diff --git a/plasmid/resource/SAMPLE-PLASMID-template.xlsx b/plasmid/resource/SAMPLE-PLASMID-template.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..fc22660c5459a37c77647c9fa956be5c98007af2 Binary files /dev/null and b/plasmid/resource/SAMPLE-PLASMID-template.xlsx differ diff --git a/plasmid/resource/eclipse/plasmid Data Store Server.launch b/plasmid/resource/eclipse/plasmid Data Store Server.launch index a0790039b7102fa1aeda1575ba518ca782fbc24e..d4bfed2f3ac7a6eefdfd59ebfeaa1833afddcaf5 100644 --- a/plasmid/resource/eclipse/plasmid Data Store Server.launch +++ b/plasmid/resource/eclipse/plasmid Data Store Server.launch @@ -7,6 +7,9 @@ <listEntry value="1"/> </listAttribute> <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/> +<listAttribute key="org.eclipse.debug.ui.favoriteGroups"> +<listEntry value="org.eclipse.debug.ui.launchGroup.run"/> +</listAttribute> <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="ch.systemsx.cisd.openbis.dss.generic.DataStoreServer"/> <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="plasmid"/> <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx512M -ea"/> diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316-1.ab1 b/plasmid/resource/example/FRP_1/PRS316-1.ab1 similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316-1.ab1 rename to plasmid/resource/example/FRP_1/PRS316-1.ab1 diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316-2.ab1 b/plasmid/resource/example/FRP_1/PRS316-2.ab1 similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316-2.ab1 rename to plasmid/resource/example/FRP_1/PRS316-2.ab1 diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316-3.ab1 b/plasmid/resource/example/FRP_1/PRS316-3.ab1 similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316-3.ab1 rename to plasmid/resource/example/FRP_1/PRS316-3.ab1 diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316.gb b/plasmid/resource/example/FRP_1/PRS316.fasta similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316.gb rename to plasmid/resource/example/FRP_1/PRS316.fasta diff --git a/plasmid/resource/example/FRP_1/PRS316.gb b/plasmid/resource/example/FRP_1/PRS316.gb new file mode 100644 index 0000000000000000000000000000000000000000..e33465983622dfc0c12a4c407740b02c146ecb2b --- /dev/null +++ b/plasmid/resource/example/FRP_1/PRS316.gb @@ -0,0 +1,229 @@ +ID PRS316 preliminary; circular DNA; SYN; 4887 BP. +XX +AC U03442; ATCC77145; +XX +DT 01-JUL-1993 (Rel. 7, Created) +DT 01-JUL-1995 (Rel. 12, Last updated, Version 1) +XX +DE Saccharomyces/E.coli phagemid vector pRS316 - complete. +XX +KW cloning vector. +XX +OS Cloning vector +OC Artificial sequences; Cloning vehicles. +XX +RN [1] +RP 1-4887 +RC pRSS56 from pBluescript KS+ & BlueScribe +RC pRS303 from pRSS56 & HIS3 gene +RC pRS304 from pRSS56 & TRP1 gene +RC pRS305 from pRSS56 & LEU2 gene +RC pRS306 from pRSS56 & URA3 gene +RC pUC19-CEN6:32 from pUC19 & CEN6 +RC pRSS83 from pUC19-CEN6:32 & pAB9, ARS +RC pRSS84 from pRSS83 +RC pRS313 from pRS303 & pRSS84 +RC pRS314 from pRS304 & pRSS84 +RC pRS315 from pRS305 & pRSS84 +RC pRS316 from pRS306 & pRSS84 +RC pRSS93 from pRSS84 & pYCF5 +RA Sikorski R.S., Hieter P.; +RT "A system of shuttle vectors and yeast host strains designed for +RT efficient manipulation of DNA in Saccharomyces cerevisiae"; +RL Genetics 122:19-27(1989). +XX +RN [2] +RC from YEp24 +RC from YCp50 +RC from YIp5 +RA Strathern J.N., Higgins D.R.; +RT "Recovery of plasmids from yeast into Escherichia coli: shuttle +RT vectors"; +RL Meth. Enzymol. 