From 7417de767e54a6c162b757002ef4120931bcc84b Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Thu, 1 Sep 2016 17:10:57 -0500
Subject: [PATCH] XNAT-4394 Updated investigators API to include projects on
which investigator is PI or associate investigator.
---
.../org/nrg/xapi/rest/data/Investigator.java | 209 ++++++++++++++++++
.../xapi/rest/data/InvestigatorService.java | 48 ++++
.../nrg/xapi/rest/data/InvestigatorsApi.java | 80 ++-----
3 files changed, 279 insertions(+), 58 deletions(-)
create mode 100644 src/main/java/org/nrg/xapi/rest/data/Investigator.java
create mode 100644 src/main/java/org/nrg/xapi/rest/data/InvestigatorService.java
diff --git a/src/main/java/org/nrg/xapi/rest/data/Investigator.java b/src/main/java/org/nrg/xapi/rest/data/Investigator.java
new file mode 100644
index 00000000..1a9ca3ac
--- /dev/null
+++ b/src/main/java/org/nrg/xapi/rest/data/Investigator.java
@@ -0,0 +1,209 @@
+package org.nrg.xapi.rest.data;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import org.apache.commons.lang3.NotImplementedException;
+import org.nrg.xdat.bean.XnatInvestigatordataBean;
+import org.nrg.xdat.model.XnatInvestigatordataI;
+import org.nrg.xdat.om.XnatInvestigatordata;
+
+import java.io.Writer;
+import java.sql.Array;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.*;
+
+/**
+ * Provides a wrapper around the {@link XnatInvestigatordata}, {@link XnatInvestigatordataI}, and {@link
+ * XnatInvestigatordataBean} classes. This omits extraneous properties (e.g. XFT integration attributes) and provides
+ * extra attributes for aggregated or synthesized properties, such as lists of projects with which the investigator is
+ * associated.
+ */
+public class Investigator implements XnatInvestigatordataI {
+ public Investigator(final XnatInvestigatordataI investigator, final Collection<String> primaryProjects, final Collection<String> investigatorProjects) {
+ _xnatInvestigatordataId = investigator.getXnatInvestigatordataId();
+ _id = investigator.getId();
+ _title = investigator.getTitle();
+ _firstname = investigator.getFirstname();
+ _lastname = investigator.getLastname();
+ _institution = investigator.getInstitution();
+ _department = investigator.getDepartment();
+ _email = investigator.getEmail();
+ _phone = investigator.getPhone();
+ _primaryProjects.addAll(primaryProjects);
+ _investigatorProjects.addAll(investigatorProjects);
+ }
+
+ public Investigator(final ResultSet resultSet) throws SQLException {
+ _xnatInvestigatordataId = resultSet.getInt(0);
+ _id = resultSet.getString(1);
+ _title = resultSet.getString(2);
+ _firstname = resultSet.getString(2);
+ _lastname = resultSet.getString(2);
+ _institution = resultSet.getString(2);
+ _department = resultSet.getString(2);
+ _email = resultSet.getString(2);
+ _phone = resultSet.getString(2);
+ _primaryProjects.addAll(getProjectIds(resultSet.getArray(10)));
+ _investigatorProjects.addAll(getProjectIds(resultSet.getArray(11)));
+ }
+
+ @Override
+ @JsonIgnore
+ public String getXSIType() {
+ return XnatInvestigatordata.SCHEMA_ELEMENT_NAME;
+ }
+
+ @Override
+ public void toXML(final Writer writer) throws Exception {
+
+ }
+
+ @Override
+ public String getTitle() {
+ return _title;
+ }
+
+ @Override
+ public void setTitle(final String title) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getFirstname() {
+ return _firstname;
+ }
+
+ @Override
+ public void setFirstname(final String firstname) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getLastname() {
+ return _lastname;
+ }
+
+ @Override
+ public void setLastname(final String lastname) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getInstitution() {
+ return _institution;
+ }
+
+ @Override
+ public void setInstitution(final String institution) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getDepartment() {
+ return _department;
+ }
+
+ @Override
+ public void setDepartment(final String department) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getEmail() {
+ return _email;
+ }
+
+ @Override
+ public void setEmail(final String email) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getPhone() {
+ return _phone;
+ }
+
+ @Override
+ public void setPhone(final String phone) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public String getId() {
+ return _id;
+ }
+
+ @Override
+ public void setId(final String v) {
+ throw new NotImplementedException("Set methods on this class are not implemented: the class is meant to be read-only and only for reference purposes.");
+ }
+
+ @Override
+ public Integer getXnatInvestigatordataId() {
+ return _xnatInvestigatordataId;
+ }
+
+ /**
+ * Gets the list of IDs for projects on which the investigator is the primary investigator.
