Revision 135
Added by Aaron Marcuse-Kubitza about 13 years ago
| scripts/test/map | ||
|---|---|---|
| 7 | 7 |
|
| 8 | 8 |
shopt -s nullglob |
| 9 | 9 |
|
| 10 |
test -n "$n" || n=2 |
|
| 11 |
let n++ # account for header row |
|
| 10 |
test -n "$n" || export n=2 |
|
| 12 | 11 |
|
| 13 | 12 |
. ../util/env_password in_password |
| 14 | 13 |
|
| ... | ... | |
| 17 | 16 |
../../mappings/extract_plot_map |
| 18 | 17 |
../../mappings/join_all_vegbank |
| 19 | 18 |
|
| 20 |
function importCsv()
|
|
| 19 |
function trace()
|
|
| 21 | 20 |
{
|
| 22 |
(set -x; head -"$n" "$in") |
|
| 21 |
( |
|
| 22 |
echo -n "$PS4" |
|
| 23 |
for arg in "$@"; do printf "%q " "$arg"; done |
|
| 24 |
echo "${_in+<$_in}" "${_out+>$_out}"
|
|
| 25 |
) >&2 |
|
| 23 | 26 |
} |
| 24 | 27 |
|
| 25 |
function importDb()
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|
| 28 |
function fromCsv()
|
|
| 26 | 29 |
{
|
| 27 |
echo "$PS4. \"$in\"" >&2
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|
| 28 |
. "$in"
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|
| 30 |
(_in="$in"; trace)
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|
| 31 |
"$1" <"$in" || exit
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|
| 29 | 32 |
} |
| 30 | 33 |
|
| 31 |
function exportXml()
|
|
| 34 |
function fromDb()
|
|
| 32 | 35 |
{
|
| 36 |
trace . "$in" |
|
| 37 |
(. "$in"; "$1") || exit |
|
| 38 |
} |
|
| 39 |
|
|
| 40 |
function toXml() |
|
| 41 |
{
|
|
| 33 | 42 |
out="$stem.$out_fmt.xml" |
| 34 | 43 |
(set -x; ../map "../../mappings/$src-$out_fmt.$table.csv" >"output/$out"\ |
| 35 | 44 |
&& diff "accepted_output/$out" "output/$out") |
| 36 | 45 |
} |
| 37 | 46 |
|
| 38 |
function exportDb()
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|
| 47 |
function toDb()
|
|
| 39 | 48 |
{
|
| 40 | 49 |
(set -x; ../map2vegbank "../../mappings/$src-VegBank.$table.csv") |
| 41 | 50 |
} |
| ... | ... | |
| 48 | 57 |
|
| 49 | 58 |
# Test exporting to XML |
| 50 | 59 |
for out_fmt in VegX VegBank; do |
| 51 |
if test "$ext" == "csv"; then importCsv|exportXml
|
|
| 52 |
elif test "$ext" == "sh"; then (importDb; exportXml)
|
|
| 60 |
if test "$ext" == "csv"; then fromCsv toXml
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|
| 61 |
elif test "$ext" == "sh"; then fromDb toXml
|
|
| 53 | 62 |
fi |
| 54 | 63 |
done |
| 55 | 64 |
|
| 56 | 65 |
# Test exporting to VegBank db |
| 57 |
if test "$ext" == "csv"; then importCsv|exportDb
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|
| 58 |
elif test "$ext" == "sh"; then (importDb; exportDb)
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|
| 66 |
if test "$ext" == "csv"; then fromCsv toDb
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|
| 67 |
elif test "$ext" == "sh"; then fromDb toDb
|
|
| 59 | 68 |
fi |
| 60 | 69 |
done |
| scripts/lib/util.py | ||
|---|---|---|
| 1 | 1 |
# Useful functions and classes |
| 2 | 2 |
|
| 3 |
def module(value): return type(value).__module__.split('.')
