Inconsistent category type in taxonomy tree
grololo06 opened this issue · comments
It looks like a Phylo taxon should not be child of a Morpho one, however:
ecotaxa=# select txo.id, coalesce(txo.nbrobj,0)+coalesce(txo.nbrobjcum,0), txo.name, ptxo.id, ptxo.name
from taxonomy txo, taxonomy ptxo
where (txo.nbrobj>0 or txo.nbrobjcum>0)
and ptxo.id=txo.parent_id
and txo.taxotype='P'
and ptxo.taxotype='M' order by txo.id;
id | ?column? | name | id | name
-------+----------+----------------------------------------+-------+---------------
38408 | 46 | dark septate | 23188 | dark
85069 | 401316 | othertocheck | 85011 | other
85154 | 2026 | tempCeratoneis closterium | 84959 | temporary
85158 | 179 | tempChaetoceros contortus | 84959 | temporary
85161 | 53975 | tempCryptophyceae | 84959 | temporary
85163 | 39 | tempKatodinium glaucum | 84959 | temporary
85168 | 2293 | tempPrasinophyceae | 84959 | temporary
85174 | 4 | tempCoccosphaerales | 84959 | temporary
85183 | 12767 | tempflagellates | 84959 | temporary
85206 | 100 | cyst 1 | 85096 | cyst
85207 | 169 | cyst 2 | 85096 | cyst
85208 | 715 | cyst 3 | 85096 | cyst
85209 | 560 | cyst 4 | 85096 | cyst
85210 | 150 | cyst 5 | 85096 | cyst
85211 | 99 | cyst 6 | 85096 | cyst
85212 | 60 | cyst 7 | 85096 | cyst
85213 | 5665 | Coccolithes | 85068 | part
85214 | 200 | Setae Corethron | 85068 | part
85215 | 2677 | Setae | 85068 | part
85216 | 2923 | shells | 85068 | part
85235 | 2866 | centric 1 temp | 85009 | centric
85236 | 2255 | centric 2 temp | 85009 | centric
85237 | 688 | centric 3 temp | 85009 | centric
85238 | 2817 | centric 4 temp | 85009 | centric
85239 | 591 | centric 5 temp | 85009 | centric
85240 | 231 | centric 6 temp | 85009 | centric
85241 | 627 | centric 7 temp | 85009 | centric
85242 | 175 | centric 8 temp | 85009 | centric
85243 | 1005 | centric 9 temp | 85009 | centric
85244 | 205 | centric 10 temp | 85009 | centric
85245 | 167 | centric 11 temp | 85009 | centric
85246 | 173 | centric 12 temp | 85009 | centric
85247 | 100 | centric 13 temp | 85009 | centric
85248 | 1974 | centric 14 temp | 85009 | centric
85249 | 999 | pennate 1 temp | 85010 | pennate
85250 | 325 | pennate 2 temp | 85010 | pennate
85251 | 2930 | pennate 3 temp | 85010 | pennate
85252 | 946 | pennate 4 temp | 85010 | pennate
85253 | 175 | pennate 5 temp | 85010 | pennate
85254 | 1431 | pennate 6 temp | 85010 | pennate
85256 | 120 | pennate 8 temp | 85010 | pennate
85257 | 1245 | pennate 9 temp | 85010 | pennate
85258 | 761 | pennate 10 temp | 85010 | pennate
85259 | 242 | pennate 11 temp | 85010 | pennate
85260 | 62 | pennate 12 temp | 85010 | pennate
85261 | 81 | pennate 13 temp | 85010 | pennate
85322 | 700 | auto 5 temp | 85097 | autotroph
85323 | 198 | auto 1 temp | 85097 | autotroph
85324 | 650 | auto 2 temp | 85097 | autotroph
85325 | 2500 | auto 3 temp | 85097 | autotroph
85326 | 143 | auto 4 temp | 85097 | autotroph
85327 | 100 | hetero 1 temp | 85098 | heterotroph
85328 | 750 | hetero 2 temp | 85098 | heterotroph
85329 | 100 | hetero 3 temp | 85098 | heterotroph
85330 | 50 | hetero 4 temp | 85098 | heterotroph
85331 | 50 | hetero 5 temp | 85098 | heterotroph
85332 | 100 | hetero 6 temp | 85098 | heterotroph
85333 | 150 | hetero 7 temp | 85098 | heterotroph
