Repository: airavata Updated Branches: refs/heads/airavata-0.15-release-branch dce8796bf -> 2b1e125c8
no access denial errors; output data staging is using task details Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/2b1e125c Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/2b1e125c Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/2b1e125c Branch: refs/heads/airavata-0.15-release-branch Commit: 2b1e125c8885a1b71267e1cf6e9c5e0a42683a2b Parents: dce8796 Author: msmemon <[email protected]> Authored: Thu Jun 11 16:55:10 2015 +0200 Committer: msmemon <[email protected]> Committed: Thu Jun 11 16:55:10 2015 +0200 ---------------------------------------------------------------------- .../gfac/bes/provider/impl/BESProvider.java | 7 +- .../bes/security/UNICORESecurityContext.java | 5 +- .../gfac/bes/utils/DataTransferrer.java | 68 ++++++++++++++------ .../gfac/bes/utils/UASDataStagingProcessor.java | 12 +++- .../airavata/gfac/bes/utils/URIUtils.java | 3 +- 5 files changed, 67 insertions(+), 28 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/2b1e125c/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java index 299e6ef..40baa22 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java @@ -132,14 +132,17 @@ public class BESProvider extends AbstractProvider implements GFacProvider, } CreateActivityDocument cad = CreateActivityDocument.Factory.newInstance(); JobDefinitionDocument jobDefDoc = JobDefinitionDocument.Factory.newInstance(); - + // create storage StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null); sc = storageCreator.createStorage(); JobDefinitionType jobDefinition = JSDLGenerator.buildJSDLInstance(jobExecutionContext, sc.getUrl()).getJobDefinition(); cad.addNewCreateActivity().addNewActivityDocument().setJobDefinition(jobDefinition); - log.info("JSDL" + jobDefDoc.toString()); + + log.debug("Submitted JSDL: " + jobDefDoc.getJobDefinition().getJobDescription()); + + // upload files if any DataTransferrer dt = new DataTransferrer(jobExecutionContext, sc); http://git-wip-us.apache.org/repos/asf/airavata/blob/2b1e125c/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java index f2ec94e..e82beeb 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java @@ -89,14 +89,13 @@ public class UNICORESecurityContext extends X509SecurityContext { boolean genCert = userData.isGenerateCert(); if(genCert) { String userDN = userData.getUserDN(); - if (userDN == null && "".equals(userDN)){ - log.warn("Cannot generate cert, falling back to container configured MyProxy credentials"); + if (userDN == null || "".equals(userDN)){ + log.warn("Cannot generate cert, falling back to GFAC configured MyProxy credentials"); return getDefaultConfiguration(enableMessageLogging); } else { log.info("Generating X.509 certificate for: "+userDN); try { - String caCertPath = ServerSettings.getSetting(BESConstants.PROP_CA_CERT_PATH, ""); String caKeyPath = ServerSettings.getSetting(BESConstants.PROP_CA_KEY_PATH, ""); String caKeyPass = ServerSettings.getSetting(BESConstants.PROP_CA_KEY_PASS, ""); http://git-wip-us.apache.org/repos/asf/airavata/blob/2b1e125c/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java index d70e4b1..d94cb20 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java @@ -95,26 +95,56 @@ public class DataTransferrer { file.mkdirs(); } - Map<String, Object> output = jobContext.getOutMessageContext().getParameters(); - Set<String> keys = output.keySet(); - - for (String outPrm : keys) { - OutputDataObjectType actualParameter = (OutputDataObjectType) output.get(outPrm); - if (DataType.STDERR == actualParameter.getType()) continue; - if (DataType.STDOUT == actualParameter.getType()) continue; - - String value = actualParameter.getValue(); - FileDownloader fileDownloader = new FileDownloader(value,downloadLocation, Mode.overwrite); - try { - fileDownloader.perform(storageClient); - String outputPath = downloadLocation + File.separator + value.substring(value.lastIndexOf('/')+1); - actualParameter.setValue(outputPath); - actualParameter.setType(DataType.URI); - jobContext.addOutputFile(outputPath); - } catch (Exception e) { - throw new GFacProviderException(e.getLocalizedMessage(),e); +// Map<String, Object> output = jobContext.getOutMessageContext().getParameters(); +// Set<String> keys = output.keySet(); +// +// for (String outPrm : keys) { +// OutputDataObjectType actualParameter = (OutputDataObjectType) output.get(outPrm); +// if (DataType.STDERR == actualParameter.getType() || +// DataType.STDOUT == actualParameter.getType() || +// DataType.URI == actualParameter.getType()) { +// continue; +// } +// +// String value = actualParameter.getValue(); +// FileDownloader fileDownloader = new FileDownloader(value,downloadLocation, Mode.overwrite); +// try { +// fileDownloader.perform(storageClient); +// String outputPath = downloadLocation + File.separator + value.substring(value.lastIndexOf('/')+1); +// actualParameter.setValue(outputPath); +// actualParameter.setType(DataType.URI); +// jobContext.addOutputFile(outputPath); +// } catch (Exception e) { +// throw new GFacProviderException(e.getLocalizedMessage(),e); +// } +// } + + List<OutputDataObjectType> applicationOutputs = jobContext.getTaskData().getApplicationOutputs(); + if (applicationOutputs != null && !applicationOutputs.isEmpty()){ + for (OutputDataObjectType output : applicationOutputs){ + if("".equals(output.getValue()) || output.getValue() == null) { + continue; } - } + + if(output.getType().equals(DataType.STRING)) { + String value = output.getValue(); + FileDownloader fileDownloader = new FileDownloader(value,downloadLocation, Mode.overwrite); + try { + fileDownloader.perform(storageClient); + String outputPath = downloadLocation + File.separator + value; + jobContext.addOutputFile(outputPath); + } catch (Exception e) { + throw new GFacProviderException(e.getLocalizedMessage(),e); + } + } + } + } + + + + + + downloadStdOuts(); } http://git-wip-us.apache.org/repos/asf/airavata/blob/2b1e125c/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java index 09c6e11..5de9593 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java @@ -113,9 +113,13 @@ public class UASDataStagingProcessor { List<OutputDataObjectType> applicationOutputs = context.getTaskData().getApplicationOutputs(); if (applicationOutputs != null && !applicationOutputs.isEmpty()){ for (OutputDataObjectType output : applicationOutputs){ - if(output.getType().equals(DataType.URI) && !output.getValue().startsWith("file:")) { + if("".equals(output.getValue()) || output.getValue() == null) { + continue; + } + + if(output.getType().equals(DataType.URI)) { createOutURIElement(value, output.getValue()); - } + } } } return value; @@ -128,8 +132,10 @@ public class UASDataStagingProcessor { if (applicationInputs != null && !applicationInputs.isEmpty()){ for (InputDataObjectType input : applicationInputs){ + if("".equals(input.getValue()) || input.getValue() == null) { + continue; + } if(input.getType().equals(DataType.URI)){ - //TODO: set the in sms url createInURISMSElement(value, smsUrl, input.getValue()); } else if(input.getType().equals(DataType.STRING)){ http://git-wip-us.apache.org/repos/asf/airavata/blob/2b1e125c/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/URIUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/URIUtils.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/URIUtils.java index fbc91da..b385368 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/URIUtils.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/URIUtils.java @@ -106,7 +106,8 @@ public class URIUtils { fragment = URIUtil.encode(fragment, URI.allowed_fragment); return beforeFragment+fragment; } - public static java.net.URI createGsiftpURI(String host, String localPath) throws URISyntaxException { + + public static java.net.URI createGsiftpURI(String host, String localPath) throws URISyntaxException { StringBuffer buf = new StringBuffer(); if (!host.startsWith("gsiftp://";)) buf.append("gsiftp://";);