+ *
+ * @return The projects on which the investigator is the primary investigator.
+ */
+ @SuppressWarnings("unused")
+ public Set<String> getPrimaryProjects() {
+ return new HashSet<>(_primaryProjects);
+ }
+
+ /**
+ * Indicates whether the investigator is a PI on the indicated project.
+ *
+ * @param project The project to test.
+ *
+ * @return Returns true if the investigator is the PI on the indicated project, false otherwise.
+ */
+ @SuppressWarnings("unused")
+ public boolean hasPrimaryProject(final String project) {
+ return _primaryProjects.contains(project);
+ }
+
+ /**
+ * Gets the list of IDs for projects on which the investigator is the primary investigator.
+ *
+ * @return The projects on which the investigator is the primary investigator.
+ */
+ @SuppressWarnings("unused")
+ public Set<String> getInvestigatorProjects() {
+ return new HashSet<>(_investigatorProjects);
+ }
+
+ /**
+ * Indicates whether the investigator is a member of the indicated project team. Note that this does not check
+ * whether the investigator is the project's PI.
+ *
+ * @param project The project to test.
+ *
+ * @return Returns true if the investigator is a member of the indicated project team, false otherwise.
+ */
+ @SuppressWarnings("unused")
+ public boolean hasInvestigatorProject(final String project) {
+ return _investigatorProjects.contains(project);
+ }
+
+ private static Collection<? extends String> getProjectIds(final Array array) throws SQLException {
+ if (array == null) {
+ return Collections.emptyList();
+ }
+ return Arrays.asList((String[]) array.getArray());
+ }
+
+ private final Integer _xnatInvestigatordataId;
+ private final String _id;
+ private final String _title;
+ private final String _firstname;
+ private final String _lastname;
+ private final String _institution;
+ private final String _department;
+ private final String _email;
+ private final String _phone;
+ private final Set<String> _primaryProjects = new HashSet<>();
+ private final Set<String> _investigatorProjects = new HashSet<>();
+}
diff --git a/src/main/java/org/nrg/xapi/rest/data/InvestigatorService.java b/src/main/java/org/nrg/xapi/rest/data/InvestigatorService.java
new file mode 100644
index 00000000..ad6e1a88
--- /dev/null
+++ b/src/main/java/org/nrg/xapi/rest/data/InvestigatorService.java
@@ -0,0 +1,48 @@
+package org.nrg.xapi.rest.data;
+
+import org.nrg.xdat.model.XnatInvestigatordataI;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.RowMapper;
+import org.springframework.stereotype.Service;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.List;
+
+/**
+ * Manages operations with {@link Investigator investigator proxy objects}. This is not a full-on Hibernate service,
+ * since the "entities" managed are not Hibernate entities but instead are composite objects that represent XFT {@link
+ * XnatInvestigatordataI} objects as well as metadata aggregated from other tables.
