TargetedMSModule.java

/*
 * Copyright (c) 2012-2019 LabKey Corporation
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.labkey.targetedms;

import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.admin.FolderSerializationRegistry;
import org.labkey.api.assay.sample.SampleAssayResultsConfig;
import org.labkey.api.assay.sample.SampleAssayResultsService;
import org.labkey.api.audit.AuditLogService;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.PropertySchema;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.data.UpgradeCode;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.files.DirectoryPattern;
import org.labkey.api.files.FileContentService;
import org.labkey.api.module.FolderTypeManager;
import org.labkey.api.module.Module;
import org.labkey.api.module.ModuleContext;
import org.labkey.api.module.ModuleHtmlView;
import org.labkey.api.module.ModuleProperty;
import org.labkey.api.module.SpringModule;
import org.labkey.api.pipeline.PipelineService;
import org.labkey.api.protein.ProteinService;
import org.labkey.api.protein.ProteomicsModule;
import org.labkey.api.protein.search.MSSearchWebpart;
import org.labkey.api.protein.search.ProteinSearchForm;
import org.labkey.api.query.QueryView;
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.ApplicationAdminPermission;
import org.labkey.api.settings.AdminConsole;
import org.labkey.api.settings.OptionalFeatureFlag;
import org.labkey.api.settings.OptionalFeatureService;
import org.labkey.api.targetedms.TargetedMSService;
import org.labkey.api.usageMetrics.UsageMetricsService;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.BaseWebPartFactory;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
import org.labkey.api.view.Portal;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartFactory;
import org.labkey.api.view.WebPartView;
import org.labkey.api.view.template.ClientDependency;
import org.labkey.panoramapremium.PanoramaPremiumController;
import org.labkey.panoramapremium.QCNotificationSender;
import org.labkey.panoramapremium.View.QCSummaryMenuCustomizer;
import org.labkey.targetedms.chart.ComparisonCategory;
import org.labkey.targetedms.chart.ReplicateLabelMinimizer;
import org.labkey.targetedms.datasource.MsDataSourceUtil;
import org.labkey.targetedms.folderImport.QCFolderImporter;
import org.labkey.targetedms.folderImport.QCFolderWriterFactory;
import org.labkey.targetedms.parser.Protein;
import org.labkey.targetedms.parser.SampleFile;
import org.labkey.targetedms.parser.SpectrumFilter;
import org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser;
import org.labkey.targetedms.passport.PassportController;
import org.labkey.targetedms.pipeline.TargetedMSPipelineProvider;
import org.labkey.targetedms.query.CrossLinkedPeptideDisplayColumn;
import org.labkey.targetedms.query.PrecursorManager;
import org.labkey.targetedms.query.SkylineListSchema;
import org.labkey.targetedms.search.ModificationSearchWebPart;
import org.labkey.targetedms.search.ProteinSearchWebPart;
import org.labkey.targetedms.view.CalibrationCurveView;
import org.labkey.targetedms.view.CrossLinkedPeptideInfo;
import org.labkey.targetedms.view.LibraryQueryViewWebPart;
import org.labkey.targetedms.view.ReplicateSummaryWebPart;
import org.labkey.targetedms.view.TargetedMSRunsWebPartView;
import org.labkey.targetedms.view.TransitionPeptideSearchViewProvider;
import org.labkey.targetedms.view.TransitionProteinSearchViewProvider;
import org.labkey.targetedms.view.passport.ProteinListView;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;

import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;

public class TargetedMSModule extends SpringModule implements ProteomicsModule
{
    // Protocol prefix for importing .sky documents from Skyline
    public static final String IMPORT_SKYDOC_PROTOCOL_OBJECT_PREFIX = "TargetedMS.ImportSky";
    // Protocol prefix for importing .zip archives from Skyline
    public static final String IMPORT_SKYZIP_PROTOCOL_OBJECT_PREFIX = "TargetedMS.ImportSkyZip";

