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Revision 5054

Added by Aaron Marcuse-Kubitza almost 12 years ago

Moved tnrs table from public (schemas/vegbien.sql) to its own TNRS schema, which is created by a new .TNRS datasource. Note that .TNRS is included in the automated testing, but not yet in the import.

View differences:

inputs/.TNRS/tnrs/map.csv
1 
TNRS,VegCore,Filter,Comments
2 
Name_number,OMIT,,
3 
Name_submitted,unscrubbedScientificNameWithAuthorship,,
4 
Overall_score,OMIT,,
5 
Name_matched,OMIT,,
6 
Name_matched_rank,OMIT,,
7 
Name_score,OMIT,,
8 
Name_matched_author,OMIT,,
9 
Name_matched_url,OMIT,,
10 
Author_matched,OMIT,,
11 
Author_score,OMIT,,
12 
Family_matched,OMIT,,
13 
Family_score,OMIT,,
14 
Name_matched_accepted_family,OMIT,,
15 
Genus_matched,OMIT,,
16 
Genus_score,OMIT,,
17 
Specific_epithet_matched,OMIT,,
18 
Specific_epithet_score,OMIT,,
19 
Infraspecific_rank,OMIT,,
20 
Infraspecific_epithet_matched,OMIT,,
21 
Infraspecific_epithet_score,OMIT,,
22 
Infraspecific_rank_2,OMIT,,
23 
Infraspecific_epithet_2_matched,OMIT,,
24 
Infraspecific_epithet_2_score,OMIT,,
25 
Annotations,OMIT,,
26 
Unmatched_terms,OMIT,,
27 
Taxonomic_status,taxonomicStatus,,
28 
Accepted_name,scientificName,,
29 
Accepted_name_author,scientificNameAuthorship,,
30 
Accepted_name_rank,taxonRank,,
31 
Accepted_name_url,OMIT,,
32 
Accepted_name_species,OMIT,,Also contains genus. Omitted because Accepted_name contains more info.
33 
Accepted_name_family,family,,
34 
Selected,OMIT,,
35 
Source,OMIT,,
36 
Warnings,OMIT,,
37 
Accepted_name_lsid,OMIT,,
inputs/.TNRS/tnrs/VegBIEN.csv
1 
TNRS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 
Accepted_name,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
3 
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,
4 
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
5 
Accepted_name_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
6 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
7 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
8 
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
9 
Accepted_name_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
10 
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
11 
Accepted_name_lsid,,** No non-empty join mapping for OMIT **
12 
Accepted_name_species,,** No non-empty join mapping for OMIT ** Also contains genus. Omitted because Accepted_name contains more info.
13 
Accepted_name_url,,** No non-empty join mapping for OMIT **
14 
Annotations,,** No non-empty join mapping for OMIT **
15 
Author_matched,,** No non-empty join mapping for OMIT **
16 
Author_score,,** No non-empty join mapping for OMIT **
17 
Family_matched,,** No non-empty join mapping for OMIT **
18 
Family_score,,** No non-empty join mapping for OMIT **
19 
Genus_matched,,** No non-empty join mapping for OMIT **
20 
Genus_score,,** No non-empty join mapping for OMIT **
21 
Infraspecific_epithet_2_matched,,** No non-empty join mapping for OMIT **
22 
Infraspecific_epithet_2_score,,** No non-empty join mapping for OMIT **
23 
Infraspecific_epithet_matched,,** No non-empty join mapping for OMIT **
24 
Infraspecific_epithet_score,,** No non-empty join mapping for OMIT **
25 
Infraspecific_rank,,** No non-empty join mapping for OMIT **
26 
Infraspecific_rank_2,,** No non-empty join mapping for OMIT **
27 
Name_matched,,** No non-empty join mapping for OMIT **
28 
Name_matched_accepted_family,,** No non-empty join mapping for OMIT **
29 
Name_matched_author,,** No non-empty join mapping for OMIT **
30 
Name_matched_rank,,** No non-empty join mapping for OMIT **
31 
Name_matched_url,,** No non-empty join mapping for OMIT **
32 
Name_number,,** No non-empty join mapping for OMIT **
33 
Name_score,,** No non-empty join mapping for OMIT **
34 
Name_submitted,,** No join mapping for unscrubbedScientificNameWithAuthorship **
35 
Overall_score,,** No non-empty join mapping for OMIT **
36 
