Revision 368
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS/verify.0.plots.sql | ||
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SELECT '# projects'; |
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SELECT count(*) FROM project; |
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SELECT ''; |
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SELECT '# plot observations'; |
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SELECT count(*) FROM plotevent; |
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SELECT ''; |
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| inputs/SALVIAS/test.0.plots.out | ||
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Inserted 0 rows |
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| inputs/SALVIAS/verify.0.plots.ref.out | ||
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# projects |
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# plot observations |
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13661 |
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| inputs/SALVIAS/verify.0.plots.out | ||
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# projects |
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# plot observations |
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13591 |
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| inputs/SALVIAS/verify.0.plots.ref.sql | ||
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SELECT '# projects'; |
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SELECT count(*) FROM projects; |
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SELECT ''; |
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SELECT '# plot observations'; |
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SELECT count(*) FROM plotMetadata; |
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SELECT ''; |
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/* |
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SELECT pr.project_id, project_name, COUNT(PlotID) |
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FROM projects pr JOIN plotMetadata p |
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ON pr.project_id=p.project_id |
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GROUP BY pr.project_id, project_name; |
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SELECT DISTINCT pr.project_id, project_name, PlotMethod, m.MethodCode, m.Description |
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FROM projects pr JOIN plotMetadata p JOIN lookup_MethodCode m |
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ON pr.project_id=p.project_id AND p.MethodCode=m.MethodCode |
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LIMIT 10; |
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SELECT p.PlotID, p.SiteCode, COUNT(*) |
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FROM projects pr JOIN plotMetadata p JOIN plotObservations o |
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ON pr.project_id=p.project_id AND p.PlotID=o.PlotID |
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WHERE p.project_id=2 |
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GROUP BY p.PlotID, p.SiteCode; |
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SELECT NoInd, COUNT(*) AS observations |
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FROM plotObservations o JOIN plotMetadata p |
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ON o.PlotID=p.PlotID |
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WHERE project_id=2 |
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GROUP BY NoInd; |
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SELECT p.PlotID, p.SiteCode, SUM(NoInd) AS Individuals |
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FROM projects pr JOIN plotMetadata p JOIN plotObservations o |
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ON pr.project_id=p.project_id AND p.PlotID=o.PlotID |
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WHERE p.project_id=2 |
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GROUP BY p.PlotID, p.SiteCode; |
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SELECT DISTINCT pr.project_id, project_name, PlotMethod, m.MethodCode, m.Description |
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FROM projects pr JOIN plotMetadata p JOIN lookup_MethodCode m |
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ON pr.project_id=p.project_id AND p.MethodCode=m.MethodCode |
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WHERE m.MethodCode=8; |
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SELECT NoInd, COUNT(*) AS observations |
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FROM plotObservations o JOIN plotMetadata p JOIN lookup_MethodCode m |
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ON o.PlotID=p.PlotID AND p.MethodCode=m.MethodCode |
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WHERE project_id=2 |
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GROUP BY NoInd; |
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SELECT p.PlotID, p.SiteCode, SUM(NoInd) AS Individuals |
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FROM projects pr JOIN plotMetadata p JOIN plotObservations o |
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ON pr.project_id=p.project_id AND p.PlotID=o.PlotID |
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WHERE p.project_id=1 |
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GROUP BY p.PlotID, p.SiteCode |
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LIMIT 10; |
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SELECT PlotMethod, MethodCode, Description, COUNT(project_id) as projects |
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FROM ( |
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SELECT DISTINCT p.PlotMethod, p.MethodCode, p.Description, p.project_id |
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FROM ( |
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SELECT project_id, PlotID, PlotMethod, m.MethodCode, m.Description |
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FROM plotMetadata p JOIN lookup_MethodCode m |
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ON p.MethodCode=m.MethodCode |
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) p JOIN plotObservations o JOIN stems s |
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ON p.PlotID=o.PlotID AND o.PlotObsID=s.PlotObsID |
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GROUP BY project_id |
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) AS a |
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GROUP BY PlotMethod, MethodCode, Description; |
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SELECT DISTINCT pr.project_id, project_name |
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FROM projects pr JOIN plotMetadata p JOIN plotObservations o JOIN stems s |
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ON pr.project_id=p.project_id AND p.PlotID=o.PlotID AND o.PlotObsID=s.PlotObsID |
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WHERE p.MethodCode=3; |
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SELECT p.PlotID, SiteName as plot, COUNT(*) AS stems |