    public static final String TARGETED_MS_SETUP = "Targeted MS Setup";
    public static final String TARGETED_MS_CHROMATOGRAM_LIBRARY_DOWNLOAD = "Chromatogram Library Download";
    public static final String TARGETED_MS_PRECURSOR_VIEW = "Targeted MS Precursor View";
    public static final String TARGETED_MS_PEPTIDE_VIEW = "Targeted MS Peptide View";
    public static final String TARGETED_MS_MOLECULE_PRECURSOR_VIEW = "Targeted MS Molecule Precursor View";
    public static final String TARGETED_MS_MOLECULE_VIEW = "Targeted MS Molecule View";
    public static final String TARGETED_MS_PEPTIDE_GROUP_VIEW = "Targeted MS Protein View";
    public static final String TARGETED_MS_RUNS_WEBPART_NAME = "Targeted MS Runs";
    public static final String TARGETED_MS_PROTEIN_SEARCH = "Targeted MS Protein Search";
    public static final String TARGETED_MS_PEPTIDE_SEARCH = "Targeted MS Peptide Search";
    public static final String TARGETED_MS_REPLICATE_SUMMARY = "Targeted MS Replicate Summary";
    public static final String TARGETED_MS_QC_PLOTS = "Targeted MS QC Plots";
    public static final String TARGETED_MS_PARETO_PLOT = "Targeted MS Pareto Plot";
    public static final String TARGETED_MS_CALIBRATION_CURVE = "Targeted MS Calibration Curve";
    public static final String TARGETED_MS_FIGURES_OF_MERIT = "Targeted MS Figures of Merit";
    public static final String TARGETED_MS_PEPTIDE_MOLECULE_SUMMARY = "Peptide/Molecule Summary";
    public static final String TARGETED_MS_PROJECT_WEBPART = "Targeted MS Project";

    public static final String PEPTIDE_TAB_NAME = "Peptides";
    public static final String PROTEIN_TAB_NAME = "Proteins";
    public static final String MOLECULE_TAB_NAME = "Molecules";

    public static final String USE_TEMP_DIR_FOR_SKYD_IMPORT = "UseTempDirForSkydImport";

    public static final String[] EXPERIMENT_FOLDER_WEB_PARTS = new String[] {MSSearchWebpart.NAME,
                                                                           TARGETED_MS_RUNS_WEBPART_NAME};

    public static final String[] LIBRARY_FOLDER_WEB_PARTS = new String[] {TARGETED_MS_CHROMATOGRAM_LIBRARY_DOWNLOAD,
                                                                          MSSearchWebpart.NAME,
                                                                          TARGETED_MS_RUNS_WEBPART_NAME};

    public static final String[] PEPTIDE_TAB_WEB_PARTS = new String[] {
            TARGETED_MS_PEPTIDE_VIEW,
            TARGETED_MS_PRECURSOR_VIEW
    };

    public static final String[] MOLECULE_TAB_WEB_PARTS = new String[] {
            TARGETED_MS_MOLECULE_VIEW,
            TARGETED_MS_MOLECULE_PRECURSOR_VIEW
    };

    public static final String[] PROTEIN_TAB_WEB_PARTS = new String[] {
            TARGETED_MS_PEPTIDE_GROUP_VIEW
    };

    public static final String[] QC_FOLDER_WEB_PARTS = new String[] {TARGETED_MS_REPLICATE_SUMMARY, TARGETED_MS_QC_PLOTS};

    public final ModuleProperty FOLDER_TYPE_PROPERTY;
    public final ModuleProperty SKYLINE_AUDIT_LEVEL_PROPERTY;
    public final ModuleProperty MAX_TRANSITION_CHROM_INFOS_PROPERTY;
    public static final int DEFAULT_MAX_TRANSITION_CHROM_INFOS = 100_000;
    public final ModuleProperty MAX_PRECURSORS_PROPERTY;
    public static final int DEFAULT_MAX_PRECURSORS = 1_000;
    public final ModuleProperty AUTO_QC_PING_TIMEOUT_PROPERTY;

    public TargetedMSModule()
    {
        FOLDER_TYPE_PROPERTY = new ModuleProperty(this, FOLDER_TYPE_PROP_NAME);
        // Set up the TargetedMS Folder Type property
        FOLDER_TYPE_PROPERTY.setDefaultValue(TargetedMSService.FolderType.Undefined.toString());
        FOLDER_TYPE_PROPERTY.setCanSetPerContainer(true);
        FOLDER_TYPE_PROPERTY.setShowDescriptionInline(true);
        addModuleProperty(FOLDER_TYPE_PROPERTY);

