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41 changes: 41 additions & 0 deletions
41
grails-app/services/org/bbop/apollo/AvailableStatusService.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| package org.bbop.apollo | ||
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| import grails.transaction.Transactional | ||
| import org.codehaus.groovy.grails.web.json.JSONArray | ||
|
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| @Transactional | ||
| class AvailableStatusService { | ||
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| JSONArray getAvailableStatuses(Organism organism, List<FeatureType> featureTypeList) { | ||
| JSONArray availableStatusesJSONArray = new JSONArray(); | ||
| // add all CC with no type and organism | ||
| List<AvailableStatus> availableStatusList = new ArrayList<>() | ||
| if (featureTypeList) { | ||
| availableStatusList.addAll(AvailableStatus.executeQuery("select cc from AvailableStatus cc join cc.featureTypes ft where ft in (:featureTypeList)", [featureTypeList: featureTypeList])) | ||
| } | ||
| availableStatusList.addAll(AvailableStatus.executeQuery("select cc from AvailableStatus cc where cc.featureTypes is empty")) | ||
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| // if there are organism filters for these canned comments for this organism, then apply them | ||
| List<AvailableStatusOrganismFilter> availableStatusOrganismFilters = AvailableStatusOrganismFilter.findAllByAvailableStatusInList(availableStatusList) | ||
| if (availableStatusOrganismFilters) { | ||
| // if the organism is in the list, that is good | ||
| AvailableStatusOrganismFilter.findAllByOrganismAndAvailableStatusInList(organism, availableStatusList).each { | ||
| availableStatusesJSONArray.put(it.availableStatus.value) | ||
| } | ||
| // we have to add anything from availableStatusList that isn't in another one | ||
| List<AvailableStatus> availableStatusesToExclude = AvailableStatusOrganismFilter.findAllByOrganismNotEqualAndAvailableStatusInList(organism, availableStatusList).availableStatus | ||
| for(AvailableStatus availableStatus in availableStatusList){ | ||
| if(!availableStatusesJSONArray.contains(availableStatus.value) && !availableStatusesToExclude.contains(availableStatus)){ | ||
| availableStatusesJSONArray.put(availableStatus.value) | ||
| } | ||
| } | ||
| } | ||
| // otherwise ignore them | ||
| else { | ||
| availableStatusList.each { | ||
| availableStatusesJSONArray.put(it.value) | ||
| } | ||
| } | ||
| return availableStatusesJSONArray | ||
| } | ||
| } |
72 changes: 72 additions & 0 deletions
72
grails-app/services/org/bbop/apollo/CannedAttributeService.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| package org.bbop.apollo | ||
|
|
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| import grails.transaction.Transactional | ||
| import org.codehaus.groovy.grails.web.json.JSONArray | ||
|
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| @Transactional | ||
| class CannedAttributeService { | ||
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| JSONArray getCannedKeys(Organism organism, List<FeatureType> featureTypeList) { | ||
| JSONArray cannedKeysJSONArray = new JSONArray(); | ||
| List<CannedKey> cannedKeyList = new ArrayList<>() | ||
| if (featureTypeList) { | ||
| cannedKeyList.addAll(CannedKey.executeQuery("select cc from CannedKey cc join cc.featureTypes ft where ft in (:featureTypeList)", [featureTypeList: featureTypeList])) | ||
| } | ||
| cannedKeyList.addAll(CannedKey.executeQuery("select cc from CannedKey cc where cc.featureTypes is empty")) | ||
|
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| // if there are organism filters for these canned comments for this organism, then apply them | ||
| List<CannedKeyOrganismFilter> cannedKeyOrganismFilters = CannedKeyOrganismFilter.findAllByCannedKeyInList(cannedKeyList) | ||
| if (cannedKeyOrganismFilters) { | ||
| CannedKeyOrganismFilter.findAllByOrganismAndCannedKeyInList(organism, cannedKeyList).each { | ||
| cannedKeysJSONArray.put(it.cannedKey.label) | ||
| } | ||
| // we have to add anything from cannedCommentList that isn't in another one | ||
| List<CannedKey> cannedKeysToExclude = CannedKeyOrganismFilter.findAllByOrganismNotEqualAndCannedKeyInList(organism, cannedKeyList).cannedKey | ||
| for(CannedKey cannedKey in cannedKeyList){ | ||
| if(!cannedKeysJSONArray.contains(cannedKey.label) && !cannedKeysToExclude.contains(cannedKey)){ | ||
| cannedKeysJSONArray.put(cannedKey.label) | ||
| } | ||
| } | ||
| } | ||
| // otherwise ignore them | ||
| else { | ||
| cannedKeyList.each { | ||
| cannedKeysJSONArray.put(it.label) | ||
| } | ||
| } | ||
| return cannedKeysJSONArray | ||
| } | ||
|
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| JSONArray getCannedValues(Organism organism, List<FeatureType> featureTypeList) { | ||
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| JSONArray cannedValuesJSONArray = new JSONArray(); | ||
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| List<CannedValue> cannedValueList = new ArrayList<>() | ||
| if (featureTypeList) { | ||
| cannedValueList.addAll(CannedValue.executeQuery("select cc from CannedValue cc join cc.featureTypes ft where ft in (:featureTypeList)", [featureTypeList: featureTypeList])) | ||
| } | ||
| cannedValueList.addAll(CannedValue.executeQuery("select cc from CannedValue cc where cc.featureTypes is empty")) | ||
|
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| // if there are organism filters for these canned comments for this organism, then apply them | ||
| List<CannedValueOrganismFilter> cannedValueOrganismFilters = CannedValueOrganismFilter.findAllByCannedValueInList(cannedValueList) | ||
| if (cannedValueOrganismFilters) { | ||
| CannedValueOrganismFilter.findAllByOrganismAndCannedValueInList(organism, cannedValueList).each { | ||
| cannedValuesJSONArray.put(it.cannedValue.label) | ||
| } | ||
| // we have to add anything from cannedValueList that isn't in another one | ||
| List<CannedValue> cannedValuesToExclude = CannedValueOrganismFilter.findAllByOrganismNotEqualAndCannedValueInList(organism, cannedValueList).cannedValue | ||
| for(CannedValue cannedValue in cannedValueList){ | ||
| if(!cannedValuesJSONArray.contains(cannedValue.label) && !cannedValuesToExclude.contains(cannedValue)){ | ||
| cannedValuesJSONArray.put(cannedValue.label) | ||
| } | ||
| } | ||
| } | ||
| // otherwise ignore them | ||
| else { | ||
| cannedValueList.each { | ||
| cannedValuesJSONArray.put(it.label) | ||
| } | ||
| } | ||
| return cannedValuesJSONArray | ||
| } | ||
| } |
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