching...' 931 @cd tmp && NCBI_SETTINGS=/ VDB_CONFIG=k $B/prefetch ERR3091357 -fy > /dev/null 932 @echo ' ... align-infoing...' 933 @cd tmp && NCBI_SETTINGS=/ VDB_CONFIG=k $B/align-info ERR3091357 \ 934 | grep -v 'false,remote::https:' > /dev/null 935 @ls tmp/ERR3091357/ERR3091357.sra tmp/wgs/JTFH01 tmp/refseq/KN707955.1 \ 936 > /dev/null 937 938 @rm -r tmp 939 940resume: 941 @ echo Verifying prefetch resume 942 @ rm -frv tmp/* 943 @ mkdir -p tmp 944 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/k 945 @ echo '/repository/site/disabled = "true"' >> tmp/k 946 @ cd tmp && PATH=$(B):$(PATH) NCBI_SETTINGS=k perl ../test-resume.pl 947 @ rm -r tmp 948 949hs37d5: 950 @ echo Verifying hs37d5 951 @ rm -frv tmp/* 952 @ mkdir -p tmp 953 @ cd tmp && NCBI_SETTINGS=k PATH=$(B):$(PATH) perl ../test-hs37d5.pl 954 @ rm -r tmp 955 956ad_as_dir: # turned off by default. Library test is in 957 # ncbi-vdb\test\vfs\managertest.cpp::TestVFSManagerCheckAd 958 @ echo we can use AD as dir/... 959 @ mkdir -p tmp 960 @ export NCBI_SETTINGS=/ && export PATH=$(DIRTOTEST):$(PATH) \ 961 && cd tmp && perl ../use-AD-as-dir.pl 962 @ rm -r tmp 963 964dump-vs-prefetch: 965 @ rm -frv tmp/* 966 @ mkdir -pv tmp 967 @ cd tmp && NCBI_SETTINGS=/ NCBI_VDB_NO_ETC_NCBI_KFG=1 PATH=$(B):$(PATH) \ 968 perl ../dump-vs-prefetch.pl 969 @ rm -r tmp 970 971quality: std 972 @ echo Testing quality 973 @ mkdir -p tmp 974 @ echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > tmp/k 975 @ cd tmp && NCBI_SETTINGS=k PATH=$(DIRTOTEST):$(BINDIR):$(PATH) \ 976 perl ../test-quality.pl 977 @ rm -r tmp 978