        List<ModuleProperty.Option> auditOptions = List.of(
            new ModuleProperty.Option("0 - No Verification", "0"),
            new ModuleProperty.Option("1 - Hash Verification", "1"),
            new ModuleProperty.Option("2 - RSA Verification", "2")
        );
        // Set up the properties for controlling how chromatograms are managed in DB vs files
        SKYLINE_AUDIT_LEVEL_PROPERTY = new ModuleProperty(this, "Audit log integrity level for the uploaded Skyline documents");
        SKYLINE_AUDIT_LEVEL_PROPERTY.setInputType(ModuleProperty.InputType.combo);
        SKYLINE_AUDIT_LEVEL_PROPERTY.setOptions(auditOptions);
        SKYLINE_AUDIT_LEVEL_PROPERTY.setDefaultValue("0");
        SKYLINE_AUDIT_LEVEL_PROPERTY.setCanSetPerContainer(true);
        SKYLINE_AUDIT_LEVEL_PROPERTY.setDescription("""
                Defines requirements for the integrity of the audit log uploaded together with a Skyline document.\s
                0 means that no audit log is required. If the log file is present in the uploaded file it will be parsed and loaded as is.
                 \
                1 means that audit log is required and its integrity will be verified using MD5 hash-based algorithm. If log integrity verification fails the document upload will be cancelled.\s
                2 means that audit log is required and its integrity will be verified using RSA-encryption algorithm. If log integrity verification fails the document upload will be cancelled.""");
        SKYLINE_AUDIT_LEVEL_PROPERTY.setShowDescriptionInline(true);
        addModuleProperty(SKYLINE_AUDIT_LEVEL_PROPERTY);
        //------------------------rr

        // setup the replicate summary webpart AutoQCPing timeout
        AUTO_QC_PING_TIMEOUT_PROPERTY = new ModuleProperty(this, "TargetedMS AutoQCPing Timeout");
        AUTO_QC_PING_TIMEOUT_PROPERTY.setDescription("The number of minutes before the most recent AutoQCPing indicator is considered stale.");
        AUTO_QC_PING_TIMEOUT_PROPERTY.setDefaultValue("15");
        AUTO_QC_PING_TIMEOUT_PROPERTY.setShowDescriptionInline(true);
        AUTO_QC_PING_TIMEOUT_PROPERTY.setCanSetPerContainer(true);
        addModuleProperty(AUTO_QC_PING_TIMEOUT_PROPERTY);

        MAX_TRANSITION_CHROM_INFOS_PROPERTY = new ModuleProperty(this, "TransitionChromInfo storage limit");
        MAX_TRANSITION_CHROM_INFOS_PROPERTY.setInputType(ModuleProperty.InputType.text);
        MAX_TRANSITION_CHROM_INFOS_PROPERTY.setDefaultValue(Integer.toString(DEFAULT_MAX_TRANSITION_CHROM_INFOS));
        // Issue 47774: Remove TargetedMS module properties related to reading chromatogram data.
        // Property can be set only at the site level.
        MAX_TRANSITION_CHROM_INFOS_PROPERTY.setCanSetPerContainer(false);
        MAX_TRANSITION_CHROM_INFOS_PROPERTY.setDescription("Large DIA Skyline documents may have many transition/replicate chromatograms which may not be very useful to store in the database. Panorama can skip importing them to save storage space and import time, if the number of separately configured precursors is also exceeded");
        MAX_TRANSITION_CHROM_INFOS_PROPERTY.setShowDescriptionInline(true);
        addModuleProperty(MAX_TRANSITION_CHROM_INFOS_PROPERTY);

        MAX_PRECURSORS_PROPERTY = new ModuleProperty(this, "Precursor storage limit");
        MAX_PRECURSORS_PROPERTY.setInputType(ModuleProperty.InputType.text);
        MAX_PRECURSORS_PROPERTY.setDefaultValue(Integer.toString(DEFAULT_MAX_PRECURSORS));
        // Issue 47774: Remove TargetedMS module properties related to reading chromatogram data.
        // Property can be set only at the site level.
        MAX_PRECURSORS_PROPERTY.setCanSetPerContainer(false);
        MAX_PRECURSORS_PROPERTY.setDescription("If a document has more than a specified number of precursors AND more than the separate transition/replicate chromatogram limit, Panorama will skip storing them in the database to save space and import time");
        MAX_PRECURSORS_PROPERTY.setShowDescriptionInline(true);
        addModuleProperty(MAX_PRECURSORS_PROPERTY);
    }

    @Override
    public String getName()
    {
        return MODULE_NAME;
    }

    @Override
    public Double getSchemaVersion()
    {
        return 26.004;
    }

