sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
53df7d35a0109b1f19fcec13c71b04184abc01e031ccf38f3c5ce7175429bbec | Java | 807 | 27 | package org.janelia.colormipsearch.dao;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import org.janelia.colormipsearch.datarequests.PagedRequest;
import org.janelia.colormipsearch.datarequests.PagedResult;
import org.janelia.colormipsearch.model.BaseEntity;
/**
* Base interface for data... |
0391ccf0e754900a9496c7ec55721374d8d68dcc4dce0792e88a9576eaeae8f7 | Java | 813 | 33 | package org.janelia.colormipsearch.results;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.janelia.colormipsearch.model.AbstractMatchEntity;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
public class GroupedMatchedEntities<M extends AbstractNeuronEntity, T ex... |
0fb48618465cd2f3805ee6d8d82bfd524d27cc6042f6d5cc8e607aa692ada52e | Java | 814 | 34 | package org.janelia.colormipsearch.dao.mongo.support;
import java.lang.reflect.Field;
import java.lang.reflect.Method;
import org.janelia.colormipsearch.model.annotations.EntityId;
class EntityIdFieldHandler implements FieldHandler {
@Override
public boolean supportsField(Field f, String defaultName) {
... |
1bc1b9d117963b59e63ad60b4e38f69f0c7f155ccf98ba321a96d01f467a579f | Java | 814 | 31 | package org.janelia.colormipsearch.cds;
public class PixelMatchScore implements ColorDepthMatchScore {
private final int matchingPixNum;
private final double matchingPixNumToMaskRatio;
private final boolean mirrored;
public PixelMatchScore(int matchingPixNum,
double matchin... |
b663ce8ea8fe38309da9701ada434b5ab76311add01ac0629fab96861067f909 | Java | 814 | 24 | package org.janelia.colormipsearch.dao.mongo;
import com.mongodb.client.MongoDatabase;
import org.janelia.colormipsearch.dao.IdGenerator;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.CDMatchEntity;
public class CDMatchesMongoDao<R extends CDMatchEntity<? exten... |
8f88b88b94f54ba42c8301ae21d4d5493e6e8a445f6abdad18909d633eed456d | Java | 820 | 36 | package org.janelia.colormipsearch.dto;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.janelia.colormipsearch.results.GroupedItems;
/**
* Metadata about result matches grouped by a given mask type.
*
* @param <T>
*/
public class ResultMatches<M extends AbstractNeuronMeta... |
ad61dd87cf02a608b32226969a3d24841fe9590c0c60824e5145e38071b0ca26 | Java | 823 | 23 | package org.janelia.colormipsearch.cmd.dataexport;
import javax.validation.Validator;
import com.fasterxml.jackson.databind.BeanDescription;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializationConfig;
import com.fasterxml.jackson.databind.ser.BeanSerializerModifier... |
a05db7e56aec6b78fe75b1ae56edf892863767a0d8b5bf5ce9b92a4bb8a3c7c4 | Java | 825 | 41 | package org.jeecg.modules.system.vo;
import lombok.Data;
import org.jeecg.modules.system.entity.SysDictItem;
import org.jeecgframework.poi.excel.annotation.Excel;
import org.jeecgframework.poi.excel.annotation.ExcelCollection;
import java.util.List;
@Data
public class SysDictPage {
/**
* 主键
*/
pri... |
dd53e6de6195adcffd51bc682ca1a8632554bd10458ed9c27079df31513df52b | Java | 827 | 24 | package org.janelia.colormipsearch.dao;
import java.util.List;
import org.junit.Test;
import static org.junit.Assert.assertTrue;
public class TimebasedIdGeneratorTest {
@Test
public void generateIdsUsingInParalelUsingALock() {
IdGenerator idGenerator = new TimebasedIdGenerator(1, "target/id.lock");... |
09fa6f4ab748abc75efd65e9bac89110e4eaa114e39c12386831066d1358686c | Java | 834 | 36 | package org.janelia.colormipsearch.dto;
import javax.validation.constraints.NotNull;
/**
* Metadata about a color depth matched target.