+ */
+@Service
+public class InvestigatorService {
+ @Autowired
+ public InvestigatorService(final JdbcTemplate template) {
+ _template = template;
+ }
+
+ public Investigator getInvestigator(final int xnatInvestigatordataId) {
+ return _template.queryForObject(INVESTIGATOR_QUERY + BY_ID_WHERE, new Object[]{xnatInvestigatordataId}, ROW_MAPPER);
+ }
+
+ public Investigator getInvestigator(final String firstname, final String lastname) {
+ return _template.queryForObject(INVESTIGATOR_QUERY + BY_FIRST_LAST_WHERE, new Object[]{firstname, lastname}, ROW_MAPPER);
+ }
+
+ public List<Investigator> getInvestigators() {
+ return _template.query(INVESTIGATOR_QUERY, ROW_MAPPER);
+ }
+
+ private static final String INVESTIGATOR_QUERY = "SELECT investigator.xnat_investigatordata_id AS xnat_investigatordata_id, investigator.id AS id, investigator.title AS title, investigator.firstname AS firstname, investigator.lastname AS lastname, investigator.institution AS institution, investigator.department AS department, investigator.email AS email, investigator.phone AS phone, (SELECT array(SELECT project.id FROM xnat_projectdata project WHERE project.pi_xnat_investigatordata_id = investigator.xnat_investigatordata_id)) AS primary_inv, (SELECT array(SELECT project_inv.xnat_projectdata_id FROM xnat_projectdata_investigator project_inv WHERE project_inv.xnat_investigatordata_xnat_investigatordata_id = investigator.xnat_investigatordata_id)) AS inv FROM xnat_investigatordata investigator";
+ private static final String BY_ID_WHERE = " WHERE investigator.xnat_investigatordata_id = ?";
+ private static final String BY_FIRST_LAST_WHERE = " WHERE investigator.firstname = ? AND investigator.lastname = ?";
+
+ private static final RowMapper<Investigator> ROW_MAPPER = new RowMapper<Investigator>() {
+ @Override
+ public Investigator mapRow(final ResultSet resultSet, final int i) throws SQLException {
+ return new Investigator(resultSet);
+ }
+ };
+ private final JdbcTemplate _template;
+}
diff --git a/src/main/java/org/nrg/xapi/rest/data/InvestigatorsApi.java b/src/main/java/org/nrg/xapi/rest/data/InvestigatorsApi.java
index db058218..be3b56eb 100644
--- a/src/main/java/org/nrg/xapi/rest/data/InvestigatorsApi.java
+++ b/src/main/java/org/nrg/xapi/rest/data/InvestigatorsApi.java
@@ -6,11 +6,11 @@ import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.annotations.XapiRestController;
-import org.nrg.xdat.bean.XnatInvestigatordataBean;
-import org.nrg.xdat.model.XnatInvestigatordataI;
import org.nrg.xdat.om.XnatInvestigatordata;
import org.nrg.xdat.rest.AbstractXapiRestController;
+import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.security.services.RoleHolder;
+import org.nrg.xdat.security.services.RoleRepositoryServiceI;
import org.nrg.xdat.security.services.UserManagementServiceI;
import org.nrg.xft.XFTItem;
import org.nrg.xft.event.EventUtils;
@@ -22,12 +22,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
-import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.core.RowMapper;
import org.springframework.web.bind.annotation.*;
-import java.sql.ResultSet;
-import java.sql.SQLException;
import java.util.List;
@Api(description = "XNAT Data Investigators API")
@@ -35,42 +31,42 @@ import java.util.List;
@RequestMapping(value = "/investigators")
public class InvestigatorsApi extends AbstractXapiRestController {
@Autowired
- public InvestigatorsApi(final UserManagementServiceI userManagementService, final RoleHolder roleHolder, final JdbcTemplate jdbcTemplate) {
+ public InvestigatorsApi(final UserManagementServiceI userManagementService, final RoleHolder roleHolder, final InvestigatorService service) {
super(userManagementService, roleHolder);
- _jdbcTemplate = jdbcTemplate;
+ _service = service;
}
- @ApiOperation(value = "Get list of investigators.", notes = "The investigators function returns a list of all investigators configured in the XNAT system.", response = XnatInvestigatordataI.class, responseContainer = "List")
+ @ApiOperation(value = "Get list of investigators.", notes = "The investigators function returns a list of all investigators configured in the XNAT system.", response = Investigator.class, responseContainer = "List")
@ApiResponses({@ApiResponse(code = 200, message = "Returns a list of all of the currently configured investigators."),
@ApiResponse(code = 500, message = "An unexpected or unknown error occurred")})
@RequestMapping(produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.GET)
@ResponseBody
