Some changes to be used in EXI

ispyb-ejb/pom.xml

@@ -493,7 +493,7 @@
 
 			<ispyb.root.folder>/data/ispyb/pyarch</ispyb.root.folder>
 			<ispyb.uploaded.root.folder>/data/ispyb/pyarch/pdb/</ispyb.uploaded.root.folder>
-			<ispyb.upload.folder.pdf>/mxn/groups/ispybstorage/pdf/</ispyb.upload.folder.pdf>
+			<ispyb.upload.folder.pdf>/data/staff/ispybstorage/pdf/</ispyb.upload.folder.pdf>
 
 			<ispyb.server.name.prod>w-v-ispyb-0.maxiv.lu.se</ispyb.server.name.prod>
 			<ispyb.server.name.prod.alias>ispyb.maxiv.lu.se</ispyb.server.name.prod.alias>

ispyb-ejb/src/main/java/ispyb/common/util/PathUtils.java

@@ -67,7 +67,7 @@ public static String getFullDNAPath(DataCollection3VO dataCollectionVO) throws E
 
 		String imageDir = getImageDirPath(dataCollectionVO);
 		if (Constants.SITE_IS_MAXIV()) {
-			imageDir = imageDir.replace("/data/visitors/","/mxn/groups/ispybstorage/visitors/");
+			imageDir = imageDir.replace("/data/visitors/","/data/staff/ispybstorage/visitors/");
 		}
 		String fullDNAPath = imageDir + Constants.IMG_DNA_URL_SUFIX;
 		if (isWindows) {

