export in_host=localhost in_user=vegbank in_password=vegbank in_database=vegbank

    # Requires that all env vars are set; otherwise returns None

    has_all = True

        if env_name in os.environ: vars_[name] = os.environ[env_name]

        else: has_all = False

    if has_all: return vars_

    else: return None

    in_is_db = in_db_config != None

    out_is_db = out_db_config != None

    in_is_xml = True

        src, in_is_xml, src_root = split_col_name(src)

        dest, out_is_xml, dest_root = split_col_name(dest)

        assert out_is_xml

            assert in_is_xml

    if out_db_config != None: # output is database

"SALVIAS","VegX:/*s/individualOrganismObservation","Comments"

"OBSERVATION_ID","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher","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."

"PLOT_ID",,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."

"plot_code","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/relatedSpatialItem/relatedItem[relationshipType=parentPlot]/relatedItemID->/*s/plot/plotUniqueIdentifier","Brad: Same as plotCode, above"

"census_no","/simpleUserdefined[name=censusNo]/value","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."

"census_date","/*ID->/*s/plotObservation/obsStartDate/_date/year",

"subplot","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier",

"individual_code","/simpleUserdefined[name=individualCode]/value","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."

"ind_id",,"Brad: OMIT"

"tag1","/*ID->/*s/individualOrganism/identificationLabel","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."

"tag2","/*ID->/*s/individualOrganism/identificationLabel","Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

"x_position","/simpleUserdefined[name=xPosition]/value","Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."

"y_position","/simpleUserdefined[name=yPosition]/value","Brad: See comment above for x_position"

"voucher_string",,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."

"coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode","Brad: Incorrect. Map instead as for voucher_string"

"collector_code",,"Brad: OMIT"

"coll_lastname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/surName","Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."

"coll_firstname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName","Brad: See comment above"

"det_type","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."

"fam_status",,"Brad: OMIT. This will be determined later by using TNRS."

"gen_status",,"Brad: OMIT. This will be determined later by using TNRS."

"species_status",,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

"family","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name",

"genus","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name",

"specific_epithet","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name",

"specific_authority","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/AccordingTo/Simple","Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss."

"infra_rank_1","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank",

"infra_ep_1","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Name",

"cf_aff","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/note","Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."

"comments",,"Brad: OMIT"

"habit","/simpleUserdefined[name=habit]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

"no_of_individuals","/simpleUserdefined[name=count]/value","Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."

"cover_percent","/simpleUserdefined[name=coverPercent]/value",

"intercept_cm","/simpleUserdefined[name=interceptCm]/value","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."

"height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob"

"ht_first_branch_m","/simpleUserdefined[name=htFirstBranchM]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob"

"stem_tag1","/*ID->/*s/individualOrganism/identificationLabel","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."

"stem_tag2","/*ID->/*s/individualOrganism/identificationLabel","Brad: see above"

"stem_dbh","/diameterBaseDistance[baseDistance=1.37]/diameter",

"basal_diam","/diameterBaseDistance[baseDistance=0]/diameter",

"stem_height_m","/simpleUserdefined[name=stemHeightM]/value","Brad: Same as for height, but applies to individuals stems, not trees. Rare."

"stem_height_first_branch_m","/simpleUserdefined[name=stemHeightFirstBranchM]/value","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."

"stem_canopy_form","/simpleUserdefined[name=stemCanopyForm]/value","Brad: Should also be userDefined for VegBank. "

"stem_canopy_position","/simpleUserdefined[name=stemCanopyPosition]/value","Brad: Should also be userDefined for VegBank. "

"stem_liana_infestation","/simpleUserdefined[name=stemLianaInfestation]/value","Brad: Should also be userDefined for VegBank. "

"notes","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text",

"orig_family","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","Brad: OMIT"

"orig_species","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","Brad: OMIT"

SALVIAS,VegBank:/taxonObservation,Comments

OBSERVATION_ID,"/{taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept:[*_ID/reference],*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_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."

plot_code,/*_ID/observation/*_ID/plot/PARENT_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/1,"Brad: Same as plotCode, above"

census_no,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=censusNo]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."

census_date,/*_ID/observation/obsStartDate/_date/year,

subplot,"/*_ID/observation/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}",

individual_code,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=individualCode]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."

tag1,/taxonImportance/stemCount/stemLocation/stemCode,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."

tag2,/taxonImportance/stemCount/stemLocation/stemCode,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

x_position,/taxonImportance/stemCount/stemLocation/stemXPosition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."

y_position,/taxonImportance/stemCount/stemLocation/stemYPosition,Brad: See comment above for x_position

coll_number,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber,Brad: Incorrect. Map instead as for voucher_string

coll_lastname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/surName,"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."

coll_firstname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/givenName,Brad: See comment above

det_type,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=determinationType]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."

family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

genus,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

specific_epithet,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

specific_authority,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/plantName/reference_ID/reference/shortName",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.

infra_rank_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/first",

infra_ep_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/last",

cf_aff,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=cfAff]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."

habit,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=habit]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

no_of_individuals,/taxonImportance/*/stemCount,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."

cover_percent,/taxonImportance/cover,

intercept_cm,"/taxonImportance/definedValue[*_ID/userDefined[tableName=taxonImportance,userDefinedName=interceptCm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."

height_m,/taxonImportance/stemCount/stemHeight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

ht_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=heightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

stem_tag1,/taxonImportance/stemCount/stemLocation/stemCode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."

stem_tag2,/taxonImportance/stemCount/stemLocation/stemCode,Brad: see above

stem_dbh,/taxonImportance/stemCount/stemDiameter,

basal_diam,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemBasalDiameter]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

stem_height_m,/taxonImportance/stemCount/stemHeight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."

stem_height_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemHeightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."

stem_canopy_form,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyForm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",Brad: Should also be userDefined for VegBank. 

stem_canopy_position,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyPosition]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",Brad: Should also be userDefined for VegBank. 

stem_liana_infestation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemLianaInfestation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",Brad: Should also be userDefined for VegBank. 

notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes,

orig_family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",Brad: OMIT

orig_species,"/taxonImportance/stemCount/stemLocation/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept/*_ID/*/plantName/_alt/2}",Brad: OMIT