|
|
| 4 |
|
|
| 5 |
def root_module(value): return module(value)[0] |
|
| 6 |
|
|
| 7 |
def first(iter_): return iter_.next() |
|
| 8 |
|
|
| 3 | 9 |
def skip(iter_, func): |
| 4 | 10 |
# Advance iter while func is True |
| 5 | 11 |
try: |
| scripts/lib/sql.py | ||
|---|---|---|
| 7 | 7 |
import ex |
| 8 | 8 |
import util |
| 9 | 9 |
|
| 10 |
def _add_cursor_info(e, cur): ex.add_msg(e, 'query: '+cur.query) |
|
| 10 |
def get_cur_query(cur): |
|
| 11 |
if hasattr(cur, 'query'): return cur.query |
|
| 12 |
elif hasattr(cur, '_last_executed'): return cur._last_executed |
|
| 13 |
else: return None |
|
| 11 | 14 |
|
| 15 |
def _add_cursor_info(e, cur): ex.add_msg(e, 'query: '+get_cur_query(cur)) |
|
| 16 |
|
|
| 12 | 17 |
class NameException(Exception): pass |
| 13 | 18 |
|
| 14 | 19 |
class DbException(ex.ExceptionWithCause): |
| ... | ... | |
| 41 | 46 |
|
| 42 | 47 |
def col(cur, idx): return cur.description[idx][0] |
| 43 | 48 |
|
| 44 |
def row(cur): return iter(lambda: cur.fetchone(), None).next()
|
|
| 49 |
def rows(cur): return iter(lambda: cur.fetchone(), None)
|
|
| 45 | 50 |
|
| 51 |
def row(cur): return rows(cur).next() |
|
| 52 |
|
|
| 46 | 53 |
def value(cur): return row(cur)[0] |
| 47 | 54 |
|
| 48 | 55 |
def with_savepoint(db, func): |
| ... | ... | |
| 57 | 64 |
return return_val |
| 58 | 65 |
|
| 59 | 66 |
def select(db, table, fields, conds, limit=None): |
| 60 |
assert type(limit) == int |
|
| 67 |
assert limit == None or type(limit) == int
|
|
| 61 | 68 |
check_name(table) |
| 62 | 69 |
map(check_name, fields) |
| 63 | 70 |
map(check_name, conds.keys()) |
| ... | ... | |
| 84 | 91 |
else: query += ' DEFAULT VALUES' |
| 85 | 92 |
return run_query(db, query, row.values()) |
| 86 | 93 |
|
| 87 |
def last_insert_id(db): return value(run_query(db, 'SELECT lastval()')) |
|
| 94 |
def last_insert_id(db): |
|
| 95 |
module = util.root_module(db) |
|
| 96 |
if module == 'psycopg2': return value(run_query(db, 'SELECT lastval()')) |
|
| 97 |
elif module == 'MySQLdb': return db.insert_id() |
|
| 98 |
else: return None |
|
| 88 | 99 |
|
| 89 | 100 |
def try_insert(db, table, row): |
| 90 | 101 |
try: return with_savepoint(db, lambda: insert(db, table, row)) |
| scripts/lib/xml_dom.py | ||
|---|---|---|
| 19 | 19 |
|
| 20 | 20 |
def set_id(node, id_): node.setAttribute('id', id_)
|
| 21 | 21 |
|
| 22 |
def is_empty(node): return node.firstChild == None |
|
| 23 |
|
|
| 22 | 24 |
class NodeElemIter: |
| 23 | 25 |
def __init__(self, node): self.child = node.firstChild |
| 24 | 26 |
|
| ... | ... | |
| 99 | 101 |
self.iter_.next() |
| 100 | 102 |
return entry |
| 101 | 103 |
|
| 104 |
def set_child(node, name, value): |
|
| 105 |
'''Note: does not remove any existing child of the same name''' |
|
| 106 |
child = node.ownerDocument.createElement(name) |
|
| 107 |
set_value(node.ownerDocument, child, value) |
|
| 108 |
node.appendChild(child) |
|
| 109 |
|
|
| 102 | 110 |
def replace(old_node, new_node): |
| 103 | 111 |
old_node.parentNode.replaceChild(new_node, old_node) # note order reversed |
| 104 | 112 |
|
| 105 | 113 |
def replace_with_text(doc, node, str_): replace(node, doc.createTextNode(str_)) |
| 106 | 114 |
|
| 107 | 115 |
def by_tag_name(node, name, last_only=False): |
| 108 |
# last_only optimization returns last (most recently inserted) matching node
|
|
| 116 |
'''last_only optimization returns last matching node'''
|
|
| 109 | 117 |
children = [] |
| 110 | 118 |
for child in NodeElemReverseIter(node): |