194:319-329(1991). +XX +RN [3] +RC pRS316 +RA Stillman D.J.; +RT ; +RL Submitted (10-NOV-1993) by: +RL Stillman D.J., Dept. of Cellular, Viral and Molecular Biology, +RL University of Utah Medical Center, Salt Lake City, UT 84132 USA. +XX +CC One of a series of pBluescript-based centromere vectors (ATCC 77142 +CC ATCC 77145, ATCC 77157 to ATCC 77158) differing in the yeast +CC selectable marker gene. [1] +CC The order of the major features in this plasmid is: URA3 - f1 ori +CC (NaeI) - T7 promoter - lacZ'/MCS - T3 promoter - pMB1 ori - bla - +CC CEN6 - ARSH4. +CC A fragment (1.112 kb) containing the URA3 gene was inserted into the +CC NdeI site and a cassette containing CEN6 and the ARS associated with +CC histone 4 (ARSH4) was inserted into the AatII site of pRSS56. All ends +CC were blunted. +CC pRSS56, constructed by ligating a PvuI fragment (bp 498-2412) of +CC pBluescript KS+ to a PvuI fragment (bp 2850-730) of pBS(+), contains +CC the KS MCS from pBluescript KS+ and the unique NdeI and AatII sites +CC between bla and f1 origin of pBS(+). [1] +CC YC-type centromere vector permitting visual detection of recombinants +CC and production of ssDNA in E.coli. Contains promoters for in vitro +CC RNA synthesis, priming sites useful for sequencing, and encodes the +CC lacZ alpha (lacZ') peptide. [1] +CC Useful in plasmid shuffle experiments. +CC Restriction digests of the clone give the following sizes (kb): +CC EcoRI--5.0; BamHI--5.0, PvuII--4.4, 0.5. (ATCC staff) +CC Medium is 1227 LB plus ampicillin. +CC NCBI gi: 417973 +CC NM (pRS316) +CC CM (yes) +CC NA (ds-DNA) +CC TP (circular) +CC ST () +CC TY (phagemid) +CC SP (ATCC) +CC HO (E.coli HB101)(Saccharomyces cerevisiae)(E.coli) +CC HO (Saccharomyces cerevisiae YPH499)(Saccharomyces cerevisiae YPH500) +CC HO (Saccharomyces cerevisiae YPH501) +CC CP () +CC FN (cloning) +CC SE () +CC PA () +CC BR (pRS314)(pRS315)(pRS313) +CC OF () +CC OR () +XX +FH Key Location/Qualifiers +FH +FT misc_feature 0..0 +FT /note="1. pUC19 HincII 2686bp 432..432 +FT 2. yeast MboII-MboII 125bp, CEN6 +FT -> pUC19-CEN6:32 2811bp +FT 1. pUC8 BamHI 2665bp 241..241 +FT 2. yeast Sau3AI-Sau3AI 374bp, histone H4 ARS/ARSH4 +FT -> pAB9 3039bp +FT 1. pUC19-CEN6:32 EcoRI-ScaI 1908bp 397..-..2180, CEN6 +FT 2. pAB9 ScaI-EcoRI 1314bp 231..-..1171, +FT \ histone H4 ARS/ARSH4 +FT -> pRSS83 3222bp [in MCS] +FT 1. pRSS83 remove SmaI-XbaI 9bp, MCS/pUC19 415..424 +FT \ 3213bp +FT Klenow:Klenow +FT -> pRSS84 3213bp +FT 1. pRSS84 HincII-PstI, CEN6/ARSH4 +FT \ pUC19 440..2686..432 +FT T4 DNA polymerase:T4 DNA polymerase +FT 2. pRS306 AatII 4373bp 848..848 +FT T4 DNA polymerase:T4 DNA polymerase +FT -> pRS316 4887bp" +FT misc_binding 0..0 +FT /note="MCS KpnI-ApaI-XhoI-SalI-ClaI-HindIII-EcoRV- +FT EcoRI-PstI-SmaI- +FT BamHI-SpeI-XbaI-EagI-NotI-BstXI-SacII-SacI" +FT misc_binding 0..0 +FT /note="SIT unique KpnI-ApaI-XhoI-SalI-ClaI-EcoRI- +FT PstI-SmaI-BamHI-SpeI-EagI-NotI-SacII-SacI-NaeI" +FT rep_origin 0..0 +FT /note="ORI E. coli pMB1 (ColE1 and pBR322)" +FT rep_origin 0..0 +FT /note="ORI bacteriophage f1" +FT promoter 0..0 +FT /note="PRO E. coli lac gene" +FT promoter 0..0 +FT /note="PRO bacteriophage T3" +FT promoter 0..0 +FT /note="PRO bacteriophage T7" +FT CDS 0..0 +FT /note="GEN E. coli beta-galactosidase gene (lacZ'); +FT reporter gene" +FT CDS 0..0 +FT /note="ANT E. coli beta-lactamase gene (bla) +FT ampicillin resistance gene (apr/amp)" +FT CDS 0..0 +FT /note="ANT yeast URA3 gene" +FT rep_origin 0..0 +FT /note="ORI yeast ARSH4" +FT misc_feature 0..0 +FT /note="yeast centromere CEN6" +XX +SQ Sequence 4887 BP; 1361 A; 1069 C; 1167 G; 1290 T; 0 other; + tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca + cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg + ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc + accacgcttt tcaattcaat tcatcatttt ttttttattc ttttttttga tttcggtttc + tttgaaattt