*
* @param <T>
*/
public class CDMatchedTarget<T extends AbstractNeuronMetadata> extends AbstractMatchedTarget<T> {
private Float normalizedScore;
private Integer matchin... |
9122a836985c698907822336efd0357a2ebba05100ccc583365b8595ef6b2e65 | Java | 834 | 39 | package org.jeecg.modules.monitor.service;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.alibaba.fastjson.JSONArray;
import org.jeecg.modules.monitor.domain.RedisInfo;
import org.jeecg.modules.monitor.exception.RedisConnectException;
public interface RedisService {
/**
* 获取 redis ... |
02a66959b841af08c4cd4936d68672085c26a519e5247a5063bdc2153f96185c | Java | 841 | 23 | package org.janelia.colormipsearch.dao.mongo.support;
import java.util.Date;
import com.fasterxml.jackson.databind.BeanDescription;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializationConfig;
import com.fasterxml.jackson.databind.module.SimpleModule;
import com.fas... |
98df61adab1cf7e102d90225d5d3b1692a48ef82406c2770f11eddac53cfef0d | Java | 852 | 32 | package org.jeecg.modules.system.mapper;
import java.util.List;
import java.util.Map;
import org.apache.ibatis.annotations.Param;
import org.apache.ibatis.annotations.Select;
import org.jeecg.modules.system.entity.SysCategory;
import org.jeecg.modules.system.model.TreeSelectModel;
import com.baomidou.mybatisplus.cor... |
cff02f8f504d7674c63deb02325f1926e2f14967bb1de526b0e6c13bef69b1e4 | Java | 858 | 30 | package org.jeecg.modules.system.service.impl;
import org.jeecg.modules.system.entity.SysDictItem;
import org.jeecg.modules.system.mapper.SysDictItemMapper;
import org.jeecg.modules.system.service.ISysDictItemService;
import com.baomidou.mybatisplus.extension.service.impl.ServiceImpl;
import org.springframework.beans.... |
5bd9f5070c67c6fa2af1a1b04d6f520c96d0e9f3f3a58be0c8d03a19ba597437 | Java | 862 | 33 | package org.janelia.colormipsearch.model;
import java.util.HashMap;
import java.util.Map;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.janelia.colormipsearch.model.annotations.PersistenceInfo;
@PersistenceInfo(storeName ="pppmURL")
public class PPPmURLs extends AbstractPublishedURLs {
priva... |
b118317c35dcb93e7585584222a1dab8ff550733242ee8ebe70690a140165774 | Java | 872 | 23 | package org.janelia.colormipsearch.dao.mongo;
import com.mongodb.client.MongoClient;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Indexes;
import org.janelia.colormipsearch.dao.IdGenerator;
import org.janelia.colormipsearch.dao.MatchSessionDao;
import org.janelia.colormipsearch.model.Abstr... |
8d475ddd6840d649dd167578baa6ce280d353f391203184f48d524520516b95d | Java | 875 | 41 | package org.jeecg.modules.system.service;
import java.util.List;
import org.jeecg.modules.system.entity.SysUser;
import org.jeecg.modules.system.entity.SysUserDepart;
import org.jeecg.modules.system.model.DepartIdModel;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* <p>
* SysUserDpeart用户组织机构s... |
e0459393fe5fd5783da90a34145680a2190c0eee414f13716384cc0addf055f6 | Java | 880 | 35 | package org.janelia.colormipsearch.imageprocessing;
import ij.ImagePlus;
/**
* ImageType specifies the pixel type such as:
* - gray - 8 bits pixel
* - gray - 16 bits pixel
* - RGB - 24 bits pixel
* R - bits 0-7
* G - bits 8-15
* B - bits 16-23
* this type is used for ARGB pixels as w... |
86659b9b26f2b06d59f49bf6159c4d82881a300f6c4af3d9d23f63334e33410d | Java | 885 | 27 | package org.janelia.colormipsearch.dao.mongo.support;
import java.io.IOException;
import java.util.Date;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import org.joda.time.DateTime;
import org.joda.time... |
017e5b5bbabc10e36a06a194cd07b45885c55b3daab580b87e70318097be55c4 | Java | 896 | 40 | package org.jeecg.modules.quartz.service;
import java.util.List;
import org.jeecg.modules.quartz.entity.QuartzJob;
import org.quartz.SchedulerException;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* @Description: 定时任务在线管理
* @Author: jeecg-boot
* @Date: 2019-04-28
* @Version: V1.1
*/
public ... |
102532bf6cd7cda5aae9d4191e318f72a437f7bdec72f38478e1d78447c0bf67 | Java | 903 | 38 | package org.janelia.colormipsearch.dto;
import javax.validation.GroupSequence;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* The default group validation for PPP target images is different because PPP targets will not have a MIP ID.