    @Override
    public boolean hasScripts()
    {
        return true;
    }

    @Override
    public boolean isAvailable(Container container)
    {
        return container.isRoot() || container.getActiveModules().contains(this);
    }

    @NotNull
    @Override
    protected Collection<WebPartFactory> createWebPartFactories()
    {
        return List.of(
            new BaseWebPartFactory(TARGETED_MS_SETUP)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    JspView<Void> view = new JspView<>("/org/labkey/targetedms/view/folderSetup.jsp");
                    view.setTitle(TargetedMSController.CONFIGURE_TARGETED_MS_FOLDER);
                    return view;
                }

                @Override
                public String getDisplayName(Container container, String location)
                {
                    return "Panorama Setup";
                }
            },

            new BaseWebPartFactory(TARGETED_MS_CHROMATOGRAM_LIBRARY_DOWNLOAD)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    JspView<Void> view = new JspView<>("/org/labkey/targetedms/view/chromatogramLibraryDownload.jsp");
                    view.setTitle(TARGETED_MS_CHROMATOGRAM_LIBRARY_DOWNLOAD);
                    return view;
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PRECURSOR_VIEW)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return LibraryQueryViewWebPart.forTable(TargetedMSSchema.TABLE_PRECURSOR, portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_MOLECULE_PRECURSOR_VIEW)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return LibraryQueryViewWebPart.forTable(TargetedMSSchema.TABLE_MOLECULE_PRECURSOR, portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PEPTIDE_VIEW)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return LibraryQueryViewWebPart.forTable(TargetedMSSchema.TABLE_PEPTIDE, portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_MOLECULE_VIEW)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return LibraryQueryViewWebPart.forTable(TargetedMSSchema.TABLE_MOLECULE, portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PEPTIDE_GROUP_VIEW)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return LibraryQueryViewWebPart.forTable(TargetedMSSchema.TABLE_PEPTIDE_GROUP, portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_RUNS_WEBPART_NAME)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return new TargetedMSRunsWebPartView(portalCtx);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PROTEIN_SEARCH)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return new ProteinSearchWebPart(new ProteinSearchForm()
                    {
                        @Override
                        public int[] getSeqId()
                        {
                            return new int[0];
                        }

                        @Override
                        public boolean isExactMatch()
                        {
                            return true;
                        }
                    });
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PEPTIDE_SEARCH)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    JspView<Void> view = new JspView<>("/org/labkey/targetedms/search/peptideSearch.jsp");
                    view.setTitle("Peptide Search");
                    return view;
                }
            },

            new BaseWebPartFactory(ModificationSearchWebPart.NAME)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    TargetedMSController.ModificationSearchForm form = TargetedMSController.ModificationSearchForm.createDefault();
                    // When rendering a webpart with LABKEY.WebPart in a wiki page, config.partConfig can be used to set the
                    // configuration parameters for the webpart. Read the parameters from the ViewContext and initialize the
                    // form accordingly.
                    // For example, partConfig: {hideIncludeSubfolder: true, includeSubfolders: true} should hide the
                    // "includeSubfolders" checkbox and set the value of "includeSubfolders" to true.
                    String inclSubFolders = (String)portalCtx.get("includeSubfolders");
                    if(!StringUtils.isBlank(inclSubFolders))
                    {
                        form.setIncludeSubfolders(Boolean.valueOf(inclSubFolders));
                    }
                    String hideIncludeSubfolder = (String)portalCtx.get("hideIncludeSubfolder");
                    if(!StringUtils.isBlank(hideIncludeSubfolder))
                    {
                        form.setHideIncludeSubfolders(Boolean.valueOf(hideIncludeSubfolder));
                    }
                    return new ModificationSearchWebPart(form);
                }
            },

            new BaseWebPartFactory(TARGETED_MS_QC_PLOTS)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    JspView<Void> result = new JspView<>("/org/labkey/targetedms/view/qcTrendPlotReport.jsp");
                    result.addClientDependency(ClientDependency.fromPath("Ext4"));
                    result.setTitle("QC Plots");
                    result.setFrame(WebPartView.FrameType.PORTAL);
                    return result;
                }
            },

            new BaseWebPartFactory(TARGETED_MS_REPLICATE_SUMMARY)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return new ReplicateSummaryWebPart(portalCtx, 3);
                }

