Examples with MetadataTemplateField ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField used on opensource projects

Example 1 with MetadataTemplateField

use of ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField in project irida by phac-nml.

the class AnalysisController method getMetadataTemplateFields.

/**
 * Generates a list of metadata fields for a five template.
 *
 * @param templateId {@link Long} id for the {@link MetadataTemplate} that the fields are required.
 * @return {@link Map}
 */
@RequestMapping("/ajax/{submissionId}/metadata-template-fields")
@ResponseBody
public Map<String, Object> getMetadataTemplateFields(@RequestParam Long templateId) {
    MetadataTemplate template = metadataTemplateService.read(templateId);
    List<MetadataTemplateField> metadataFields = template.getFields();
    List<String> fields = new ArrayList<>();
    for (MetadataTemplateField metadataField : metadataFields) {
        fields.add(metadataField.getLabel());
    }
    return ImmutableMap.of("fields", fields);
}

Example 2 with MetadataTemplateField

use of ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField in project irida by phac-nml.

the class ProjectLineListController method saveMetadataTemplate.

/**
 * Save a list a {@link MetadataTemplateField} as a {@link MetadataTemplate}
 *
 * @param projectId  identifier for the current {@link Project}
 * @param fields     {@link List} of {@link String} names of {@link MetadataTemplateField}
 * @param name       {@link String} name for the new template.
 * @param templateId ID of the template to update.  Will create new template if null
 * @param locale     Locale of teh logged in user
 * @return the saved {@link MetadataTemplate} and a response message
 */
@RequestMapping(value = "/templates", method = RequestMethod.POST)
@ResponseBody
public Map<String, Object> saveMetadataTemplate(@PathVariable long projectId, @RequestParam String name, @RequestParam(value = "fields[]") List<String> fields, @RequestParam(required = false) Long templateId, Locale locale) {
    Project project = projectService.read(projectId);
    List<MetadataTemplateField> metadataFields = new ArrayList<>();
    for (String label : fields) {
        // Check to see if this field already exists.
        MetadataTemplateField metadataField = metadataTemplateService.readMetadataFieldByLabel(label);
        // If it does not exist, create a new field.
        if (metadataField == null) {
            metadataField = new MetadataTemplateField(label, "text");
            metadataTemplateService.saveMetadataField(metadataField);
        }
        metadataFields.add(metadataField);
    }
    MetadataTemplate template;
    String message;
    // If the template already has an ID, it is an existing template, so just update it.
    if (templateId != null) {
        template = metadataTemplateService.read(templateId);
        template.setFields(metadataFields);
        template.setName(name);
        metadataTemplateService.updateMetadataTemplateInProject(template);
        message = messageSource.getMessage("linelist.create-template.update-success", new Object[] { name }, locale);
    } else {
        template = new MetadataTemplate(name, metadataFields);
        ProjectMetadataTemplateJoin join = metadataTemplateService.createMetadataTemplateInProject(template, project);
        template = join.getObject();
        message = messageSource.getMessage("linelist.create-template.success", new Object[] { name }, locale);
    }
    return ImmutableMap.of("template", template, "message", message);
}

Example 3 with MetadataTemplateField

use of ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField in project irida by phac-nml.

the class ProjectLineListController method getAllProjectMetadataFields.

/**
 * Get the template the the line list table.  This becomes the table headers.
 *
 * @param projectId
 * 		{@link Long} identifier of the current {@link Project}
 *
 * @return {@link Set} containing unique metadata fields
 */
private List<String> getAllProjectMetadataFields(Long projectId, Locale locale) {
    Project project = projectService.read(projectId);
    Set<String> fields = new HashSet<>();
    List<MetadataTemplateField> metadataFieldsForProject = metadataTemplateService.getMetadataFieldsForProject(project);
    fields.addAll(metadataFieldsForProject.stream().map(MetadataTemplateField::getLabel).collect(Collectors.toSet()));
    // Get all the fields from the templates.
    List<ProjectMetadataTemplateJoin> metadataTemplateJoins = metadataTemplateService.getMetadataTemplatesForProject(project);
    for (ProjectMetadataTemplateJoin join : metadataTemplateJoins) {
        MetadataTemplate template = join.getObject();
        fields.addAll(template.getFields().stream().map(MetadataTemplateField::getLabel).collect(Collectors.toSet()));
    }
    return new ArrayList<>(fields);
}

Example 4 with MetadataTemplateField

use of ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField in project irida by phac-nml.

the class ProjectSampleMetadataController method saveProjectSampleMetadata.

