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Revision 518

VegBIEN: Renamed museumaccessionnumber to sourceaccessionnumber

View differences:

test/accepted_output/SALVIAS.organisms.VegBIEN.xml
87 87
            <party_id>
88 88
                <party/>
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            </party_id>
90
            <museumaccessionnumber>607771</museumaccessionnumber>
90
            <sourceaccessionnumber>607771</sourceaccessionnumber>
91 91
        </taxondetermination>
92 92
        <taxondetermination>
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            <role_id>
......
372 372
            <party_id>
373 373
                <party/>
374 374
            </party_id>
375
            <museumaccessionnumber>607722</museumaccessionnumber>
375
            <sourceaccessionnumber>607722</sourceaccessionnumber>
376 376
        </taxondetermination>
377 377
        <taxondetermination>
378 378
            <role_id>
test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml
73 73
            <party_id>
74 74
                <party/>
75 75
            </party_id>
76
            <museumaccessionnumber>1</museumaccessionnumber>
76
            <sourceaccessionnumber>1</sourceaccessionnumber>
77 77
        </taxondetermination>
78 78
        <taxondetermination>
79 79
            <role_id>
......
349 349
            <party_id>
350 350
                <party/>
351 351
            </party_id>
352
            <museumaccessionnumber>2</museumaccessionnumber>
352
            <sourceaccessionnumber>2</sourceaccessionnumber>
353 353
        </taxondetermination>
354 354
        <taxondetermination>
355 355
            <role_id>
test/accepted_output/NYBG.organisms.VegBIEN.xml
310 310
            <party_id>
311 311
                <party/>
312 312
            </party_id>
313
            <museumaccessionnumber>816590</museumaccessionnumber>
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            <sourceaccessionnumber>816590</sourceaccessionnumber>
314 314
        </taxondetermination>
315 315
        <taxondetermination>
316 316
            <role_id>
......
525 525
            <party_id>
526 526
                <party/>
527 527
            </party_id>
528
            <museumaccessionnumber>220541</museumaccessionnumber>
528
            <sourceaccessionnumber>220541</sourceaccessionnumber>
529 529
        </taxondetermination>
530 530
        <taxondetermination>
531 531
            <role_id>
inputs/SALVIAS/maps/VegBIEN.organisms.csv
28 28
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}",
29 29
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT
30 30
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
schemas/vegbien.sql
2513 2513
    taxonfit character varying(50),
2514 2514
    taxonconfidence character varying(50),
2515 2515
    museum_id integer,
2516
    museumaccessionnumber character varying(100),
2516
    sourceaccessionnumber character varying(100),
2517 2517
    grouptype character varying(20),
2518 2518
    notes text,
2519 2519
    notespublic boolean,
......
4359 4359
--
4360 4360

  
4361 4361
ALTER TABLE ONLY taxondetermination
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    ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, individualplant_id, role_id, plantname_id, museumaccessionnumber);
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    ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, individualplant_id, role_id, plantname_id, sourceaccessionnumber);
4363 4363

  
4364 4364

  
4365 4365
--
mappings/SALVIAS_db-VegBIEN.organisms.csv
28 28
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}",
29 29
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT
30 30
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
31
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
mappings/VegX-VegBIEN.organisms.csv
121 121
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc/_namePart/last}"
122 122
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first,/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first}
123 123
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}"
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/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}"
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/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}"
mappings/NYBG-VegBIEN.organisms.csv
38 38
Species,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",
39 39
InstitutionCode,/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/first},
40 40
CollectionCode,"/{taxondetermination[role_id/aux_role/rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen:[*_id/reference]/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
41
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
41
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv
28 28
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/last,*_id/plantconcept/*_id/*/plantname/_name/last}",
29 29
OrigFamily,"/taxondetermination[rolecode=identifier,plantlevel=Family]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
30 30
OrigSpecies,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}",Brad: OMIT
31
PlotObsID,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
31
PlotObsID,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
mappings/for_review/VegX-VegBIEN.organisms.csv
121 121
//party/organizationName,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname,aggregateoccurrence/individualplant/specimen/collectioncode_dwc/_namePart/last}"
122 122
//party/organizationName/_name/first,/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first}
123 123
//party/organizationName/_name/last,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}"
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//taxonNameUsageConcept/voucher,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}"
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//taxonNameUsageConcept/voucher,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}"
mappings/for_review/NYBG-VegBIEN.organisms.csv
38 38
Species,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}",
39 39
InstitutionCode,/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/first},
40 40
CollectionCode,"/{taxondetermination[rolecode=collector]/museum_id/party/organizationname/_name/last,aggregateoccurrence/individualplant/specimen/collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
41
UniqueNYInternalRecordNumber,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
41
UniqueNYInternalRecordNumber,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
mappings/for_review/SALVIAS-VegBIEN.organisms.csv
37 37
infra_ep_1,"/taxondetermination[rolecode=computer,plantlevel=Subspecies]/{*_id/*/plantname/_name/last,*_id/plantconcept/*_id/*/plantname/_name/last}",
38 38
orig_family,"/taxondetermination[rolecode=identifier,plantlevel=Family]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}",Brad: OMIT
39 39
orig_species,"/{taxondetermination[rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[rolecode=identifier,plantlevel=Species]/{*_id/*/plantname,*_id/plantconcept/*_id/*/plantname}}",Brad: OMIT
40
OBSERVATION_ID,"/{taxondetermination[rolecode=collector]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
40
OBSERVATION_ID,"/{taxondetermination[rolecode=collector]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
mappings/SALVIAS-VegBIEN.organisms.csv
37 37
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}",
38 38
orig_family,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT
39 39
orig_species,"/{taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2,taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}}",Brad: OMIT
40
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
40
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/sourceaccessionnumber,*_id/plotevent/sourceid/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/sourceid/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."

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