git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-publishing/gCat-Feeder-Suite@179492 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
c89eb7d5bd
commit
b304a9b78a
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@ -9,6 +9,18 @@
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<name>gCat Controller</name>
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<description>Controller implementation for GCat Service</description>
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<dependencyManagement>
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<dependencies>
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||||
<dependency>
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<groupId>org.gcube.distribution</groupId>
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<artifactId>gcube-bom</artifactId>
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<version>LATEST</version>
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<type>pom</type>
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<scope>import</scope>
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</dependency>
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||||
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</dependencies>
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</dependencyManagement>
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<dependencies>
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<dependency>
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@ -32,6 +44,20 @@
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<scope>provided</scope>
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</dependency>
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</dependencies>
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<build>
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@ -63,7 +63,7 @@ public class GCatController implements CatalogueController{
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try {
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builder= factory.newDocumentBuilder();
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expr= xpath.compile("string(/bookstore/book/title/@lang)");
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expr= xpath.compile("string(//metadataformat/@type)");
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} catch (ParserConfigurationException | XPathExpressionException e) {
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throw new RuntimeException("Unable to initialize Controller");
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}
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@ -141,7 +141,7 @@ public class GCatController implements CatalogueController{
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}
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log.debug("Publishing Item..");
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String itemResp=createItem(itemNode.asText());
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String itemResp=createItem(itemNode.toString(),itemNode.path("name").textValue());
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String itemId = getId(itemResp);
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log.debug("Pubilshed Item with ID {} ",itemId);
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@ -263,13 +263,17 @@ public class GCatController implements CatalogueController{
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}
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private String createItem(String toCreate) throws WrongObjectFormatException, PublicationException{
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private String createItem(String toCreate,String name) throws WrongObjectFormatException, PublicationException{
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Item item=null;
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try{
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if(isForcedUrl())
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item = new Item(getForcedUrl());
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else item=new Item();
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return item.create(toCreate);
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if(existsItem(item,name))
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return item.update(name, toCreate);
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else return item.create(toCreate);
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}catch(WebApplicationException e) {
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handleWebException(e);
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return null;
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@ -280,7 +284,15 @@ public class GCatController implements CatalogueController{
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}
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private boolean existsItem(Item item,String name) {
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try {
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item.read(name);
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return true;
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}catch(WebApplicationException e) {