85334 | 100 | hetero 8 temp | 85098 | heterotroph
85335 | 450 | hetero 9 temp | 85098 | heterotroph
92027 | 1091 | tempTorodinium robustum | 84959 | temporary
92031 | 1 | tempPeridiniella catenata | 84959 | temporary
92335 | 157 | Fossula arctica | 92329 | temporary
92336 | 163 | Fragilariopsis doliolus | 92329 | temporary
92339 | 2 | Guinardia cylindrus | 92329 | temporary
92340 | 4 | Hemiaulus hauckii | 92329 | temporary
92341 | 1 | Hemiaulus indicus | 92329 | temporary
92343 | 51 | Hemidiscus cuneiformis | 92329 | temporary
92344 | 129 | Leptocylindrus mediterraneus | 92329 | temporary
92345 | 8 | Lioloma delicatulum | 92329 | temporary
92347 | 2 | Lioloma pacificum | 92329 | temporary
92349 | 85 | Nanoneis hasleae | 92329 | temporary
92357 | 1 | Neodelphineis indica | 92329 | temporary
92358 | 2 | Nitzschia bicapitata | 92329 | temporary
92361 | 1 | Plagiotropis lepidoptera | 92329 | temporary
92367 | 1 | Rhizosolenia bergonii | 92329 | temporary
92369 | 4 | Rhizosolenia chunii | 92329 | temporary
92375 | 1 | Rhizosolenia sima f sima | 92329 | temporary
92378 | 1 | Rossithidium petersenii | 92329 | temporary
92379 | 17 | Roperia tesselata | 92329 | temporary
92380 | 2 | Shionodiscus oestrupii | 92329 | temporary
92382 | 1 | Shionodiscus oestrupii var. venrickae | 92329 | temporary
92386 | 12 | Thalassionema pseudonitzschioides | 92329 | temporary
92387 | 8 | Thalassiosira antarctica var. borealis | 92329 | temporary
92389 | 2 | Bacterosira constricta | 92329 | temporary
92390 | 1 | Thalassiosira decipiens | 92329 | temporary
92393 | 1 | Thalassiosira gracilis var. gracilis | 92329 | temporary
92394 | 3 | Thalassiosira hyalina | 92329 | temporary
92397 | 1 | Thalassiosira subtilis | 92329 | temporary
92398 | 6 | Thalassiosira tealata | 92329 | temporary
92399 | 3 | Thalassiosira tubifera | 92329 | temporary
92402 | 80 | Thalassiothrix sp. | 92329 | temporary
92407 | 1 | Actiniscus pentasterias | 92329 | temporary
92416 | 25 | Blepharocysta splendor-maris | 92329 | temporary
92424 | 5 | Ceratocorys gourretii | 92329 | temporary
92425 | 2 | Ceratocorys sp. | 92329 | temporary
92427 | 3 | Citharistes regius | 92329 | temporary
92428 | 102 | Cladopyxis brachiolata | 92329 | temporary
92429 | 3 | Cladopyxis caryophyllum | 92329 | temporary
92431 | 34 | Corythodinium sp. | 92329 | temporary
92432 | 3 | Corythodinium constrictum | 92329 | temporary
92435 | 27 | Corythodinium tesselatum | 92329 | temporary
92440 | 4 | Dinophysis ovum | 92329 | temporary
92443 | 1 | Dinophysis sacculus | 92329 | temporary
92444 | 5 | Dinophysis schuettii | 92329 | temporary
92450 | 62 | Goniodoma polyedricum | 92329 | temporary
92453 | 7 | Gonyaulax birostris | 92329 | temporary
92458 | 4 | Gonyaulax fragilis | 92329 | temporary
92459 | 11 | Gonyaulax fusiformis | 92329 | temporary
92463 | 1 | Gonyaulax monacantha | 92329 | temporary
92467 | 4 | Gonyaulax sphaeroidea | 92329 | temporary
92479 | 4 | Histioneis elongata | 92329 | temporary
92482 | 1 | Histioneis mediterranea | 92329 | temporary
92498 | 8 | Histioneis variabilis | 92329 | temporary
92499 | 7 | Mesoporos perforatus | 92329 | temporary
92501 | 148 | Micracanthodinium quadrispinum | 92329 | temporary
92508 | 8 | Oxytoxum crassum | 92329 | temporary