Selected,,** No non-empty join mapping for OMIT **
37 
Source,,** No non-empty join mapping for OMIT **
38 
Specific_epithet_matched,,** No non-empty join mapping for OMIT **
39 
Specific_epithet_score,,** No non-empty join mapping for OMIT **
40 
Taxonomic_status,,** No join mapping for taxonomicStatus **
41 
Unmatched_terms,,** No non-empty join mapping for OMIT **
42 
Warnings,,** No non-empty join mapping for OMIT **
inputs/.TNRS/tnrs/test.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <_simplifyPath id="-1">
4 
        <next>parent_id</next>
5 
        <path>
6 
            <location>
7 
                <locationevent>
8 
                    <taxonoccurrence>
9 
                        <authortaxoncode>$Accepted_name</authortaxoncode>
10 
                        <taxondetermination>
11 
                            <taxonpath_id>
12 
                                <taxonpath>
13 
                                    <author>$Accepted_name_author</author>
14 
                                    <family>$Accepted_name_family</family>
15 
                                    <subspecies>$Accepted_name_rank</subspecies>
16 
                                    <taxonomicname>$Accepted_name</taxonomicname>
17 
                                    <taxonomicnamewithauthor>
18 
                                        <_join_words>
19 
                                            <1>$Accepted_name</1>
20 
                                            <2>$Accepted_name_author</2>
21 
                                        </_join_words>
22 
                                    </taxonomicnamewithauthor>
23 
                                </taxonpath>
24 
                            </taxonpath_id>
25 
                        </taxondetermination>
26 
                    </taxonoccurrence>
27 
                </locationevent>
28 
            </location>
29 
        </path>
30 
    </_simplifyPath>
31 
</VegBIEN>
32 
Inserted 7 new rows into database
inputs/.TNRS/tnrs/+header.csv
1 
Name_number,Name_submitted,Overall_score,Name_matched,Name_matched_rank,Name_score,Name_matched_author,Name_matched_url,Author_matched,Author_score,Family_matched,Family_score,Name_matched_accepted_family,Genus_matched,Genus_score,Specific_epithet_matched,Specific_epithet_score,Infraspecific_rank,Infraspecific_epithet_matched,Infraspecific_epithet_score,Infraspecific_rank_2,Infraspecific_epithet_2_matched,Infraspecific_epithet_2_score,Annotations,Unmatched_terms,Taxonomic_status,Accepted_name,Accepted_name_author,Accepted_name_rank,Accepted_name_url,Accepted_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid
inputs/.TNRS/tnrs/new_terms.csv
1 
Name_number,OMIT,,
2 
Name_submitted,unscrubbedScientificNameWithAuthorship,,
3 
Overall_score,OMIT,,
4 
Name_matched,OMIT,,
5 
Name_matched_rank,OMIT,,
6 
Name_score,OMIT,,
7 
Name_matched_author,OMIT,,
8 
Name_matched_url,OMIT,,
9 
Author_matched,OMIT,,
10 
Author_score,OMIT,,
11 
Family_matched,OMIT,,
12 
Family_score,OMIT,,
13 
Name_matched_accepted_family,OMIT,,
14 
Genus_matched,OMIT,,
15 
Genus_score,OMIT,,
16 
Specific_epithet_matched,OMIT,,
17 
Specific_epithet_score,OMIT,,
18 
Infraspecific_rank,OMIT,,
19 
Infraspecific_epithet_matched,OMIT,,
20 
Infraspecific_epithet_score,OMIT,,
21 
Infraspecific_rank_2,OMIT,,
22 
Infraspecific_epithet_2_matched,OMIT,,
23 
Infraspecific_epithet_2_score,OMIT,,
24 
Annotations,OMIT,,
25 
Unmatched_terms,OMIT,,
26 
Accepted_name,scientificName,,
27 
Accepted_name_author,scientificNameAuthorship,,
28 
Accepted_name_rank,taxonRank,,
29 
Accepted_name_url,OMIT,,
30 
Accepted_name_species,OMIT,,Also contains genus. Omitted because Accepted_name contains more info.
31 
Accepted_name_family,family,,
32 
Selected,OMIT,,
33 
Source,OMIT,,
34 
Warnings,OMIT,,
35 
Accepted_name_lsid,OMIT,,
inputs/.TNRS/tnrs/unmapped_terms.csv
1 
unscrubbedScientificNameWithAuthorship
2 
taxonomicStatus
schemas/vegbien.my.sql
2633 2633 