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log.debug("Read Item returned error. Assuming it's missing ",e);
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return false;
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}
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}
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@ -339,6 +351,7 @@ public class GCatController implements CatalogueController{
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}
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private static String getId(String publishResponse) {
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try {
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return mapper.readTree(publishResponse).path("result").path("id").asText();
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@ -1,21 +1,39 @@
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{
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"profile": "<metadataformat type=\"Algorithm\">\n <metadatafield>\n <fieldName>Input Parameter</fieldName>\n <dataType>String</dataType>\n <mandatory>false</mandatory>\n <note>Input parameter expected for the execution of the algorithm</note>\n </metadatafield> \n</metadataformat>",
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"profileID": "DataMiner Process",
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"profile": "<metadataformat type=\"DataMiner Process\">\n\t<metadatafield>\n\t\t<fieldName>Input Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Input parameter expected for the execution of the process</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Output Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Output parameter expected from the execution of the process\n\t\t</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Process Author</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<maxOccurs>*</maxOccurs>\n\t\t<defaultValue />\n\t\t<note>The name of the author, with email and ORCID. The format should\n\t\t\tbe: family, given[, email][, ORCID]. Example: Smith, John,\n\t\t\tjs@acme.org, orcid.org/0000-0002-1825-0097</note>\n\t\t<validator>\n\t\t\t<regularExpression>^[a-zA-ZÀ-ÿ .'-]+, [a-zA-ZÀ-ÿ .'-]+[,\n\t\t\t\t]*([a-zA-Z0-9_!#$%’*+=?`{|}~^.-]+@[a-zA-Z0-9À-ÿ.-]+)?[,\n\t\t\t\t]*(orcid.org\\/0000-000(1-[5-9]|2-[0-9]|3-[0-4])\\d\\d\\d-\\d\\d\\d[\\dX])?$</regularExpression>\n\t\t</validator>\n\t</metadatafield>\n</metadataformat>",
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"item":
|
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{
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||||
"name": "step_4_vpa_iccat_bft_e_report_in_nextnext",
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"title": "Step 4 Vpa Iccat Bft E Report in NextNext",
|
||||
"description": "ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD",
|
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"name": "grid_cwp_to_coordinates_in_prevre",
|
||||
"title": "Grid Cwp To Coordinates in preVRE",
|
||||
"description": "An algorithm that adds longitude, latitude and resolution columns analysing a column containing FAO Ocean Area codes (CWP format).",
|
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"version": null,
|
||||
"visibility": null,
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||||
"license": "CC-BY-NC-SA-4.0",
|
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"author": "gianpaolo.coro",
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"maintainer": "gianpaolo.coro",
|
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"tags": ["Iccat Eastern Bft Stock Assessment"],
|
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"license_id": "CC-BY-NC-SA-4.0",
|
||||
"author": null,
|
||||
"maintainer": null,
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"tags": [
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||||
{
|
||||
"name": "Geo Processing"
|
||||
},
|
||||
{
|
||||
"name": "preVRE"
|
||||
},
|
||||
{
|
||||
"name": "WPS"
|
||||
},
|
||||
{
|
||||
"name": "Analytics"
|
||||
}],
|
||||
"extras": [
|
||||
{
|
||||
"key": "system",
|
||||
"value": "Algorithm"
|
||||
}]
|
||||
"key": "system:type",
|
||||
"value": "DataMiner Process"
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}],
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"private": true
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},
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"resources": []
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"resources": [
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{
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"name": "Gateway Link",
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"url": "https://pre.d4science.org/group/prevre/dataminer-manager?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GRID_CWP_TO_COORDINATES",
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"description": "Link to the GUI designed to operate with DataMiner"
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}]
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||||
}
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@ -0,0 +1,101 @@
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|||
{
|
||||
"profile": null,
|
||||