| 111 | 119 |
if child.tagName == name: |
| ... | ... | |
| 117 | 125 |
return xml.dom.minidom.getDOMImplementation().createDocument(None, root, |
| 118 | 126 |
None) |
| 119 | 127 |
|
| 128 |
def writexml(writer, node): node.writexml(writer, addindent=' ', newl='\n') |
|
| 129 |
|
|
| 120 | 130 |
# xml.dom.minidom modifications |
| 121 | 131 |
|
| 122 | 132 |
def _write_data(writer, data): writer.write(escape(data)) |
| scripts/lib/xpath.py | ||
|---|---|---|
| 142 | 142 |
if last_only == None: last_only = create |
| 143 | 143 |
|
| 144 | 144 |
if create and not is_positive(xpath): return None |
| 145 |
doc = parent.ownerDocument |
|
| 145 | 146 |
for elem_idx, elem in enumerate(xpath): |
| 146 | 147 |
# Find possible matches |
| 147 | 148 |
children = [] |
| ... | ... | |
| 216 | 217 |
if value != None: set_value(xpath, value) |
| 217 | 218 |
get(doc, xpath, True) |
| 218 | 219 |
|
| 219 |
def path2xml(xpath): |
|
| 220 |
doc = xml_dom.create_doc() |
|
| 221 |
get(doc, xpath, True) |
|
| 222 |
return doc.documentElement |
|
| 220 |
def path2xml(xpath, first_branch=True): |
|
| 221 |
root = xml_dom.create_doc().documentElement |
|
| 222 |
get(root.ownerDocument, xpath, True) |
|
| 223 |
if first_branch: root = root.firstChild |
|
| 224 |
return root |
|
| 223 | 225 |
|
| 224 | 226 |
def str2xml(xpath): return path2xml(parse(xpath)) |
| scripts/lib/db_xml.py | ||
|---|---|---|
| 37 | 37 |
if pkeys == None: pkeys = {}
|
| 38 | 38 |
def pkey(table): return sql.pkey(db, pkeys, table) |
| 39 | 39 |
|
| 40 |
table = name_of(node) |
|
| 41 |
pkey_ = pkey(table) |
|
| 42 |
|
|
| 43 |
fields = [] |
|
| 44 |
conds = {}
|
|
| 40 | 45 |
for child in xml_dom.NodeElemIter(node): |
| 41 |
assert xml_dom.is_text(child) |
|
| 46 |
child_name = name_of(child) |
|
| 47 |
if xml_dom.is_empty(child): fields.append(child_name) |
|
| 48 |
elif xml_dom.is_text(child): conds[child_name] = xml_dom.value(child) |
|
| 49 |
else: raise Exception('Joins not supported yet')
|
|
| 50 |
id_ = xml_dom.get_id(node) |
|
| 51 |
if id_ != '': conds[pkey(table)] = id_ # replace any existing pkey value |
|
| 52 |
if fields == []: fields.append(pkey_) |
|
| 42 | 53 |
|
| 43 |
return []
|
|
| 54 |
return sql.select(db, table, fields, conds)
|
|
| 44 | 55 |
|
| 45 | 56 |
def put(db, node, store_ids=False, row_ct_ref=None, pkeys=None, parent_id=None): |
| 46 | 57 |
# store_ids enables searching the tree for missing fields |
| scripts/lib/opts.py | ||
|---|---|---|
| 4 | 4 |
|
| 5 | 5 |
def env_flag(name): return name in os.environ and os.environ[name] != '' |
| 6 | 6 |
|
| 7 |
def get_env_var(name, default, env_names_ref=None): |
|
| 8 |
if env_names_ref != None: env_names_ref.append(name) |
|
| 9 |
return os.getenv(name, default) |
|
| 10 |
|
|
| 7 | 11 |
def get_env_vars(names, prefix=None, env_names_ref=None): |
| 8 | 12 |
vars_ = {}
|
| 9 | 13 |
for name in names: |
| scripts/map | ||
|---|---|---|
| 3 | 3 |
# For outputting an XML file to a PostgreSQL database, use the general format of |
| 4 | 4 |
# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml |
| 5 | 5 |
|
| 6 |
import os |
|
| 7 | 6 |
import os.path |
| 8 | 7 |
import sys |
| 9 | 8 |
import xml.dom.minidom |
| ... | ... | |
| 25 | 24 |
def usage_err(): |
| 26 | 25 |
raise SystemExit('Usage: '+opts.env_usage(env_names, True)
|
| 27 | 26 |
+' [commit=1] '+sys.argv[0]+' [map_path] [<input] [>output]') |
| 27 |
limit = int(opts.get_env_var('n', sys.maxint, env_names))