- public ResponseEntity<List<XnatInvestigatordataI>> getInvestigators() {
- return new ResponseEntity<>(_jdbcTemplate.query(PI_QUERY + PI_ORDERBY, PI_ROWMAPPER), HttpStatus.OK);
+ public ResponseEntity<List<Investigator>> getInvestigators() {
+ return new ResponseEntity<>(_service.getInvestigators(), HttpStatus.OK);
}
- @ApiOperation(value = "Gets the requested investigator.", notes = "Returns the investigator with the specified ID.", response = XnatInvestigatordataI.class)
+ @ApiOperation(value = "Gets the requested investigator.", notes = "Returns the investigator with the specified ID.", response = Investigator.class)
@ApiResponses({@ApiResponse(code = 200, message = "Returns the requested investigator."),
@ApiResponse(code = 404, message = "The requested investigator wasn't found."),
@ApiResponse(code = 500, message = "An unexpected or unknown error occurred.")})
@RequestMapping(value = "{investigatorId}", produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.GET)
@ResponseBody
- public ResponseEntity<XnatInvestigatordataI> getInvestigator(@PathVariable("investigatorId") final int investigatorId) {
- final XnatInvestigatordataI investigator = getXnatInvestigator(investigatorId);
+ public ResponseEntity<Investigator> getInvestigator(@PathVariable("investigatorId") final int investigatorId) {
+ final Investigator investigator = _service.getInvestigator(investigatorId);
if (investigator == null) {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
}
return new ResponseEntity<>(investigator, HttpStatus.OK);
}
- @ApiOperation(value = "Creates a new investigator from the submitted attributes.", notes = "Returns the newly created investigator with the submitted attributes.", response = XnatInvestigatordataI.class)
+ @ApiOperation(value = "Creates a new investigator from the submitted attributes.", notes = "Returns the newly created investigator with the submitted attributes.", response = Investigator.class)
@ApiResponses({@ApiResponse(code = 200, message = "Returns the newly created investigator."),
@ApiResponse(code = 403, message = "Insufficient privileges to create the submitted investigator."),
@ApiResponse(code = 404, message = "The requested investigator wasn't found."),
@ApiResponse(code = 500, message = "An unexpected or unknown error occurred.")})
@RequestMapping(consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST)
@ResponseBody
- public ResponseEntity<XnatInvestigatordataI> createInvestigator(@RequestBody final XnatInvestigatordataBean investigator) throws Exception {
+ public ResponseEntity<Investigator> createInvestigator(@RequestBody final Investigator investigator) throws Exception {
if (StringUtils.isBlank(investigator.getFirstname()) || StringUtils.isBlank(investigator.getLastname())) {
_log.error("User {} tried to create investigator without a first or last name.", getSessionUser().getUsername());
return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
@@ -88,10 +84,10 @@ public class InvestigatorsApi extends AbstractXapiRestController {
_log.error("Failed to create a new investigator for user {}. Check the logs for possible errors or exceptions.", user.getUsername());
return new ResponseEntity<>(HttpStatus.CONFLICT);
}
- return new ResponseEntity<>(getXnatInvestigator(investigator.getFirstname(), investigator.getLastname()), HttpStatus.OK);
+ return new ResponseEntity<>(_service.getInvestigator(investigator.getFirstname(), investigator.getLastname()), HttpStatus.OK);
}
- @ApiOperation(value = "Updates the requested investigator from the submitted attributes.", notes = "Returns the updated investigator.", response = XnatInvestigatordataI.class)
+ @ApiOperation(value = "Updates the requested investigator from the submitted attributes.", notes = "Returns the updated investigator.", response = Investigator.class)
@ApiResponses({@ApiResponse(code = 200, message = "Returns the updated investigator."),
@ApiResponse(code = 304, message = "The requested investigator is the same as the submitted investigator."),
@ApiResponse(code = 403, message = "Insufficient privileges to edit the requested investigator."),
@@ -99,8 +95,9 @@ public class InvestigatorsApi extends AbstractXapiRestController {
@ApiResponse(code = 500, message = "An unexpected or unknown error occurred.")})
@RequestMapping(value = "{investigatorId}", consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.PUT)
@ResponseBody
- public ResponseEntity<XnatInvestigatordataI> updateInvestigator(@PathVariable("investigatorId") final int investigatorId, @RequestBody final XnatInvestigatordataBean investigator) throws Exception {