"item": {
|
||||
"license_title": "Creative Commons Attribution Share-Alike 4.0",
|
||||
"maintainer": null,
|
||||
"searchable": "true",
|
||||
"relationships_as_object": [],
|
||||
"private": true,
|
||||
"maintainer_email": null,
|
||||
"num_tags": 2,
|
||||
"metadata_created": "2019-03-19T15:03:28.482434",
|
||||
"metadata_modified": "2019-03-19T15:03:30.676258",
|
||||
"author": "luca_frosini",
|
||||
"author_email": "luca.frosini@gcube.ckan.org",
|
||||
"state": "active",
|
||||
"version": null,
|
||||
"creator_user_id": "287b2eec-4cd7-4e50-817f-e6dce19995c7",
|
||||
"type": "dataset",
|
||||
"tags": [
|
||||
{
|
||||
"vocabulary_id": null,
|
||||
"state": "active",
|
||||
"display_name": "Other",
|
||||
"id": "8ca635e2-4f72-48ed-8460-6734e9070a00",
|
||||
"name": "Other"
|
||||
},
|
||||
{
|
||||
"vocabulary_id": null,
|
||||
"state": "active",
|
||||
"display_name": "REST",
|
||||
"id": "3d481290-b3cd-466f-8142-51608c616e60",
|
||||
"name": "REST"
|
||||
}
|
||||
],
|
||||
"groups": [],
|
||||
"license_id": "CC-BY-SA-4.0",
|
||||
"extras": [
|
||||
{
|
||||
"key": "FSKX_model_parameters:Input Parameter",
|
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"value": "standard desviation of Temperatures( sdTemp): 2.9 °c( Double)"
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||||
},
|
||||
{
|
||||
"key": "FSKX_model_parameters:Output Parameter",
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||||
"value": ""
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||||
},
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||||
{
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||||
"key": "FSKX_model_scope:Hazard",
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||||
"value": ""
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||||
},
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{
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"key": "FSKX_model_scope:Population",
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"value": ""
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},
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{
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"key": "FSKX_model_scope:Product",
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"value": ""
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},
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{
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"key": "Item URL",
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"value": "http://data.d4science.org/ctlg/AGINFRAplusDev/my_first_restful_transaction_model"
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},
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{
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"key": "Model Author",
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"value": ""
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||||
},
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||||
{
|
||||
"key": "Model Creator",
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||||
"value": ""
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||||
},
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||||
{
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"key": "Model ID",
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||||
"value": ""
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||||
},
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||||
{
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||||
"key": "Model Language",
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"value": "Other"
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||||
},
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||||
{
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||||
"key": "Population",
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||||
"value": "Italian"
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||||
},
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||||
{
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||||
"key": "ReadMe",
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||||
"value": ""
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||||
},
|
||||
{
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||||
"key": "Reference Description",
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||||
"value": ""
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||||
},
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||||
{
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||||
"key": "Related Identifier",
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||||
"value": ""
|
||||
},
|
||||
{
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||||
"key": "system:type",
|
||||
"value": "My Profile"
|
||||
}
|
||||
]
|
||||
},
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||||
"resources": null
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||||
}
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||||
|
|
@ -1,5 +1,5 @@
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|||
#Generated by Maven Integration for Eclipse
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#Wed May 08 18:18:34 CEST 2019
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#Mon May 20 17:18:44 CEST 2019