*/
@GroupSequenc... |
6aa890e23dffbdd8a0b963bbb5d504f56cccfabfbdd301ec96498f83a9b7b54d | Java | 903 | 24 | package org.janelia.colormipsearch.dao.mongo;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Indexes;
import org.janelia.colormipsearch.dao.IdGenerator;
import org.janelia.colormipsearch.dao.MatchSessionDao;
import org.janelia.colormipsearch.model.AbstractSessionEntity;
public class MatchSe... |
fdb5be69e96d4973952bcb4e9895b9e4ea68ad73e38c57469cef56c0d8e346ff | Java | 919 | 30 | package org.janelia.colormipsearch.dao.mongo.support;
import com.fasterxml.jackson.databind.ser.BeanPropertyWriter;
import com.fasterxml.jackson.databind.ser.PropertyWriter;
import com.fasterxml.jackson.databind.ser.impl.SimpleBeanPropertyFilter;
import org.janelia.colormipsearch.model.annotations.DoNotPersist;
publ... |
4ad099bf23607588fac45608c047e2860c45ed648afee3777675c1b9bd565c9e | Java | 927 | 25 | package org.jeecg.modules.system.mapper;
import java.util.List;
import org.apache.ibatis.annotations.Param;
import org.jeecg.modules.system.entity.SysAnnouncement;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
import com.baomidou.mybatisplus.extension.plugins.pagination.Page;
/**
* @Description: 系统通告表
*... |
af39e065df1d201ff5f7af9c25aca9d76f56521f705e92703c4e2a0c8315b32f | Java | 931 | 31 | package org.jeecg.modules.system.mapper;
import java.util.List;
import org.apache.ibatis.annotations.Param;
import org.jeecg.modules.system.entity.SysAnnouncementSend;
import org.jeecg.modules.system.model.AnnouncementSendModel;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
import com.baomidou.mybatisplus.... |
44f1471803a04faa508c7968757e1532978d6ac6f8dd1508c7204054c8350be2 | Java | 936 | 36 | package org.janelia.colormipsearch.model;
import java.util.LinkedHashMap;
import java.util.Map;
import org.janelia.colormipsearch.model.annotations.PersistenceInfo;
/**
* This is the representation of a color depth or PPP match run.