                @Override
                public List<String> getLegacyNames()
                {
                    return List.of("Targeted MS QC Summary");
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PARETO_PLOT)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    JspView<Void> result = new JspView<>("/org/labkey/targetedms/view/paretoPlot.jsp");
                    result.addClientDependency(ClientDependency.fromPath("Ext4"));
                    result.setTitle("Pareto Plots");
                    result.setFrame(WebPartView.FrameType.PORTAL);
                    return result;
                }
            },

            new BaseWebPartFactory("Passport")
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    QueryView v =  ProteinListView.createView(portalCtx);
                    v.setTitle("Passport");
                    v.setFrame(WebPartView.FrameType.PORTAL);
                    return v;
                }
            },

            new BaseWebPartFactory(TARGETED_MS_CALIBRATION_CURVE)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    String calCurveIdString = webPart.getPropertyMap().get("calibrationCurveId");
                    long calCurveId = 0;
                    if (calCurveIdString != null)
                    {
                        try
                        {
                            calCurveId = Long.parseLong(calCurveIdString);
                        }
                        catch (NumberFormatException ignored) {}
                    }
                    return new CalibrationCurveView(portalCtx.getUser(), portalCtx.getContainer(), calCurveId);
                }

                @Override
                public boolean isAvailable(Container c, String scope, String location)
                {
                    return false;
                }
            },

            new BaseWebPartFactory(TARGETED_MS_FIGURES_OF_MERIT)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    String idString = webPart.getPropertyMap().get("generalMoleculeId");
                    long id = 0;
                    if (idString != null)
                    {
                        try
                        {
                            id = Long.parseLong(idString);
                        }
                        catch (NumberFormatException ignored) {}
                    }
                    return TargetedMSController.getFiguresOfMeritView(portalCtx.getUser(), portalCtx.getContainer(), id, true);
                }

                @Override
                public boolean isAvailable(Container c, String scope, String location)
                {
                    return false;
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PEPTIDE_MOLECULE_SUMMARY)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return ModuleHtmlView.get(getModule(), "peptideSummary");
                }
            },

            new BaseWebPartFactory(TARGETED_MS_PROJECT_WEBPART)
            {
                @Override
                public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
                {
                    return ModuleHtmlView.get(getModule(), "msProject");
                }
            }
        );
    }

    @NotNull
    @Override
    public Collection<String> getSummary(Container c)
    {
        return Collections.emptyList();
    }

    @Override
    @NotNull
    public Set<String> getSchemaNames()
    {
        return PageFlowUtil.set(TargetedMSManager.get().getSchemaName());
    }

    @Override
    protected void init()
    {
        addController("targetedms", TargetedMSController.class);
        addController("passport", PassportController.class);
        addController(PanoramaPremiumController.NAME, PanoramaPremiumController.class);

        Portal.registerNavTreeCustomizer("Targeted MS QC Plots", viewContext -> {
            List<NavTree> result = new ArrayList<>();
            if (viewContext.hasPermission(AdminPermission.class))
            {
                NavTree save = new NavTree("Save as Default View");
                save.setScript("LABKEY.targetedms.PlotSettingsUtil.saveAsDefault()");
                result.add(save);
            }
            if (!viewContext.getUser().isGuest())
            {
                NavTree save = new NavTree("Revert to Default View");
                save.setScript("LABKEY.targetedms.PlotSettingsUtil.revertToDefault()");
                result.add(save);
            }

            return result;
        });

        TargetedMSSchema.register(this);
        SkylineListSchema.register(this);

        UsageMetricsService svc = UsageMetricsService.get();
        if (null != svc)
        {
            svc.registerUsageMetrics(MODULE_NAME, () ->
            {
                Map<String, Object> metric = new HashMap<>();
                DbSchema schema = TargetedMSManager.getSchema();
                metric.put("runCount", new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.Runs WHERE Deleted = ?", Boolean.FALSE).getObject(Long.class));
                metric.put("guideSetCount", new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.GuideSet").getObject(Long.class));
                metric.put("guideSetContainerCount", new SqlSelector(schema, "SELECT COUNT(DISTINCT Container) FROM TargetedMS.GuideSet").getObject(Long.class));