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||||
version=1.0.0-SNAPSHOT
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groupId=org.gcube.data-publishing.gCat-Feeder
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||||
m2e.projectName=gCat-Controller
|
||||
|
|
|
|||
|
|
@ -9,6 +9,18 @@
|
|||
<name>gCat Controller</name>
|
||||
<description>Controller implementation for GCat Service</description>
|
||||
|
||||
<dependencyManagement>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-bom</artifactId>
|
||||
<version>LATEST</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
</dependencyManagement>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
|
|
@ -32,6 +44,20 @@
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|||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-databind</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>org.slf4j</groupId>
|
||||
<artifactId>slf4j-api</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
|
|
|
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Binary file not shown.
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@ -1,21 +1,39 @@
|
|||
{
|
||||
"profile": "<metadataformat type=\"Algorithm\">\n <metadatafield>\n <fieldName>Input Parameter</fieldName>\n <dataType>String</dataType>\n <mandatory>false</mandatory>\n <note>Input parameter expected for the execution of the algorithm</note>\n </metadatafield> \n</metadataformat>",
|
||||
"profileID": "DataMiner Process",
|
||||
"profile": "<metadataformat type=\"DataMiner Process\">\n\t<metadatafield>\n\t\t<fieldName>Input Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Input parameter expected for the execution of the process</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Output Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Output parameter expected from the execution of the process\n\t\t</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Process Author</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<maxOccurs>*</maxOccurs>\n\t\t<defaultValue />\n\t\t<note>The name of the author, with email and ORCID. The format should\n\t\t\tbe: family, given[, email][, ORCID]. Example: Smith, John,\n\t\t\tjs@acme.org, orcid.org/0000-0002-1825-0097</note>\n\t\t<validator>\n\t\t\t<regularExpression>^[a-zA-ZÀ-ÿ .'-]+, [a-zA-ZÀ-ÿ .'-]+[,\n\t\t\t\t]*([a-zA-Z0-9_!#$%’*+=?`{|}~^.-]+@[a-zA-Z0-9À-ÿ.-]+)?[,\n\t\t\t\t]*(orcid.org\\/0000-000(1-[5-9]|2-[0-9]|3-[0-4])\\d\\d\\d-\\d\\d\\d[\\dX])?$</regularExpression>\n\t\t</validator>\n\t</metadatafield>\n</metadataformat>",
|
||||
"item":
|
||||
{
|
||||
"name": "step_4_vpa_iccat_bft_e_report_in_nextnext",
|
||||
"title": "Step 4 Vpa Iccat Bft E Report in NextNext",
|
||||
"description": "ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD",
|
||||
"name": "grid_cwp_to_coordinates_in_prevre",
|
||||
"title": "Grid Cwp To Coordinates in preVRE",
|
||||
"description": "An algorithm that adds longitude, latitude and resolution columns analysing a column containing FAO Ocean Area codes (CWP format).",
|
||||
"version": null,
|
||||
"visibility": null,
|
||||
"license": "CC-BY-NC-SA-4.0",
|
||||
"author": "gianpaolo.coro",
|
||||
"maintainer": "gianpaolo.coro",
|
||||
"tags": ["Iccat Eastern Bft Stock Assessment"],
|
||||
"license_id": "CC-BY-NC-SA-4.0",
|
||||
"author": null,
|
||||
"maintainer": null,
|
||||
"tags": [
|
||||
{
|
||||
"name": "Geo Processing"
|
||||
},
|
||||
{
|
||||
"name": "preVRE"
|
||||
},
|
||||
{
|
||||
"name": "WPS"
|
||||
},
|
||||
{
|
||||
"name": "Analytics"
|
||||
}],
|
||||
"extras": [
|
||||
{
|
||||
"key": "system",
|
||||
"value": "Algorithm"
|
||||
}]
|
||||
"key": "system:type",
|
||||
"value": "DataMiner Process"
|
||||
}],
|
||||
"private": true
|
||||
},
|
||||
"resources": []
|
||||
"resources": [
|
||||
{
|
||||
"name": "Gateway Link",
|
||||
"url": "https://pre.d4science.org/group/prevre/dataminer-manager?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GRID_CWP_TO_COORDINATES",
|
||||
"description": "Link to the GUI designed to operate with DataMiner"
|
||||
}]
|
||||
}
|
||||
|
|
@ -0,0 +1,101 @@
|
|||
{
|
||||
"profile": null,
|
||||
"item": {
|
||||
"license_title": "Creative Commons Attribution Share-Alike 4.0",
|
||||
"maintainer": null,
|
||||
"searchable": "true",
|
||||
"relationships_as_object": [],
|
||||
"private": true,
|
||||
"maintainer_email": null,
|
||||
"num_tags": 2,
|
||||
"metadata_created": "2019-03-19T15:03:28.482434",
|
||||
"metadata_modified": "2019-03-19T15:03:30.676258",
|
||||
"author": "luca_frosini",
|
||||
"author_email": "luca.frosini@gcube.ckan.org",
|
||||
"state": "active",
|
||||
"version": null,
|
||||
"creator_user_id": "287b2eec-4cd7-4e50-817f-e6dce19995c7",
|
||||
"type": "dataset",
|
||||
"tags": [
|
||||
{
|
||||
"vocabulary_id": null,
|
||||
"state": "active",
|
||||
"display_name": "Other",
|
||||
"id": "8ca635e2-4f72-48ed-8460-6734e9070a00",
|
||||
"name": "Other"
|
||||
},
|
||||
{
|
||||
"vocabulary_id": null,
|
||||
"state": "active",
|
||||
"display_name": "REST",
|
||||
"id": "3d481290-b3cd-466f-8142-51608c616e60",
|
||||
"name": "REST"
|
||||
}
|
||||
],
|
||||
"groups": [],
|
||||
"license_id": "CC-BY-SA-4.0",
|
||||
"extras": [
|
||||
{
|
||||
"key": "FSKX_model_parameters:Input Parameter",
|
||||