ttttgattcg gtaatctccg aacagaagga agaacgaagg aaggagcaca + gacttagatt ggtatatata cgcatatgta gtgttgaaga aacatgaaat tgcccagtat + tcttaaccca actgcacaga acaaaaacct gcaggaaacg aagataaatc atgtcgaaag + ctacatataa ggaacgtgct gctactcatc ctagtcctgt tgctgccaag ctatttaata + tcatgcacga aaagcaaaca aacttgtgtg cttcattgga tgttcgtacc accaaggaat + tactggagtt agttgaagca ttaggtccca aaatttgttt actaaaaaca catgtggata + tcttgactga tttttccatg gagggcacag ttaagccgct aaaggcatta tccgccaagt + acaatttttt actcttcgaa gacagaaaat ttgctgacat tggtaataca gtcaaattgc + agtactctgc gggtgtatac agaatagcag aatgggcaga cattacgaat gcacacggtg + tggtgggccc aggtattgtt agcggtttga agcaggcggc agaagaagta acaaaggaac + ctagaggcct tttgatgtta gcagaattgt catgcaaggg ctccctatct actggagaat + atactaaggg tactgttgac attgcgaaga gcgacaaaga ttttgttatc ggctttattg + ctcaaagaga catgggtgga agagatgaag gttacgattg gttgattatg acacccggtg + tgggtttaga tgacaaggga gacgcattgg gtcaacagta tagaaccgtg gatgatgtgg + tctctacagg atctgacatt attattgttg gaagaggact atttgcaaag ggaagggatg + ctaaggtaga gggtgaacgt tacagaaaag caggctggga agcatatttg agaagatgcg + gccagcaaaa ctaaaaaact gtattataag taaatgcatg tatactaaac tcacaaatta + gagcttcaat ttaattatat cagttattac cctgcggtgt gaaataccgc acagatgcgt + aaggagaaaa taccgcatca ggaaattgta aacgttaata ttttgttaaa attcgcgtta + aatttttgtt aaatcagctc attttttaac caataggccg aaatcggcaa aatcccttat + aaatcaaaag aatagaccga gatagggttg agtgttgttc cagtttggaa caagagtcca + ctattaaaga acgtggactc caacgtcaaa gggcgaaaaa ccgtctatca gggcgatggc + ccactacgtg aaccatcacc ctaatcaagt tttttggggt cgaggtgccg taaagcacta + aatcggaacc ctaaagggag cccccgattt agagcttgac ggggaaagcc ggcgaacgtg + gcgagaaagg aagggaagaa agcgaaagga gcgggcgcta gggcgctggc aagtgtagcg + gtcacgctgc gcgtaaccac cacacccgcc gcgcttaatg cgccgctaca gggcgcgtcg + cgccattcgc cattcaggct gcgcaactgt tgggaagggc gatcggtgcg ggcctcttcg + ctattacgcc agctggcgaa ggggggatgt gctgcaaggc gattaagttg ggtaacgcca + gggttttccc agtcacgacg ttgtaaaacg acggccagtg aattgtaata cgactcacta + tagggcgaat tggagctcca ccgcggtggc ggccgctcta gaactagtgg atcccccggg + ctgcaggaat tcgatatcaa gcttatcgat accgtcgacc tcgagggggg gcccggtacc + cagcttttgt tccctttagt gagggttaat tccgagcttg gcgtaatcat ggtcatagct + gtttcctgtg tgaaattgtt atccgctcac aattccacac aacataggag ccggaagcat + aaagtgtaaa gcctggggtg cctaatgagt gaggtaactc acattaattg cgttgcgctc + actgcccgct ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg + cgcggggaga ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct + gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt + atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc + caggaaccgt aaaaaggccg cgttgctggc gtttttccat aggctcggcc cccctgacga + gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata + ccaggcgttc ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac + cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcaat gctcacgctg + taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc + cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag + acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt + aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaaggacagt + atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg + atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac + gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca + gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac + ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac + ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt + tcgttcatcc atagttgcct gactgcccgt cgtgtagata actacgatac gggagggctt + accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt + atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc + cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa + tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg + tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt + gtgaaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc + agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt + aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg + gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac + tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc + gctgttgaga tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt + tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg + aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag + catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa + acaaataggg gttccgcgca catttccccg aaaagtgcca cctgggtcct tttcatcacg + tgctataaaa ataattataa tttaaatttt ttaatataaa tatataaatt aaaaatagaa + agtaaaaaaa gaaattaaag aaaaaatagt ttttgttttc cgaagatgta aaagactcta + gggggatcgc caacaaatac taccttttat cttgctcttc ctgctctcag gtattaatgc + cgaattgttt catcttgtct gtgtagaaga ccacacacga aaatcctgtg attttacatt + ttacttatcg ttaatcgaat gtatatctat ttaatctgct tttcttgtct aataaatata + tatgtaaagt acgctttttg ttgaaatttt ttaaaccttt gtttattttt ttttcttcat + tccgtaactc ttctaccttc tttatttact ttctaaaatc caaatacaaa acataaaaat + aaataaacac agagtaaatt cccaaattat tccatcatta aaagatacga ggcgcgtgta + agttacaggc aagcgatccg tcctaagaaa ccattattat catgacatta acctataaaa + ataggcgtat cacgaggccc tttcgtc +// diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316.png b/plasmid/resource/example/FRP_1/PRS316.png similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316.png rename to plasmid/resource/example/FRP_1/PRS316.png diff --git a/plasmid/resource/example/BOX_1:FRP_1/PRS316.tiff b/plasmid/resource/example/FRP_1/PRS316.tiff similarity index 100% rename from plasmid/resource/example/BOX_1:FRP_1/PRS316.tiff rename to plasmid/resource/example/FRP_1/PRS316.tiff diff --git a/plasmid/resource/plasmids-YeastLab.sql b/plasmid/resource/plasmids-YeastLab.sql index 8c1bb7a57d8c4aa9589f20b7b66095ac1ad4fd7f..f14bdbfde99412059189e2ecb6e5ee56f861189e 100644 --- a/plasmid/resource/plasmids-YeastLab.sql +++ b/plasmid/resource/plasmids-YeastLab.sql @@ -2123,7 +2123,7 @@ COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_manage COPY data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) FROM stdin; 1 UNKNOWN \N 1 2010-05-26 17:41:21.272491+02 \N \N -2 SEQ_FILE \N 1 2010-05-26 17:41:21.272491+02 \N \N +2 SEQ_FILE \N 1 2010-05-26 17:41:21.272491+02 generated\*.png \N 3 RAW_DATA \N 1 2010-05-26 17:41:58.696032+02 \N \N 4 VERIFICATION \N 1 2010-05-26 17:42:07.328466+02 *.* \N \. diff --git a/plasmid/resource/plasmids.sql b/plasmid/resource/plasmids.sql index 171d4dd83f4f26127cae15d09a8cd78b3be79452..ea0e9f85c151f88e736ec0c6be83bc5ed4d8959b 100644 --- a/plasmid/resource/plasmids.sql +++ b/plasmid/resource/plasmids.sql @@ -2078,7 +2078,7 @@ COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_manage COPY data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) FROM stdin; 1 UNKNOWN \N 1 2010-05-26 17:41:21.272491+02 \N \N -2 SEQ_FILE \N 1 2010-05-26 17:41:21.272491+02 \N \N +2 SEQ_FILE \N 1 2010-05-26 17:41:21.272491+02 generated\*.png \N 3 RAW_DATA \N 1 2010-05-26 17:41:58.696032+02 \N \N 4 VERIFICATION \N 1 2010-05-26 17:42:07.328466+02 *.* \N \. diff --git a/plasmid/resource/recreate_db.sh b/plasmid/resource/recreate_db.sh new file mode 100755 index 0000000000000000000000000000000000000000..ba2468948f716c25ccffdc640e133b39e12b0c48 --- /dev/null +++ b/plasmid/resource/recreate_db.sh @@ -0,0 +1,4 @@ +OWNER=buczekp +psql -U postgres -c "drop database openbis_plasmids;" +psql -U postgres -c "create database openbis_plasmids with owner $OWNER encoding = 'UNICODE';" +psql -U $OWNER -d openbis_plasmids -f plasmids-YeastLab.sql