+ public ResponseEntity<Investigator> updateInvestigator(@PathVariable("investigatorId") final int investigatorId, @RequestBody final Investigator investigator) throws Exception {
final UserI user = getSessionUser();
+
final XnatInvestigatordata existing = XnatInvestigatordata.getXnatInvestigatordatasByXnatInvestigatordataId(investigatorId, user, false);
if (existing == null) {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
@@ -142,7 +139,7 @@ public class InvestigatorsApi extends AbstractXapiRestController {
_log.error("Failed to save the investigator with ID {}. Check the logs for possible errors or exceptions.");
return new ResponseEntity<>(HttpStatus.CONFLICT);
}
- return new ResponseEntity<>(getXnatInvestigator(investigatorId), HttpStatus.OK);
+ return new ResponseEntity<>(_service.getInvestigator(investigatorId), HttpStatus.OK);
}
return new ResponseEntity<>(HttpStatus.NOT_MODIFIED);
@@ -150,12 +147,16 @@ public class InvestigatorsApi extends AbstractXapiRestController {
@ApiOperation(value = "Deletes the requested investigator.", notes = "Returns true if the requested investigator was successfully deleted. Returns false otherwise.", response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Returns true to indicate the requested investigator was successfully deleted."),
+ @ApiResponse(code = 403, message = "The user doesn't have permission to delete investigators."),
@ApiResponse(code = 404, message = "The requested investigator wasn't found."),
@ApiResponse(code = 500, message = "An unexpected or unknown error occurred.")})
@RequestMapping(value = "{investigatorId}", produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.DELETE)
@ResponseBody
public ResponseEntity<Boolean> deleteInvestigator(@PathVariable("investigatorId") final int investigatorId) throws Exception {
final UserI user = getSessionUser();
+ if (!Roles.isSiteAdmin(user)) {
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
+ }
final XnatInvestigatordata investigator = XnatInvestigatordata.getXnatInvestigatordatasByXnatInvestigatordataId(investigatorId, user, false);
if (investigator == null) {
return new ResponseEntity<>(false, HttpStatus.NOT_FOUND);
@@ -164,44 +165,7 @@ public class InvestigatorsApi extends AbstractXapiRestController {
return new ResponseEntity<>(true, HttpStatus.OK);
}
- private XnatInvestigatordataI getXnatInvestigator(final int investigatorId) {
- final List<XnatInvestigatordataI> investigators = _jdbcTemplate.query(PI_QUERY + PI_BY_ID, new Object[]{investigatorId}, PI_ROWMAPPER);
- if (investigators.size() == 0) {
- return null;
- }
- return investigators.get(0);
- }
-
- private XnatInvestigatordataI getXnatInvestigator(final String firstname, final String lastname) {
- final List<XnatInvestigatordataI> investigators = _jdbcTemplate.query(PI_QUERY + PI_BY_NAME, new Object[]{firstname, lastname}, PI_ROWMAPPER);
- if (investigators.size() == 0) {
- return null;
- }
- return investigators.get(0);
- }
-
private static final Logger _log = LoggerFactory.getLogger(InvestigatorsApi.class);
- // TODO: InvestigatorListResource uses a query that adds the PI's login. XnatInvestigatordataBean has no setter for login, so leaving it off for now.
- private static final String PI_QUERY = "SELECT DISTINCT ON (lastname, firstname) xnat_investigatorData_id, title, firstname, lastname, institution, department, email, phone FROM xnat_investigatorData ";
- private static final String PI_ORDERBY = "ORDER BY lastname, firstname";
- private static final String PI_BY_ID = "WHERE xnat_investigatordata_id = ?";
- private static final String PI_BY_NAME = "WHERE firstname = ? AND lastname = ?";
- private final static RowMapper<XnatInvestigatordataI> PI_ROWMAPPER = new RowMapper<XnatInvestigatordataI>() {
- @Override
- public XnatInvestigatordataI mapRow(final ResultSet resultSet, final int i) throws SQLException {
- return new XnatInvestigatordataBean() {{
- setXnatInvestigatordataId(resultSet.getInt("xnat_investigatordata_id"));
- setTitle(resultSet.getString("title"));
- setFirstname(resultSet.getString("firstname"));
- setLastname(resultSet.getString("lastname"));
- setDepartment(resultSet.getString("department"));
- setInstitution(resultSet.getString("institution"));
- setEmail(resultSet.getString("email"));
- setPhone(resultSet.getString("phone"));
- }};
- }
- };
-
- private final JdbcTemplate _jdbcTemplate;
+ private final InvestigatorService _service;
}
--
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