"value": "standard desviation of Temperatures( sdTemp): 2.9 °c( Double)"
|
||||
},
|
||||
{
|
||||
"key": "FSKX_model_parameters:Output Parameter",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "FSKX_model_scope:Hazard",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "FSKX_model_scope:Population",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "FSKX_model_scope:Product",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Item URL",
|
||||
"value": "http://data.d4science.org/ctlg/AGINFRAplusDev/my_first_restful_transaction_model"
|
||||
},
|
||||
{
|
||||
"key": "Model Author",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Model Creator",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Model ID",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Model Language",
|
||||
"value": "Other"
|
||||
},
|
||||
{
|
||||
"key": "Population",
|
||||
"value": "Italian"
|
||||
},
|
||||
{
|
||||
"key": "ReadMe",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Reference Description",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "Related Identifier",
|
||||
"value": ""
|
||||
},
|
||||
{
|
||||
"key": "system:type",
|
||||
"value": "My Profile"
|
||||
}
|
||||
]
|
||||
},
|
||||
"resources": null
|
||||
}
|
||||
|
|
@ -4,15 +4,6 @@
|
|||
<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
|
||||
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
|
||||
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
|
||||
<dependent-module archiveName="collectors-plugin-framework-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/collectors-plugin-framework/collectors-plugin-framework">
|
||||
<dependency-type>uses</dependency-type>
|
||||
</dependent-module>
|
||||
<dependent-module archiveName="commons-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/commons/commons">
|
||||
<dependency-type>uses</dependency-type>
|
||||
</dependent-module>
|
||||
<dependent-module archiveName="catalogue-plugin-framework-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/catalogue-plugin-framework/catalogue-plugin-framework">
|
||||
<dependency-type>uses</dependency-type>
|
||||
</dependent-module>
|
||||
<property name="context-root" value="gCat-Feeder"/>
|
||||
<property name="java-output-path" value="/gCat-Feeder/target/classes"/>
|
||||
</wb-module>
|
||||
|
|
|
|||
|
|
@ -7,8 +7,8 @@ public interface LocalConfiguration {
|
|||
public static final String POOL_MIN_IDLE="db.pools.min_total";
|
||||
|
||||
|
||||
public static final String MAPPING_DB_ENDPOINT_NAME="db.ep.name";
|
||||
public static final String MAPPING_DB_ENDPOINT_CATEGORY="db.ep.category";
|
||||
public static final String DB_ENDPOINT_NAME="db.ep.name";
|
||||
public static final String DB_ENDPOINT_CATEGORY="db.ep.category";
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -59,16 +59,17 @@ public class ConnectionManagerImpl implements ConnectionManager {
|
|||
@Inject
|
||||
private LocalConfiguration configuration;
|
||||
|
||||
private synchronized DatabaseConnectionDescriptor getDB() throws InternalError {
|
||||
private synchronized DatabaseConnectionDescriptor getDB() throws InternalError {
|
||||
if(!databases.containsKey(infrastructure.getCurrentContext()))
|
||||
databases.put(infrastructure.getCurrentContext(), infrastructure.queryForDatabase(
|
||||
configuration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_CATEGORY),
|
||||
configuration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_NAME)));
|
||||
configuration.getProperty(LocalConfiguration.DB_ENDPOINT_CATEGORY),
|
||||
configuration.getProperty(LocalConfiguration.DB_ENDPOINT_NAME)));
|
||||
return databases.get(infrastructure.getCurrentContext());
|
||||
}
|
||||
|
||||
@Override
|
||||
public Connection getConnection() throws SQLException, InternalError {
|
||||
log.debug("Getting DB connection in {} ",infrastructure.getCurrentContext());
|
||||
DataSource ds=getDataSource();
|
||||
Connection conn=ds.getConnection();
|
||||
conn.setAutoCommit(false);
|
||||
|
|
@ -119,8 +120,8 @@ public class ConnectionManagerImpl implements ConnectionManager {
|
|||
Connection conn=null;
|
||||
try{
|
||||
conn=dataSource.getConnection();
|
||||
conn.createStatement().executeUpdate(Queries.getInitDB(db.getFlavor()));
|
||||
conn.commit();
|
||||
conn.setAutoCommit(true);
|
||||
conn.createStatement().executeUpdate(Queries.getInitDB(db.getFlavor()));
|
||||
}catch(SQLException e) {
|
||||
throw new InternalError("Unable to Init database "+db,e);
|
||||
}finally {
|
||||
|
|
|
|||
|
|
@ -106,7 +106,7 @@ public class PersistenceManagerImpl implements PersistenceManager {
|
|||
throws PersistenceError, InvalidRequest {
|
||||
Connection conn=null;
|
||||
try {
|
||||
log.debug("Looking for execution according to filter {} ",filter);
|
||||
log.debug("Looking for execution according to filter {}",filter);
|
||||
conn=connections.getConnection();
|
||||
ArrayList<ExecutionDescriptor> toReturn=new ArrayList<>();
|
||||
PreparedStatement psGet=Queries.GET_ALL.get(conn, filter);
|
||||
|
|
|
|||
|
|
@ -2,5 +2,5 @@ db.pools.max_idle=5
|
|||
db.pools.max_total=50
|
||||
db.pools.min_total=3
|
||||
|
||||
mapping-db.ep.name=Feeder_DB
|
||||
mapping-db.ep.category=Database
|
||||
db.ep.name=Feeder_DB
|
||||
db.ep.category=Database
|
||||
Loading…
Reference in New Issue