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FROM plotMetadata p JOIN plotObservations o JOIN stems s |
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ON p.PlotID=o.PlotID AND o.PlotObsID=s.PlotObsID |
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WHERE p.project_id=2 |
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GROUP BY p.PlotID, SiteName |
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LIMIT 10; |
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SELECT p.PlotID, SiteName AS plot, COUNT(DISTINCT Family, Genus, Species) AS SpeciesCount |
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE project_id=2 |
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GROUP BY p.PlotID, SiteName; |
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SELECT DISTINCT p.PlotID, SiteName AS plot, Family, CONCAT_WS(' ',IFNULL(Genus,''), IFNULL(Species,'')) AS SpeciesName
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=298; |
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SELECT name_status, count(*) FROM plotObservations GROUP BY name_status; |
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SELECT DISTINCT p.PlotID, SiteName AS plot, Family, |
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CONCAT_WS(' ',IFNULL(Genus,''), IFNULL(Species,'')) AS SpeciesName, name_status
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=298; |
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SELECT DISTINCT p.PlotID, SiteName AS plot, Family, |
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CONCAT_WS(' ',IFNULL(Genus,''), IFNULL(Species,'')) AS SpeciesName, name_status
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=298 AND name_status=1; |
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SELECT p.PlotID, SiteCode AS plot, o.Line as subplot, COUNT(*) AS individuals |
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=298 |
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GROUP BY p.PlotID, plot, subplot; |
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SELECT p.PlotID, SiteCode AS plot, o.Line as subplot, SUM(NoInd) AS individuals |
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=298 |
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GROUP BY p.PlotID, plot, subplot; |
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SELECT p.PlotID, SiteCode AS plot, o.Line as subplot, SUM(NoInd) AS individuals |
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=1 |
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GROUP BY p.PlotID, plot, subplot; |
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SELECT COUNT(*) FROM plotMetadata WHERE MethodCode=1; |
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SELECT PlotID FROM plotMetadata WHERE MethodCode=1 LIMIT 1; |
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SELECT p.PlotID, SiteCode AS plot, Family, |
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CONCAT_WS(' ',IFNULL(Genus,''), IFNULL(Species,'')) AS SpeciesName, cover_percent
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FROM plotMetadata p JOIN plotObservations o |
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ON p.PlotID=o.PlotID |
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WHERE p.PlotID=24589; |
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SELECT p.PlotID, p.SiteCode as plot, Country, PolDiv1 AS stateProvince, pol2 AS countyParish, |
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LatDec as latitude, LongDec as longitude, Elev as elevation |
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FROM projects pr JOIN plotMetadata p |
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ON pr.project_id=p.project_id |
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WHERE pr.project_id=1 |
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LIMIT 20; |
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SELECT AccessCode, COUNT(*) |
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FROM plotMetadata |
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GROUP BY AccessCode; |
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SELECT pr.project_id, project_name, project_pi, allow_download_all, PlotID, SiteCode, Country |
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FROM projects pr JOIN plotMetadata p |
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ON pr.project_id=p.project_id |
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WHERE p.AccessCode=1; |
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*/ |
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| inputs/input.Makefile | ||
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selfDir_3d1bc249 := $(dir $(lastword $(MAKEFILE_LIST))) |
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# Make |
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addBeforeExt = $(basename $(2))$(1)$(suffix $(2)) |
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# Commands |
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DIFF = diff --unified=1 $(+:_%=) |
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table = $(shell s="$(*F)"; echo "$${s\#\#*.}")# remove sort order prefix
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vegxMaps := $(wildcard map.VegX.*.csv) |
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vegbienMaps := $(subst .VegX.,.VegBIEN.,$(vegxMaps)) |
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tables := $(vegbienMaps:map.VegBIEN.%.csv=%) |
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table = $(shell s="$(*F)"; echo "$${s\#\#*.}")# remove sort order prefix
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root := $(selfDir_3d1bc249).. |
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psqlAsBien := $(root)/bin/psql_vegbien |
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root := ../.. |
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map := env out_database=vegbien $(root)/map |
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##### |
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all: _not_file # empty rule since must be first target in file
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all: _not_file maps import verify
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.SUFFIXES: |
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_not_file: |
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.PHONY: _not_file |
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all := $(wildcard output.*) $(vegbienMaps) |
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clean: _not_file |
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$(RM) $(all) |
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rm-%: _not_file |
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$(RM) $* |
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%.out: % _not_file |
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./$* >$@ |
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.PRECIOUS: %.out |
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##### |
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reinstall: _not_file uninstall install |
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##### |
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maps: $(vegbienMaps) _not_file |