/**
 * Save uploaded metadata to the
 *
 * @param locale
 * 		{@link Locale} of the current user.
 * @param session
 * 		{@link HttpSession}
 * @param projectId
 * 		{@link Long} identifier for the current project
 *
 * @return {@link Map} of potential errors.
 */
@RequestMapping(value = "/upload/save", method = RequestMethod.POST)
@ResponseBody
public Map<String, Object> saveProjectSampleMetadata(Locale locale, HttpSession session, @PathVariable long projectId) {
    Map<String, Object> errors = new HashMap<>();
    Project project = projectService.read(projectId);
    SampleMetadataStorage stored = (SampleMetadataStorage) session.getAttribute("pm-" + projectId);
    if (stored == null) {
        errors.put("stored-error", true);
    }
    List<Sample> samplesToUpdate = new ArrayList<>();
    List<Map<String, String>> found = stored.getFound();
    if (found != null) {
        // Lets try to get a sample
        String sampleNameColumn = stored.getSampleNameColumn();
        List<String> errorList = new ArrayList<>();
        try {
            for (Map<String, String> row : found) {
                String name = row.get(sampleNameColumn);
                Sample sample = sampleService.getSampleBySampleName(project, name);
                row.remove(sampleNameColumn);
                Map<MetadataTemplateField, MetadataEntry> newData = new HashMap<>();
                // Need to overwrite duplicate keys
                for (Entry<String, String> entry : row.entrySet()) {
                    MetadataTemplateField key = metadataTemplateService.readMetadataFieldByLabel(entry.getKey());
                    if (key == null) {
                        key = metadataTemplateService.saveMetadataField(new MetadataTemplateField(entry.getKey(), "text"));
                    }
                    newData.put(key, new MetadataEntry(entry.getValue(), "text"));
                }
                sample.mergeMetadata(newData);
                // Save metadata back to the sample
                samplesToUpdate.add(sample);
            }
            sampleService.updateMultiple(samplesToUpdate);
        } catch (EntityNotFoundException e) {
            // This really should not happen, but hey, you never know!
            errorList.add(messageSource.getMessage("metadata.results.save.sample-not-found", new Object[] { e.getMessage() }, locale));
        }
        if (errorList.size() > 0) {
            errors.put("save-errors", errorList);
        }
    } else {
        errors.put("found-error", messageSource.getMessage("metadata.results.save.found-error", new Object[] {}, locale));
    }
    if (errors.size() == 0) {
        return ImmutableMap.of("success", messageSource.getMessage("metadata.results.save.success", new Object[] { found.size() }, locale));
    }
    return errors;
}

Example 5 with MetadataTemplateField

use of ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField in project irida by phac-nml.

the class ProjectSamplesMetadataTemplateController method saveMetadataTemplate.

/**
 * Save or update a {@link MetadataTemplate} within a {@link Project}
 *
 * @param projectId
 * 		{@link Long} identifier for a {@link Project}
 * @param template
 * 		A {@link UIMetadataTemplate} to save to a {@link Project}
 *
 * @return {@link String} redirects to the template page.
 */
@RequestMapping(value = "/save", method = RequestMethod.POST)
public String saveMetadataTemplate(@PathVariable Long projectId, UIMetadataTemplate template) {
    Project project = projectService.read(projectId);
    List<MetadataTemplateField> metadataFields = new ArrayList<>();
    for (String field : template.getFields()) {
        MetadataTemplateField metadataTemplateField = metadataTemplateService.readMetadataFieldByLabel(field);
        if (metadataTemplateField == null) {
            metadataTemplateField = new MetadataTemplateField(field, "text");
            metadataTemplateService.saveMetadataField(metadataTemplateField);
        }
        metadataFields.add(metadataTemplateField);
    }
    MetadataTemplate metadataTemplate;
    if (template.getId() != null) {
        metadataTemplate = metadataTemplateService.read(template.getId());
        metadataTemplate.setName(template.getName());
        metadataTemplate.setFields(metadataFields);
        metadataTemplateService.updateMetadataTemplateInProject(metadataTemplate);
    } else {
        ProjectMetadataTemplateJoin projectMetadataTemplateJoin = metadataTemplateService.createMetadataTemplateInProject(new MetadataTemplate(template.getName(), metadataFields), project);
        metadataTemplate = projectMetadataTemplateJoin.getObject();
    }
    return "redirect:/projects/" + projectId + "/metadata-templates/" + metadataTemplate.getId();
}