                SQLFragment folderTypeSQL = new SQLFragment("SELECT p.value, COUNT(*) AS FolderCount FROM ");
                folderTypeSQL.append(PropertySchema.getInstance().getTableInfoProperties(), "p");
                folderTypeSQL.append(" INNER JOIN ");
                folderTypeSQL.append(PropertySchema.getInstance().getTableInfoPropertySets(), "ps");
                folderTypeSQL.append(" ON p.\"set\" = ps.\"set\" WHERE ps.category = 'moduleProperties.TargetedMS' ");
                folderTypeSQL.append(" AND p.name = ? GROUP BY value");
                folderTypeSQL.add(FOLDER_TYPE_PROP_NAME);

                Map<String, Long> folderCounts = new HashMap<>();
                new SqlSelector(PropertySchema.getInstance().getSchema(), folderTypeSQL).forEach(rs ->
                        folderCounts.put(rs.getString("value"), rs.getLong("FolderCount")));

                metric.put("folderCounts", folderCounts);

                SQLFragment annotationFolderCountSQL = new SQLFragment("SELECT at.Name, COUNT(DISTINCT a.Container) AS FolderCount FROM ");
                annotationFolderCountSQL.append(TargetedMSManager.getTableInfoQCAnnotationType(), "at");
                annotationFolderCountSQL.append(" INNER JOIN " );
                annotationFolderCountSQL.append(TargetedMSManager.getTableInfoQCAnnotation(), "a");
                annotationFolderCountSQL.append(" ON at.Id = a.qcAnnotationTypeId GROUP BY at.Name");

                Map<String, Long> annotationFolderCounts = new HashMap<>();
                new SqlSelector(PropertySchema.getInstance().getSchema(), annotationFolderCountSQL).forEach(rs ->
                        annotationFolderCounts.put(rs.getString("Name"), rs.getLong("FolderCount")));

                metric.put("annotationFolderCounts", annotationFolderCounts);

                return metric;
            });
        }
        TargetedMSService.setInstance(new TargetedMSServiceImpl());

        SampleAssayResultsService sampleAssayService = SampleAssayResultsService.get();
        if (sampleAssayService != null)
            sampleAssayService.registerConfig(this, new SampleAssayResultsConfig(
                    "Skyline Documents", "targetedms", "SampleFileAssayResults", null,
                    "Name", "SampleName", ContainerFilter.Type.AllFolders
            ));

        FolderSerializationRegistry folderRegistry = FolderSerializationRegistry.get();
        if (null != folderRegistry)
        {
            folderRegistry.addFactories(new QCFolderWriterFactory(), new QCFolderImporter.Factory());
        }

        OptionalFeatureService.get().addFeatureFlag(
            new OptionalFeatureFlag(
                USE_TEMP_DIR_FOR_SKYD_IMPORT,
                "Stage SKYD files to a temporary local file for import purposes",
                "When using a non-local file system, the latency for random access requests can be significantly slower than first copying to local storage",
                false, false, OptionalFeatureService.FeatureType.Optional
            )
        );
    }

    @Override
    protected void startupAfterSpringConfig(ModuleContext moduleContext)
    {
        PipelineService service = PipelineService.get();
        service.registerPipelineProvider(new TargetedMSPipelineProvider(this));

        ExperimentService.get().registerExperimentDataHandler(new TargetedMSDataHandler());
        ExperimentService.get().registerExperimentDataHandler(new SkylineBinaryDataHandler());

        ExperimentService.get().registerExperimentRunTypeSource(container -> {
            if (container == null || container.getActiveModules().contains(TargetedMSModule.this))
            {
                return Collections.singleton(TargetedMSService.get().getExperimentRunType());
            }
            return Collections.emptySet();
        });

        //register the Targeted MS folder type
        FolderTypeManager.get().registerFolderType(this, new TargetedMSFolderType(this));

        ProteinService proteinService = ProteinService.get();
        proteinService.registerProteinSearchView(new TransitionProteinSearchViewProvider());
        proteinService.registerPeptideSearchView(new TransitionPeptideSearchViewProvider());
        proteinService.registerProteinSearchFormView(new ProteinSearchWebPart.ProteinSearchFormViewProvider());

        AuditLogService.get().registerAuditType(new TargetedMsRepresentativeStateAuditProvider());

        TargetedMSListener listener = new TargetedMSListener();
        ContainerManager.addContainerListener(listener);

        ActionURL chromatogramURL = new ActionURL(TargetedMSController.ChromatogramCrawlerAction.class, ContainerManager.getRoot());
        AdminConsole.addLink(AdminConsole.SettingsLinkType.Premium, "Targeted MS Chromatogram Crawler", chromatogramURL, ApplicationAdminPermission.class);