  		




  2634
  2634
  
    

  		




  2635
  2635
  
    
--


  		




  2636
  
  
    
-- Name: tnrs; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  2637
  
  
    
--


  		




  2638
  
  
    

  		




  2639
  
  
    
CREATE TABLE tnrs (


  		




  2640
  
  
    
    `Name_number` text,


  		




  2641
  
  
    
    `Name_submitted` text,


  		




  2642
  
  
    
    `Overall_score` text,


  		




  2643
  
  
    
    `Name_matched` text,


  		




  2644
  
  
    
    `Name_matched_rank` text,


  		




  2645
  
  
    
    `Name_score` text,


  		




  2646
  
  
    
    `Name_matched_author` text,


  		




  2647
  
  
    
    `Name_matched_url` text,


  		




  2648
  
  
    
    `Author_matched` text,


  		




  2649
  
  
    
    `Author_score` text,


  		




  2650
  
  
    
    `Family_matched` text,


  		




  2651
  
  
    
    `Family_score` text,


  		




  2652
  
  
    
    `Name_matched_accepted_family` text,


  		




  2653
  
  
    
    `Genus_matched` text,


  		




  2654
  
  
    
    `Genus_score` text,


  		




  2655
  
  
    
    `Specific_epithet_matched` text,


  		




  2656
  
  
    
    `Specific_epithet_score` text,


  		




  2657
  
  
    
    `Infraspecific_rank` text,


  		




  2658
  
  
    
    `Infraspecific_epithet_matched` text,


  		




  2659
  
  
    
    `Infraspecific_epithet_score` text,


  		




  2660
  
  
    
    `Infraspecific_rank_2` text,


  		




  2661
  
  
    
    `Infraspecific_epithet_2_matched` text,


  		




  2662
  
  
    
    `Infraspecific_epithet_2_score` text,


  		




  2663
  
  
    
    `Annotations` text,


  		




  2664
  
  
    
    `Unmatched_terms` text,


  		




  2665
  
  
    
    `Taxonomic_status` text,


  		




  2666
  
  
    
    `Accepted_name` text,


  		




  2667
  
  
    
    `Accepted_name_author` text,


  		




  2668
  
  
    
    `Accepted_name_rank` text,


  		




  2669
  
  
    
    `Accepted_name_url` text,


  		




  2670
  
  
    
    `Accepted_name_species` text,


  		




  2671
  
  
    
    `Accepted_name_family` text,


  		




  2672
  
  
    
    `Selected` text,


  		




  2673
  
  
    
    `Source` text,


  		




  2674
  
  
    
    `Warnings` text,


  		




  2675
  
  
    
    `Accepted_name_lsid` text


  		




  2676
  
  
    
);


  		




  2677
  
  
    

  		




  2678
  
  
    

  		




  2679
  
  
    
--


  		




  2680
  2636
  
    
-- Name: trait; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  2681
  2637
  
    
--


  		




  2682
  2638
  
    

  		












  

    
      schemas/vegbien.sql
    
  





  3252
  3252
  
    

  		




  3253
  3253
  
    

  		




  3254
  3254
  
    
--


  		