ispyb-ejb/src/main/java/ispyb/common/util/export/ExiCsvExporter.java

@@ -0,0 +1,317 @@
+/*******************************************************************************
+ * This file is part of ISPyB.
+ * 
+ * ISPyB is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * ISPyB is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with ISPyB.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * Contributors : S. Delageniere, R. Leal, L. Launer, K. Levik, S. Veyrier, P. Brenchereau, M. Bodin, A. De Maria Antolinos
+ ******************************************************************************/
+
+package ispyb.common.util.export;
+
+import ispyb.common.util.Constants;
+import ispyb.server.common.services.sessions.Session3Service;
+import ispyb.server.common.util.ejb.Ejb3ServiceLocator;
+import ispyb.server.mx.services.autoproc.SpaceGroup3Service;
+import ispyb.server.mx.services.collections.DataCollection3Service;
+import ispyb.server.mx.services.sample.BLSample3Service;
+import ispyb.server.mx.vos.autoproc.SpaceGroup3VO;
+import ispyb.server.mx.vos.collections.DataCollection3VO;
+import ispyb.server.mx.vos.collections.DataCollectionGroup3VO;
+import ispyb.server.mx.vos.collections.Session3VO;
+import org.apache.log4j.Logger;
+
+import java.io.ByteArrayOutputStream;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.text.SimpleDateFormat;
+import java.util.List;
+import java.util.*;
+
+/**
+ * allows creation of CSV report - general report for EXI, available in the
+ * 
+ * @author Solange Delageniere
+ * 
+ */
+public class ExiCsvExporter {
+
+	private final static Logger LOG = Logger.getLogger(ExiCsvExporter.class);
+
+	//proposalId
+	int proposalId;
+
+	// proposal code
+	String proposalCode;
+
+	// session info
+	Integer sessionId;
+
+	private Session3VO slv;
+
+	List<DataCollection3VO> dataCollections = new ArrayList<>();
+
+	DecimalFormat df1;
+
+	DecimalFormat df2;
+
+	DecimalFormat df3;
+
+	DecimalFormat df4;
+
+	private final Ejb3ServiceLocator ejb3ServiceLocator = Ejb3ServiceLocator.getInstance();
+
+	private Session3Service sessionService;
+
+	private DataCollection3Service dataCollectionService;
+
+	private BLSample3Service sampleService;
+
+	private DataCollection3Service dcService;
+
+	private SpaceGroup3Service spacegroupService;
+
+
+	public ExiCsvExporter(int proposalId, String proposalCode, Integer sessionId,
+						  List<DataCollection3VO> dataCollections) throws Exception {
+		this.proposalCode = proposalCode;
+		this.sessionId = sessionId;
+		this.dataCollections = dataCollections;
+		init();
+	}
+
+	private void init() throws Exception {
+		df1 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df1.applyPattern("#####0.0");
+		df2 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df2.applyPattern("#####0.00");
+		df3 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df3.applyPattern("#####0.000");
+		df4 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df4.applyPattern("#####0.0000");
+
+		sessionService = (Session3Service) ejb3ServiceLocator
+				.getLocalService(Session3Service.class);
+		dcService = (DataCollection3Service) ejb3ServiceLocator
+				.getLocalService(DataCollection3Service.class);
+		spacegroupService = (SpaceGroup3Service) ejb3ServiceLocator
+				.getLocalService(SpaceGroup3Service.class);
+
+		dataCollectionService = (DataCollection3Service) ejb3ServiceLocator.getLocalService(DataCollection3Service.class);
+		sampleService = (BLSample3Service) ejb3ServiceLocator.getLocalService(BLSample3Service.class);
+
+		slv = sessionService.findByPk(sessionId, false/*withDataCollectionGroup*/, false/*withEnergyScan*/, false/*withXFESpectrum*/);
+	}
+
+	/**
+	 * export datacollection report
+	 *
+	 * @return
+	 * @throws Exception
+	 */
+	public ByteArrayOutputStream exportDataCollectionReport() throws Exception {
+
+		this.init();
+		String doc = "";
+		// create simple doc and write to a ByteArrayOutputStream
+		ByteArrayOutputStream baos = new ByteArrayOutputStream();
+		final String CSV_DELIMITER = ",";
+
+		if (this.dataCollections.isEmpty()) {
+			doc += "There is no data collection in this report";
+			baos.write(doc.getBytes());
+			return baos;
+		}
+
+
+		// Header
+		doc += "Image prefix,";
+		doc += "Beamline,";
+		doc += "Run no,";
+		doc += "Start Time,";
+		doc += "Sample Name,";
+		doc += "Protein Acronym,";
+		doc += "# images,";
+		doc += "Wavelength (angstrom),";
+		doc += "Distance (mm),";
+		doc += "Exp. Time (sec),";
+		doc += "Phi start (deg),";
+		doc += "Phi range (deg),";
+		doc += "Xbeam (mm),";
+		doc += "Ybeam (mm),";
+		doc += "Detector resol. (angstrom),";
+		if (this.proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX))
+			doc += "Crystal class,";
+		doc += "Comments";
+		doc += "\n";
+
+		// Data
+		DecimalFormat df2 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df2.applyPattern("#####0.00");
+		DecimalFormat df3 = (DecimalFormat) NumberFormat.getInstance(Locale.US);
+		df3.applyPattern("#####0.000");
+
+
+		Iterator<DataCollection3VO> it = this.dataCollections.iterator();
+		int i = 1;
+		while (it.hasNext()) {
+
+			DataCollection3VO col = (DataCollection3VO) it.next();
+			DataCollectionGroup3VO dcGroup = col.getDataCollectionGroupVO();
+			Session3VO slv = sessionService.findByPk(dcGroup.getSessionVOId(), false, false, false);
+			col = dataCollectionService.loadEager(col);
+			if(dcGroup.getBlSampleVO() != null){
+				dcGroup.setBlSampleVO(sampleService.loadEager(dcGroup.getBlSampleVO()));
+			}
+
+			// ImagePrefix
+			if (col.getImagePrefix() != null)
+				doc += col.getImagePrefix() + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Beamline
+			if (slv.getBeamlineName() != null)
+				doc += slv.getBeamlineName() + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Run number
+			if (col.getDataCollectionNumber() != null)
+				doc += col.getDataCollectionNumber().toString() + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Start Time
+			if (col.getStartTime() != null) {
+				SimpleDateFormat simple1 = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
+				String date = simple1.format(col.getStartTime());
+				doc += date + CSV_DELIMITER;
+			} else
+				doc += CSV_DELIMITER;
+
+			// Sample name
+			String sampleName = null;
+			if (dcGroup.getBlSampleVO() != null)
+				//sampleName = samples.findByPrimaryKey(col.getBlSampleVO()).getName();
+				sampleName = dcGroup.getBlSampleVO().getName();
+			if (sampleName != null)
+				doc += sampleName + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Protein acronym
+			String proteinAcronym = null;
+			if (dcGroup.getBlSampleVO() != null && dcGroup.getBlSampleVO().getCrystalVO() != null && dcGroup.getBlSampleVO().getCrystalVO().getProteinVO() != null)
+				//proteinAcronym = samples.findByPrimaryKey(col.getBlSampleId()).getAcronym();
+				proteinAcronym = dcGroup.getBlSampleVO().getCrystalVO().getProteinVO().getAcronym();
+			if (proteinAcronym != null)
+				doc += proteinAcronym + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Number of images
+			if (col.getNumberOfImages() != null)
+				doc += col.getNumberOfImages().toString() + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Wavelength
+			if (col.getWavelength() != null)
+				doc += df3.format(col.getWavelength()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Detector distance
+			if (col.getDetectorDistance() != null)
+				doc += df2.format(col.getDetectorDistance()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Exposure time
+			if (col.getExposureTime() != null)
+				doc += df3.format(col.getExposureTime()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Axis start
+			if (col.getAxisStart() != null)
+				doc += df2.format(col.getAxisStart()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Axis range
+			if (col.getAxisRange() != null)
+				doc += df2.format(col.getAxisRange()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Xbeam
+			if (col.getXbeam() != null)
+				doc += df2.format(col.getXbeam()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Ybeam
+			if (col.getYbeam() != null)
+				doc += df2.format(col.getYbeam()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// Resolution
+			if (col.getResolution() != null)
+				doc += df2.format(col.getResolution()) + CSV_DELIMITER;
+			else
+				doc += CSV_DELIMITER;
+
+			// SrystalClass (only for IFX proposal in case of MXPress experiment)
+			if (this.proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX)) {
+				if (dcGroup.getCrystalClass() != null && dcGroup.getCrystalClass() != "")
+					doc += dcGroup.getCrystalClass() + CSV_DELIMITER;
+				else
+					doc += CSV_DELIMITER;
+			}
+
+			// Comments
+			if (col.getComments() != null && col.getComments() != "") {
+				doc += "\"" + col.getComments().replaceAll("\"", "\"\"") + "\"";
+			} else
+				doc += "";
+
+			i++;
+
+			doc += "\n";
+		}
+
+		baos.write(doc.getBytes());
+
+		return baos;
+
+	}
+
+
+
+	private String getDecimalFormat(String value, DecimalFormat df) {
+		String ret = "";
+		if (value == null || value.isEmpty()) 
+			return ret;
+		try {
+			Double paramValue = new Double(value);
+			ret = df.format(paramValue);
+		} catch (NumberFormatException e) {
+			return "";
+		}
+
+		return ret;
+	}
+}