        FileContentService fcs = FileContentService.get();
        if(null != fcs)
        {
            DirectoryPattern extWatersRaw = new DirectoryPattern(this);
            extWatersRaw.setExt(".*\\.raw$");
            extWatersRaw.setFileExt("^_FUNC.*\\.DAT$");

            DirectoryPattern extAgilentRaw = new DirectoryPattern(this);
            extAgilentRaw.setExt(".*\\.d$");

            DirectoryPattern extAgilentRawSubDir = new DirectoryPattern(this);
            extAgilentRawSubDir.setExt("^AcqData$");
            extAgilentRaw.setSubDirectory(extAgilentRawSubDir);

            DirectoryPattern extBrukerRaw1 = new DirectoryPattern(this);
            extBrukerRaw1.setExt(".*\\.d$");
            extBrukerRaw1.setFileExt("^analysis.baf$");

            DirectoryPattern extBrukerRaw2 = new DirectoryPattern(this);
            extBrukerRaw2.setExt(".*\\.d$");
            extBrukerRaw2.setFileExt("^analysis.tdf$");

            fcs.addZiploaderPattern(extWatersRaw);
            fcs.addZiploaderPattern(extAgilentRaw);
            fcs.addZiploaderPattern(extBrukerRaw1);
            fcs.addZiploaderPattern(extBrukerRaw2);
        }

        Portal.registerNavTreeCustomizer(TARGETED_MS_REPLICATE_SUMMARY, new QCSummaryMenuCustomizer("configureQCGroups", "Configure Included and Excluded Precursors"));
        Portal.registerNavTreeCustomizer(TARGETED_MS_QC_PLOTS, new QCSummaryMenuCustomizer("configureQCGroups", "Configure Included and Excluded Precursors"));

        Portal.registerNavTreeCustomizer(TARGETED_MS_REPLICATE_SUMMARY, new QCSummaryMenuCustomizer("configureQCMetric", "Configure QC Metrics"));
        Portal.registerNavTreeCustomizer(TARGETED_MS_QC_PLOTS, new QCSummaryMenuCustomizer("configureQCMetric", "Configure QC Metrics"));

        Portal.registerNavTreeCustomizer(TARGETED_MS_REPLICATE_SUMMARY, new QCSummaryMenuCustomizer("subscribeOutlierNotifications", "Subscribe to Outlier Notification Emails"));
        Portal.registerNavTreeCustomizer(TARGETED_MS_QC_PLOTS, new QCSummaryMenuCustomizer("subscribeOutlierNotifications", "Subscribe to Outlier Notification Emails"));

        TargetedMSService.get().registerSkylineDocumentImportListener(QCNotificationSender.get());
    }

    @Override
    public @NotNull Set<Class<?>> getIntegrationTests()
    {
        return Set.of(
            MsDataSourceUtil.TestCase.class,
            SkylineAuditLogManager.TestCase.class
        );
    }

    @Override
    public @NotNull Set<Class<?>> getUnitTests()
    {
        return Set.of(
            ComparisonCategory.TestCase.class,
            ReplicateLabelMinimizer.TestCase.class,
            SampleFile.TestCase.class,
            SkylineAuditLogParser.TestCase.class,
            TargetedMSController.TestCase.class,
            PrecursorManager.TestCase.class,
            CrossLinkedPeptideInfo.TestCase.class,
            Protein.TestCase.class,
            SpectrumFilter.TestCase.class,
            CrossLinkedPeptideDisplayColumn.TestCase.class
        );
    }

    @Override
    public UpgradeCode getUpgradeCode()
    {
        return new TargetedMSUpgradeCode();
    }

    public static TargetedMSService.FolderType getFolderType(@NotNull Container container)
    {
        TargetedMSModule targetedMSModule = null;
        for (Module m : container.getActiveModules())
        {
            if (m instanceof TargetedMSModule)
            {
                targetedMSModule = (TargetedMSModule) m;
                break;
            }
        }
        if (targetedMSModule != null)
        {
            ModuleProperty moduleProperty = targetedMSModule.getModuleProperties().get(FOLDER_TYPE_PROP_NAME);
            return TargetedMSService.FolderType.valueOf(moduleProperty.getValueContainerSpecific(container));
        }

        return null;
    }
}