Revision 89
Added by Aaron Marcuse-Kubitza over 12 years ago
| scripts/lib/xml_func.py | ||
|---|---|---|
| 19 | 19 |
|
| 20 | 20 |
def date(items): |
| 21 | 21 |
items = dict(items) |
| 22 |
return '-'.join([items['year'], items.get('month', '1'),
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|
| 22 |
return ' '.join([items['year'], items.get('month', '1'),
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|
| 23 | 23 |
items.get('day', '1')])
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| 24 | 24 |
|
| 25 |
def name(items): |
|
| 26 |
items = dict(items) |
|
| 27 |
return ' '.join([items['first'], items['last']]) |
|
| 28 |
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|
| 25 | 29 |
# Function names must start with _ to avoid collisions with real tags |
| 26 | 30 |
# Functions have take arguments (doc, node) |
| 27 |
funcs = {'_range': range_, '_avg': avg, '_date': date}
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| 31 |
funcs = {'_range': range_, '_avg': avg, '_date': date, '_name': name}
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|
| 28 | 32 |
|
| 29 | 33 |
def process(doc, node=None): |
| 30 | 34 |
if node == None: node = doc.documentElement |
| scripts/lib/sql.py | ||
|---|---|---|
| 24 | 24 |
|
| 25 | 25 |
class NullValueException(ExceptionWithColumn): pass |
| 26 | 26 |
|
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class EmptyRowException(DbException): pass |
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| 28 |
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|
| 27 | 29 |
def check_name(name): |
| 28 | 30 |
if re.search(r'\W', name) != None: raise NameException('Name "'+name
|
| 29 | 31 |
+'" may contain only alphanumeric characters and _') |
| ... | ... | |
| 64 | 66 |
else: cond_ += '=' |
| 65 | 67 |
cond_ += ' %s' |
| 66 | 68 |
return cond_ |
| 67 |
return run_query(db, 'SELECT '+', '.join(fields)+' FROM '+table+' WHERE ' |
|
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+' AND '.join(map(cond, conds.iteritems())), conds.values()) |
|
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query = 'SELECT '+', '.join(fields)+' FROM '+table |
|
| 70 |
if conds != {}:
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query += ' WHERE '+' AND '.join(map(cond, conds.iteritems())) |
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return run_query(db, query, conds.values()) |
|
| 69 | 73 |
|
| 70 | 74 |
def insert(db, table, row): |
| 71 | 75 |
check_name(table) |
| 72 | 76 |
cols = row.keys() |
| 73 | 77 |
map(check_name, cols) |
| 74 |
return run_query(db, 'INSERT INTO '+table+' ('+', '.join(cols)
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+') VALUES ('+', '.join(['%s']*len(cols))+')', row.values())
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query = 'INSERT INTO '+table |
|
| 79 |
if row != {}: query += ' ('+', '.join(cols)+') VALUES ('\
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+', '.join(['%s']*len(cols))+')' |
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else: query += ' DEFAULT VALUES' |
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return run_query(db, query, row.values()) |
|
| 76 | 83 |
|
| 77 | 84 |
def last_insert_id(db): return value(run_query(db, 'SELECT lastval()')) |
| 78 | 85 |
|
| ... | ... | |
| 93 | 100 |
return col(run_query(db, 'SELECT * FROM '+table+' LIMIT 0'), 0) |
| 94 | 101 |
|
| 95 | 102 |
def get(db, table, row, pkey, create=False, row_ct_ref=None): |
| 103 |
if row == []: raise EmptyRowException(table) # nothing to insert/filter by |
|
| 96 | 104 |
try: return value(select(db, table, [pkey], row)) |
| 97 | 105 |
except StopIteration: |
| 98 | 106 |
if not create: raise |
| mappings/VegX-VegBank.organisms.csv | ||
|---|---|---|
| 26 | 26 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID]/partyWithRole[role=identifier]/*ID->/parties/party/individualName/{givenName,surName}","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/*_ID/party/{givenName,middleName,surName}"
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| 27 | 27 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/collectionNumber" |
| 28 | 28 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/note/text","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/notes" |
| 29 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/firstName","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/firstName"
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"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/lastName","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/lastName"
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| 29 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/first"
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"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/last"
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| 31 | 31 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher","/{taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museumAccessionNumber,*_ID/observation/*_ID/plot/authorPlotCode}"
|
| 32 | 32 |
"/*ID->/*s/individualOrganism/identificationLabel","/taxonImportance/stemCount/stemLocation/stemCode" |
| 33 | 33 |
"/*ID->/*s/individualOrganism/simpleUserdefined[name=sex]/value","/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/definedValue[@fkey=tableRecord_ID,userDefined[tableName=taxonInterpretation,userDefinedName=sex]]/definedValue" |
| mappings/NYBG-VegX.organisms.csv | ||
|---|---|---|
| 3 | 3 |
":1","/simpleUserdefined[name=count]/value" |
| 4 | 4 |
"key", |
| 5 | 5 |
"DateLastModified", |
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"InstitutionCode","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/firstName"
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"CollectionCode","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/lastName"
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"InstitutionCode","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/first" |
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"CollectionCode","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName/_name/last" |
|
| 8 | 8 |
"CatalogNumber", |
| 9 | 9 |
"ScientificName","/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonName)/Simple" |
| 10 | 10 |
"BasisOfRecord", |
| mappings/joins/NYBG-VegBank.organisms.csv | ||
|---|---|---|
| 1 | 1 |
NYBG,VegBank:/taxonObservation |
| 2 | 2 |
:0,/*_ID/observation/*_ID/plot/confidentialityStatus |
| 3 | 3 |
:1,/taxonImportance/*/stemCount |
| 4 |
InstitutionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/firstName
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| 5 |
CollectionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/lastName
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| 4 |
InstitutionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/first |
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| 5 |
CollectionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/museum_ID/party/OrganizationName/_name/last |
|
| 6 | 6 |
ScientificName,/taxonImportance/stemCount/stemLocation/taxonInterpretation(/*_ID/plantConcept[plantStatus/plantLevel=Species])/*_ID/*/plantName |
| 7 | 7 |
Kingdom,/taxonImportance/stemCount/stemLocation/taxonInterpretation(/*_ID/plantConcept[plantStatus/plantLevel=Kingdom])/*_ID/*/plantName |
| 8 | 8 |
Phylum,/taxonImportance/stemCount/stemLocation/taxonInterpretation(/*_ID/plantConcept[plantStatus/plantLevel=Subkingdom])/*_ID/*/plantName |
Also available in: Unified diff
Added support for name XML function. Added error handling for empty rows.