|
|
| 28 |
commit = opts.env_flag('commit')
|
|
| 28 | 29 |
|
| 29 | 30 |
# Get db config from env vars |
| 30 | 31 |
db_config_names = ['engine', 'host', 'user', 'password', 'database'] |
| ... | ... | |
| 39 | 40 |
map_path = None |
| 40 | 41 |
try: _prog_name, map_path = sys.argv |
| 41 | 42 |
except ValueError: |
| 42 |
if in_is_db or not out_is_db: usage_err() |
|
| 43 |
commit = opts.env_flag('commit')
|
|
| 43 |
if in_is_db: usage_err() |
|
| 44 | 44 |
|
| 45 | 45 |
# Load map header |
| 46 | 46 |
in_is_xpaths = True |
| ... | ... | |
| 84 | 84 |
|
| 85 | 85 |
import db_xml |
| 86 | 86 |
|
| 87 |
src_root = xpath.str2xml(src_root) |
|
| 88 |
mappings = [(in_, xpath.path2xml(out)) for in_, out in mappings] |
|
| 87 |
src_root = xpath.parse(src_root) |
|
| 88 |
src_root_xml = xpath.path2xml(src_root) |
|
| 89 |
mappings = [(xpath.path2xml(in_), out) for in_, out in mappings] |
|
| 89 | 90 |
|
| 90 | 91 |
in_db = sql.connect(in_db_config) |
| 91 | 92 |
in_pkeys = {}
|
| 92 |
for row_id in db_xml.get(in_db, src_root, in_pkeys): |
|
| 93 |
for row_idx, row in enumerate(sql.rows(db_xml.get(in_db, |
|
| 94 |
src_root_xml, in_pkeys))): |
|
| 95 |
if not row_idx < limit: break |
|
| 96 |
row_id, = row |
|
| 97 |
row_id = str(row_id) |
|
| 98 |
|
|
| 93 | 99 |
def put_col(path, value): |
| 94 | 100 |
xpath.put_obj(doc1, path, row_id, has_types, value) |
| 95 | 101 |
for value, out in metadata: put_col(out, value) |
| 96 | 102 |
for in_, out in mappings: |
| 97 |
put_col(out, db_xml.get(in_db, in_, in_pkeys)) |
|
| 98 |
xpath.put_obj(doc1, out, row_id, has_types, ) |
|
| 103 |
root = xpath.get(in_.ownerDocument, src_root) |
|
| 104 |
xml_dom.replace(root, root.cloneNode(False)) |
|
| 105 |
xml_dom.set_id(root, row_id) |
|
| 106 |
|
|
| 107 |
cur = db_xml.get(in_db, in_, in_pkeys) |
|
| 108 |
try: value = sql.value(cur) |
|
| 109 |
except StopIteration: continue |
|
| 110 |
put_col(out, str(value)) |
|
| 99 | 111 |
in_db.close() |
| 100 | 112 |
elif in_is_xml: raise SystemExit('XML input not supported yet')
|
| 101 | 113 |
else: # input is CSV |
| ... | ... | |
| 103 | 115 |
reader = csv.reader(sys.stdin) |
| 104 | 116 |
cols = reader.next() |
| 105 | 117 |
for row_idx, row in enumerate(reader): |
| 118 |
if not row_idx < limit: break |
|
| 106 | 119 |
row_id = str(row_idx) |
| 120 |
|
|
| 107 | 121 |
def put_col(path, value): |
| 108 | 122 |
xpath.put_obj(doc1, path, row_id, has_types, value) |
| 109 | 123 |
for value, out in metadata: put_col(out, value) |
| ... | ... | |
| 127 | 141 |
finally: |
| 128 | 142 |
out_db.rollback() |
| 129 | 143 |
out_db.close() |
| 130 |
else: doc1.writexml(sys.stdout, addindent=' ', newl='\n') # output is XML
|
|
| 144 |
else: xml_dom.writexml(sys.stdout, doc1) # output is XML
|
|
| 131 | 145 |
|
| 132 | 146 |
try: main() |
| 133 | 147 |
except SyntaxException, ex: raise SystemExit(str(ex)) |
| mappings/SALVIAS_db-VegX.organisms.csv | ||
|---|---|---|
| 1 | 1 |
"SALVIAS:/plotObservations","VegX:/*s/individualOrganismObservation","Comments" |
| 2 |
"/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."
|
|
| 3 |
"/PLOT_ID",,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 4 |
"/plot_code","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/relatedSpatialItem/relatedItem[relationshipType=parentPlot]/relatedItemID->/*s/plot/plotUniqueIdentifier","Brad: Same as plotCode, above"
|
|
| 2 |
"/PlotObsID","/*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."