  3255
  
  
    
-- Name: tnrs; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  3256
  
  
    
--


  		




  3257
  
  
    

  		




  3258
  
  
    
CREATE TABLE tnrs (


  		




  3259
  
  
    
    "Name_number" text,


  		




  3260
  
  
    
    "Name_submitted" text,


  		




  3261
  
  
    
    "Overall_score" text,


  		




  3262
  
  
    
    "Name_matched" text,


  		




  3263
  
  
    
    "Name_matched_rank" text,


  		




  3264
  
  
    
    "Name_score" text,


  		




  3265
  
  
    
    "Name_matched_author" text,


  		




  3266
  
  
    
    "Name_matched_url" text,


  		




  3267
  
  
    
    "Author_matched" text,


  		




  3268
  
  
    
    "Author_score" text,


  		




  3269
  
  
    
    "Family_matched" text,


  		




  3270
  
  
    
    "Family_score" text,


  		




  3271
  
  
    
    "Name_matched_accepted_family" text,


  		




  3272
  
  
    
    "Genus_matched" text,


  		




  3273
  
  
    
    "Genus_score" text,


  		




  3274
  
  
    
    "Specific_epithet_matched" text,


  		




  3275
  
  
    
    "Specific_epithet_score" text,


  		




  3276
  
  
    
    "Infraspecific_rank" text,


  		




  3277
  
  
    
    "Infraspecific_epithet_matched" text,


  		




  3278
  
  
    
    "Infraspecific_epithet_score" text,


  		




  3279
  
  
    
    "Infraspecific_rank_2" text,


  		




  3280
  
  
    
    "Infraspecific_epithet_2_matched" text,


  		




  3281
  
  
    
    "Infraspecific_epithet_2_score" text,


  		




  3282
  
  
    
    "Annotations" text,


  		




  3283
  
  
    
    "Unmatched_terms" text,


  		




  3284
  
  
    
    "Taxonomic_status" text,


  		




  3285
  
  
    
    "Accepted_name" text,


  		




  3286
  
  
    
    "Accepted_name_author" text,


  		




  3287
  
  
    
    "Accepted_name_rank" text,


  		




  3288
  
  
    
    "Accepted_name_url" text,


  		




  3289
  
  
    
    "Accepted_name_species" text,


  		




  3290
  
  
    
    "Accepted_name_family" text,


  		




  3291
  
  
    
    "Selected" text,


  		




  3292
  
  
    
    "Source" text,


  		




  3293
  
  
    
    "Warnings" text,


  		




  3294
  
  
    
    "Accepted_name_lsid" text


  		




  3295
  
  
    
);


  		




  3296
  
  
    

  		




  3297
  
  
    

  		




  3298
  
  
    
--


  		




  3299
  3255
  
    
-- Name: trait; Type: TABLE; Schema: public; Owner: -; Tablespace: 


  		




  3300
  3256
  
    
--


  		




  3301
  3257
  
    

  		












  

    
      lib/forwarding.Makefile
    
  





  1
  1
  
    
##### Subdir forwarding


  		




  2
  2
  
    

  		




  3
  
  
    
subdirs := $(wildcard */)


  		




  
  3
  
    
subdirs := .TNRS/ $(wildcard */)


  		




  4
  4
  
    
allSubdirs := $(subdirs) .public/


  		




  5
  5
  
    

  		




  6
  6
  
    
define subdirTargets


  		












  

    
      bin/vegbien_dest
    
  





  19
  19
  
    
    ${prefix}user=bien \


  		




  20
  20
  
    
    ${prefix}password="$(cat "$selfDir/../config/bien_password")" \


  		




  21
  21
  
    
    ${prefix}database=vegbien \


  		




  22
  
  
    
    ${prefix}schemas=temp,public,functions,py_functions


  		




  
  22
  
    
    ${prefix}schemas=temp,public,TNRS,functions,py_functions


  		




  23
  23
  
    
}


  		




  24
  24
  
    
vegbien_dest_main "$@"


  		












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