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all += $(vegbienMaps) |
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map.VegBIEN.%.csv: map.VegX.%.csv |
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$(root)/bin/join_sort <$< $(root)/mappings/VegX-VegBIEN.$(table).csv >$@ |
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.PRECIOUS: map.VegBIEN.%.csv |
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##### |
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import: _not_file $(addprefix import-,$(tables)) |
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log = $*$(if $(n),.n=$(n),).log |
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logs := $(wildcard *.log) |
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all += $(logs) |
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rm_logs: _not_file |
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$(RM) $(logs) |
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##### |
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verify: _not_file $(addprefix verify-,$(tables)) |
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verify-%: verify.%.ref.out verify.%.out _not_file |
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$(DIFF) |
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all += $(wildcard verify.*.out) |
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##### |
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test: _not_file $(addprefix test-,$(tables)) |
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test-%: test.%.ref.out test.%.out _not_file |
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$(DIFF) |
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all += $(filter-out %.ref.out,$(wildcard test.*.out)) |
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##### |
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ifdef db |
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ifndef dbEngine |
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$(error dbEngine variable must be set. Possible values: MySQL, PostgreSQL) |
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endif |
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mapEnv := in_engine=$(dbEngine) in_database=$(db) |
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all: _not_file $(vegbienMaps:map.VegBIEN.%.csv=import-%)
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####
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log = $*$(if $(n),.n=$(n),).log
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ifeq ($(dbEngine),MySQL)
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bienPassword := $(shell cat $(root)/config/bien_password) |
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mysqlAs = mysql --user=$(1) --password='$(bienPassword)' |
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mysqlAsRoot := $(call mysqlAs,root) |
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mysqlAsBien := $(call mysqlAs,bien) |
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import-%: map.VegBIEN.%.csv _not_file |
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$(importCmd) |
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importCmd = (set -x; "time" env commit=1 $(mapEnv) $(map) $<) \
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$(if $(n),,>>$(log)) 2>&1 $(if $(n),| tee -a $(log))
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importCmd = (set -x; "time" env commit=1 $(map) $<) \ |
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$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
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##
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all += $(wildcard *.out)
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%.ref.out: %.ref.sql |
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$(mysqlAsBien) --skip-column-names $(db) <$< >$@ |
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.PRECIOUS: %.ref.out |
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### |
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install: _not_file db |
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uninstall: _not_file rm_db |
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bienPassword := $(shell cat $(root)/config/bien_password) |
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mysql := mysql --user=root --password='$(bienPassword)' |
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db: $(db).sql _not_file |
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-$(mysql) <$< |
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echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysql) |
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-$(mysqlAsRoot) <$<
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echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
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# ignore errors in db import so that GRANT will still be run |
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rm_db: _not_file |
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-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysql) |
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echo "DROP DATABASE IF EXISTS $(db);"|$(mysql) |
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-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
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echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
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# ignore errors if grant not defined |
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### |
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else |
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$(error dbEngine variable must be one of the following: MySQL, PostgreSQL) |
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endif |
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#### |
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test.%.out: map.VegBIEN.%.csv _not_file |
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env n=2 $(map) $< >$@ 2>&1 |
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.PRECIOUS: test.%.out |
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##### |
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else |
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$(error db variable must be set) |
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endif |
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##### |
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# Must come after mapEnv is set |
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map := env $(mapEnv) out_database=vegbien $(root)/map |
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# Must come after %.ref.out and test.%.out so they get checked first |
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%.out: %.sql _not_file |
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$(psqlAsBien) --no-align --tuples-only <$< >$@ |
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.PRECIOUS: %.out |
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Also available in: Unified diff
input.Makefile: Added rules to verify inserted data and run tests