|
|
| 3 |
"/PlotID",,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 4 |
"/PlotCode","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier","Brad: Same as plotCode, above"
|
|
| 5 | 5 |
"/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." |
| 6 | 6 |
"/census_date","/*ID->/*s/plotObservation/obsStartDate/_date/year", |
| 7 |
"/subplot","/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier", |
|
| 8 |
"/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." |
|
| 7 |
"/OrigRecordID",, |
|
| 8 |
"/Line",, |
|
| 9 |
"/Ind","/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." |
|
| 9 | 10 |
"/ind_id",,"Brad: OMIT" |
| 10 | 11 |
"/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." |
| 11 | 12 |
"/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." |
| 12 | 13 |
"/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." |
| 13 | 14 |
"/y_position","/simpleUserdefined[name=yPosition]/value","Brad: See comment above for x_position" |
| 14 |
"/voucher_string",,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 15 |
"/dist",, |
|
| 16 |
"/perp_dist",, |
|
| 17 |
"/SourceVoucher",,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 15 | 18 |
"/coll_number","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode","Brad: Incorrect. Map instead as for voucher_string" |
| 16 | 19 |
"/collector_code",,"Brad: OMIT" |
| 20 |
"/coll_inits",, |
|
| 17 | 21 |
"/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." |
| 18 | 22 |
"/coll_firstname","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName","Brad: See comment above" |
| 19 |
"/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." |
|
| 23 |
"/DetType","/*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." |
|
| 24 |
"/det_by",, |
|
| 20 | 25 |
"/fam_status",,"Brad: OMIT. This will be determined later by using TNRS." |
| 21 | 26 |
"/gen_status",,"Brad: OMIT. This will be determined later by using TNRS." |
| 22 |
"/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." |
|
| 23 |
"/family","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name", |
|
| 24 |
"/genus","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name", |
|
| 25 |
"/specific_epithet","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name", |
|
| 26 |
"/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." |
|
| 27 |
"/name_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." |
|
| 28 |
"/SpAuthStatus",, |
|
| 29 |
"/Family","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name", |
|
| 30 |
"/Genus","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name", |
|
| 31 |
"/GenAuth",, |
|
| 32 |
"/Species","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name", |
|
| 33 |
"/auth","/*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." |
|
| 27 | 34 |
"/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", |
| 28 | 35 |
"/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", |
| 29 |
"/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." |
|
| 30 |
"/comments",,"Brad: OMIT" |
|
| 31 |
"/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." |
|
| 32 |
"/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." |
|
| 36 |
"/infra_auth_1",, |
|
| 37 |
"/common_name",, |
|
| 38 |
"/morphoname",, |
|
| 39 |
"/species_code",, |
|
| 40 |
"/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." |
|
| 41 |
"/height_class",, |
|
| 42 |
"/height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
|
| 43 |
"/height_m_commercial",, |
|
| 44 |
"/ht_first_branch_m","/simpleUserdefined[name=htFirstBranchM]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
|
| 45 |
"/NoInd","/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." |
|
| 33 | 46 |
"/cover_percent","/simpleUserdefined[name=coverPercent]/value", |
| 34 | 47 |
"/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." |
| 35 |
"/height_m","/height","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
|
| 36 |
"/ht_first_branch_m","/simpleUserdefined[name=htFirstBranchM]/value","Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob" |
|
| 37 |
"/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." |
|
| 38 |
"/stem_tag2","/*ID->/*s/individualOrganism/identificationLabel","Brad: see above" |
|
| 39 |
"/stem_dbh","/diameterBaseDistance[baseDistance=1.37]/diameter", |
|
| 40 |
"/basal_diam","/diameterBaseDistance[baseDistance=0]/diameter", |
|
| 41 |
"/stem_height_m","/simpleUserdefined[name=stemHeightM]/value","Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
|
| 42 |
"/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." |
|
| 43 |
"/stem_canopy_form","/simpleUserdefined[name=stemCanopyForm]/value","Brad: Should also be userDefined for VegBank. " |
|
| 44 |
"/stem_canopy_position","/simpleUserdefined[name=stemCanopyPosition]/value","Brad: Should also be userDefined for VegBank. " |
|
| 45 |
"/stem_liana_infestation","/simpleUserdefined[name=stemLianaInfestation]/value","Brad: Should also be userDefined for VegBank. " |
|
| 46 |
"/notes","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text", |
|
| 47 |
"/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" |
|
| 48 |
"/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" |
|
| 48 |
"/cfaff","/*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." |
|
| 49 |
"/other_annotations",, |
|
| 50 |
"/morphocf",, |
|
| 51 |
"/IsMorpho",, |
|
| 52 |
"/OrigFamily","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","Brad: OMIT" |
|
| 53 |
"/OrigGenus",, |
|
| 54 |
"/OrigSpecies","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","Brad: OMIT" |
|
| 55 |
"/OrigAuth",, |
|
| 56 |
"/phenology",, |
|
| 57 |
"/canopy_position","/simpleUserdefined[name=canopyPosition]/value","Brad: Should also be userDefined for VegBank. " |