92509 | 4 | Oxytoxum curvatum | 92329 | temporary
92511 | 2 | Oxytoxum galdiolus | 92329 | temporary
92514 | 12 | Oxytoxum milneri | 92329 | temporary
92515 | 5 | Oxytoxum obliquum | 92329 | temporary
92517 | 1 | Oxytoxum punctulatum | 92329 | temporary
92519 | 17 | Oxytoxum sceptrum | 92329 | temporary
92520 | 5 | Oxytoxum scolopax | 92329 | temporary
92524 | 25 | Oxytoxum variabile | 92329 | temporary
92526 | 32 | Palaeophalacroma unicinctum | 92329 | temporary
92534 | 14 | Prorocentrum balticum | 92329 | temporary
92537 | 4 | Prorocentrum nux | 92329 | temporary
92538 | 18 | Prorocentrum rostratum | 92329 | temporary
92540 | 1 | Protoceratium areolatum | 92329 | temporary
92541 | 30 | Protoceratium spinulosum | 92329 | temporary
92544 | 11 | Protoperidinium brevipes | 92329 | temporary
92545 | 3 | Protoperidinium crassipyrum | 92329 | temporary
92547 | 1 | Protoperidinium crassipes | 92329 | temporary
92551 | 6 | Protoperidinium granii | 92329 | temporary
92552 | 15 | Protoperidinium incertum | 92329 | temporary
92555 | 9 | Protoperidinium marukawai | 92329 | temporary
92566 | 27 | Protoperidinium steinii | 92329 | temporary
92568 | 1 | Protoperidinium subsphaericum | 92329 | temporary
92571 | 6 | Ptychodiscus noctiluca | 92329 | temporary
92572 | 3 | Pyrocystis elegans | 92329 | temporary
92581 | 2 | Tripos arcticus | 92329 | temporary
92582 | 3 | Tripos arietinus | 92329 | temporary
92584 | 3 | Tripos azoricus | 92329 | temporary
92586 | 8 | Tripos brevis | 92329 | temporary
92587 | 10 | Tripos candelabrus | 92329 | temporary
92588 | 8 | Tripos carriensis | 92329 | temporary
92591 | 1 | Tripos contortum | 92329 | temporary
92592 | 38 | Tripos contrarius | 92329 | temporary
92593 | 66 | Tripos declinatus | 92329 | temporary
92594 | 2 | Tripos digitatus | 92329 | temporary
92595 | 1 | Tripos divaricatus | 92329 | temporary
92598 | 320 | Tripos furca | 92329 | temporary
92600 | 400 | Tripos fusus | 92329 | temporary
92603 | 59 | Tripos gibberius | 92329 | temporary
92605 | 1 | Tripos hexacanthus | 92329 | temporary
92608 | 2 | Tripos lineatus | 92329 | temporary
92611 | 2 | Tripos macroceros | 92329 | temporary
92612 | 13 | Tripos massiliensis | 92329 | temporary
92613 | 7 | Tripos minutus | 92329 | temporary
92614 | 169 | Tripos muelleri | 92329 | temporary
92617 | 215 | Tripos pentagonus | 92329 | temporary
92620 | 4 | Tripos praelongus | 92329 | temporary
92624 | 444 | Tripos teres | 92329 | temporary
92625 | 46 | Tripos trichoceros | 92329 | temporary
92627 | 1 | Calcidiscus leptoporus | 92329 | temporary
92628 | 3 | Calciopappus sp. | 92329 | temporary
92640 | 1 | Hyalolithus neolepis | 92329 | temporary
92648 | 1 | Rhabdosphaera claviger | 92329 | temporary
92651 | 1 | Dinobryon balticum | 92329 | temporary
92660 | 4 | Octactis octonaria | 92329 | temporary
92677 | 4416 | Radiozoa | 92329 | temporary
92678 | 2361 | Undetermined flagellate | 92329 | temporary
92679 | 6 | Coccolithophores | 92329 | temporary
92887 | 217 | Trochophora | 92838 | trochozoa
93165 | 1 | Xanthichthys | 92893 | balistidae
93194 | 1 | Balistes | 92893 | balistidae
93274 | 2 | Holocentrus | 92906 | holocentridae
(178 lignes)
@jiho , if it's OK with you then let's forbid the bad pattern creation.