ispyb-ejb/src/main/java/ispyb/server/mx/services/autoproc/AutoProcProgramAttachment3Service.java

@@ -85,4 +85,10 @@ public List<AutoProcProgramAttachment3VO> findAll()
 	 */
 	public List<AutoProcProgramAttachment3VO> findNoanomCorrect(final Integer autoProcProgramId) throws Exception;
 
+	/**
+	 * find aimless files attachments
+	 * @return
+	 * @throws Exception
+	 */
+	public List<AutoProcProgramAttachment3VO> findAimless(final Integer autoProcProgramId) throws Exception;
 }

ispyb-ejb/src/main/java/ispyb/server/mx/services/autoproc/AutoProcProgramAttachment3ServiceBean.java

@@ -70,6 +70,11 @@ private static final String FIND_ALL() {
 			"WHERE  autoProcProgramId = :autoProcProgramId AND " +
 			"fileName like '%_noanom_aimless%' ";
 
+	private static final String FIND_AUTOPROC_AIMLESS = "SELECT * " +
+			"FROM AutoProcProgramAttachment  " +
+			"WHERE  autoProcProgramId = :autoProcProgramId AND " +
+			"fileName like '%_aimless%' ";
+
 	@PersistenceContext(unitName = "ispyb_db")
 	private EntityManager entityManager;
 
@@ -208,6 +213,25 @@ public List<AutoProcProgramAttachment3VO> findNoanomCorrect(final Integer autoPr
 		}
 	}
 
+	/**
+	 * find anom correct files attachments
+	 * @return
+	 * @throws Exception
+	 */
+	@SuppressWarnings("unchecked")
+	public List<AutoProcProgramAttachment3VO> findAimless(final Integer autoProcProgramId) throws Exception {
+
+		String query = FIND_AUTOPROC_AIMLESS ;
+		try{
+
+			List<AutoProcProgramAttachment3VO> listVOs = this.entityManager.createNativeQuery(query, "autoProcProgramAttachmentNativeQuery")
+					.setParameter("autoProcProgramId", autoProcProgramId).getResultList();
+			return listVOs;
+		}catch(Exception e){
+			return null;
+		}
+	}
+
 	/* Private methods ------------------------------------------------------ */
 
 	/**