|
| 58 |
"/canopy_form","/simpleUserdefined[name=canopyForm]/value","Brad: Should also be userDefined for VegBank. " |
|
| 59 |
"/liana_infestation","/simpleUserdefined[name=lianaInfestation]/value","Brad: Should also be userDefined for VegBank. " |
|
| 60 |
"/Notes","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text", |
|
| 61 |
"/temp_dbh","/diameterBaseDistance[baseDistance=1.37]/diameter", |
|
| 62 |
"/temp_liandbh",, |
|
| 63 |
"/tmp_del",, |
|
| mappings/SALVIAS_db-VegBank.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS:/plotObservations,VegBank:/taxonObservation,Comments |
| 2 |
/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."
|
|
| 3 |
/plot_code,/*_ID/observation/*_ID/plot/PARENT_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/1,"Brad: Same as plotCode, above"
|
|
| 2 |
/PlotObsID,"/{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."
|
|
| 3 |
/PlotCode,"/*_ID/observation/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}","Brad: Same as plotCode, above"
|
|
| 4 | 4 |
/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." |
| 5 | 5 |
/census_date,/*_ID/observation/obsStartDate/_date/year, |
| 6 |
/subplot,"/*_ID/observation/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}",
|
|
| 7 |
/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." |
|
| 6 |
/Ind,"/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." |
|
| 8 | 7 |
/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." |
| 9 | 8 |
/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." |
| 10 | 9 |
/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." |
| ... | ... | |
| 12 | 11 |
/coll_number,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber,Brad: Incorrect. Map instead as for voucher_string |
| 13 | 12 |
/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." |
| 14 | 13 |
/coll_firstname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/givenName,Brad: See comment above |
| 15 |
/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."
|
|
| 16 |
/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",
|
|
| 17 |
/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",
|
|
| 18 |
/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",
|
|
| 19 |
/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.
|
|
| 14 |
/DetType,"/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."
|
|
| 15 |
/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",
|
|
| 16 |
/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",
|
|
| 17 |
/Species,"/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",
|
|
| 18 |
/auth,"/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.
|
|
| 20 | 19 |
/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", |
| 21 | 20 |
/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", |
| 22 |
/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." |
|
| 23 |
/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." |
|
| 24 |
/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." |
|
| 21 |
/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." |
|
| 22 |
/height_m,/taxonImportance/stemCount/stemHeight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 23 |
/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 |
|
| 24 |
/NoInd,/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." |
|
| 25 | 25 |
/cover_percent,/taxonImportance/cover, |
| 26 | 26 |
/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." |
| 27 |
/height_m,/taxonImportance/stemCount/stemHeight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 28 |
/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 |
|
| 29 |
/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." |
|
| 30 |
/stem_tag2,/taxonImportance/stemCount/stemLocation/stemCode,Brad: see above |
|
| 31 |
/stem_dbh,/taxonImportance/stemCount/stemDiameter, |
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| 32 |
/basal_diam,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemBasalDiameter]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue", |
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| 33 |
/stem_height_m,/taxonImportance/stemCount/stemHeight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
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| 34 |
/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." |
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| 35 |
/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. |
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| 36 |
/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. |
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| 37 |
/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. |
|
| 38 |
/notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes, |
|
| 39 |
/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 |
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| 40 |
/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
|
|
| 27 |
/cfaff,"/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." |
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| 28 |
/OrigFamily,"/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 |
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| 29 |
/OrigSpecies,"/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
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| 30 |
/Notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes, |
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| 31 |
/temp_dbh,/taxonImportance/stemCount/stemDiameter, |
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Also available in: Unified diff
map: Implemented DB input support for querying a single table