BTW, any other rule in this area?
Yes, the pattern should be forbidden.
In the cases above:
- most of those child of
temporarywere created there to be quick and dirty, waiting for UniEuk/WoRMS to come along - the children of
pennate,autotrophetc. should be morpho balistidae,holocentridaeshould be phylo.
balistidae, holocentridae -> corrected onto EcoTaxoserver, and propagated fine to EcoTaxa.
living>temporary should be Morpho, which solves the temporary issues.
The rest is in WoRMS move Google sheet
Log of execution onto ecotaxoserver. As the direct SQL does not propagate, same commands were ran onto EcoTaxa DB.
ecotaxoserver=# update taxonomy set taxotype='M' where id in (17263,17264,27675,27676,13364,13363,85234,85323,85324,85325,85326,85322,92688,92689,92230,92231,92232,85235,85244,85245,85246,85247,85248,85236,85237,85238,85239,85240,85241,85242,85243,85230,85231,85195,85196,85197,92273,92266,92304,92272,92265,11880,11879,11878,11877,11876,92271,92264,92274,92267,92306,85302,85311,85312,85313,85314,85315,85316,85317,85318,85319,85303,85304,85305,85306,85307,85308,85309,85310,85213,92323,92316,92315,92317,92320,92322,92321,92275,92268,92307,92255,85202,85203,85204,85206,85207,85208,85209,85210,85211,85212,38408,85217,85340,85346,85341,85347,85342,85348,85343,85349,85344,85350,85345,85351,92237,85337,93602,92682,92277,92270,92253,92309,92258,92312,92247,92313,92327,85263,85264,24576,85275,85276,85277,85278,85279,85280,85281,85282,85283,85266,85267,85268,85269,85270,85271,85272,85273,85284,85285,85286,85287,58306,58319,58322,85299,85300,85301,85327,85328,85329,85330,85331,85332,85333,85334,85335,58458,92269,92252,92276,92314,92256,92308,93601,92245,92236,85069,85249,85258,85259,85260,85261,85250,85251,85252,85253,85254,85255,85256,85257,27304,27303,27302,85289,85290,85291,85292,85293,85294,85295,85297,91419,85218,85219,85220,85221,85222,85223,85198,85199,85320,85321,85215,85214,85216,85226,85225,85228,85227,85224,85036,85038,85039,85037,85148,85154,85158,85229,85174,85161,85183,85163,92031,85168,92027,85298,93528,92587,92591,92603,92887,8982,92678,26325,51958,6);
UPDATE 237
Temps : 172,201 ms
ecotaxoserver=# update taxonomy set taxotype='P' where id=92329;
UPDATE 1
Temps : 0,656 ms
ecotaxoserver=# select txo.id, coalesce(txo.nbrobj,0)+coalesce(txo.nbrobjcum,0), txo.name, ptxo.id, ptxo.name
ecotaxoserver-# from taxonomy txo, taxonomy ptxo
ecotaxoserver-# where (txo.nbrobj>0 or txo.nbrobjcum>0)
ecotaxoserver-# and ptxo.id=txo.parent_id
ecotaxoserver-# and txo.taxotype='P'
ecotaxoserver-# and ptxo.taxotype='M' order by txo.id;
id | ?column? | name | id | name
----+----------+------+----+------
(0 ligne)
Temps : 64,544 ms