*/
@PersistenceInfo(storeName ="matchSession")
public abstract class AbstractSessi... |
748c0a2e24c7b912fdc34a52aea4c1fee2a0e740a65644594263a47740d6065b | Java | 936 | 28 | package org.jeecg.modules.message.service.impl;
import org.jeecg.common.system.base.service.impl.JeecgServiceImpl;
import org.jeecg.modules.message.entity.SysMessageTemplate;
import org.jeecg.modules.message.mapper.SysMessageTemplateMapper;
import org.jeecg.modules.message.service.ISysMessageTemplateService;
import or... |
d9eb402d61d8be85dcd4eefaa9cdf2a683dbc654936162c17246f792389c83e6 | Java | 936 | 41 | package org.janelia.colormipsearch.cmd_v2;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
import java.io.Serializable;
import java.util.Map;
class PublishedImage implements Serializable {
@JsonProperty("_id")
String id;
@JsonProperty
Str... |
291f68165c09a8216f56c4ec1a0675026d673749ab20561cf3232e446aa9d8a7 | Java | 937 | 30 | package org.jeecg.modules.system.service;
import org.jeecg.modules.system.entity.SysDepartPermission;
import com.baomidou.mybatisplus.extension.service.IService;
import org.jeecg.modules.system.entity.SysPermissionDataRule;
import java.util.List;
/**
* @Description: 部门权限表
* @Author: jeecg-boot
* @Date: 2020-02-... |
0becd279b0e2e2f66083fb83c9ef1bc05b8f9a571535c7c0c95aa6d505b86ea7 | Java | 948 | 37 | package org.jeecg.modules.system.mapper;
import org.apache.ibatis.annotations.Delete;
import org.apache.ibatis.annotations.Param;
import org.apache.ibatis.annotations.Update;
import org.jeecg.modules.system.entity.SysRole;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
/**
* <p>
* 角色表 Mapper 接口
* </p>
*... |
beaab235f89d518dc1928d776c2a06b7e8e84e6bbf94c2ac4fd593ccb0b2f64e | Java | 951 | 36 | package org.janelia.colormipsearch.dao.mongo;
import java.util.List;
import org.janelia.colormipsearch.AbstractITest;
import org.janelia.colormipsearch.dao.Dao;
import org.janelia.colormipsearch.dao.DaosProvider;
import org.janelia.colormipsearch.model.BaseEntity;
import org.junit.BeforeClass;
public abstract class ... |
cd4ca628c0edcffc84b723955e88057f5ab7f13ef32129a22be81de77c59f0f7 | Java | 954 | 43 | package jaolho.data.lma.implementations;
import jaolho.data.lma.LMAFunction;
/**
* LMA polynomial y = a_n * x^n + ... + a_2 * x^2 + a_1 * x + a_0
*/
public class Polynomial extends LMAFunction {
/**
* @return The partial derivate of the polynomial which is
* x to the power of the parameter index.
*/
public... |
a6a186d2f9d935e7daa5ca0a51b16d07d27edce2d6faaff45c796383783ead21 | Java | 958 | 44 | package org.janelia.colormipsearch.dto;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.janelia.colormipsearch.results.GroupedItems;
/**
* Metadata about result matches grouped by a given mask type.
*
* @param <T>
*/
public class ResultMatches<M extends AbstractNeuronMeta... |
999e30461d9501d861975161784fc492e2cf66390e6dd1d470a43bd3f941ce1f | Java | 959 | 43 | package org.jeecg.modules.system.service;
import com.baomidou.mybatisplus.extension.service.IService;
import org.jeecg.common.api.vo.Result;
import org.jeecg.modules.system.entity.SysRole;
import org.jeecgframework.poi.excel.entity.ImportParams;
import org.springframework.web.multipart.MultipartFile;
/**
* <p>
* 角色... |
19fac7a793ec51d6067ff67b16aa25e300f346b3b61895db265d9c34e4efc741 | Java | 972 | 29 | package org.janelia.colormipsearch.dao.mongo.support;
import java.io.IOException;
import java.math.BigInteger;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonN... |
e9bc11b047b8876ada5a3f6ad4d5bcf6e2b81af4633f65dafbbd44afe8fc8d24 | Java | 977 | 44 | package org.jeecg.modules.system.model;
import java.io.Serializable;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import lombok.Data;
/**
* @Title: DuplicateCheckVo
* @Description: 重复校验VO
* @Author 张代浩
* @Date 2019-03-25
* @Version V1.0
*/
@Data
@ApiModel(value="重复校验数据... |
b1e627bc1b2a5e01d1d73a1e8d6e51ae0e29219b4041847c7056052a12e176cc | Java | 986 | 29 | package org.janelia.colormipsearch.dao.mongo.support;
import java.io.IOException;
import java.math.BigInteger;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonN... |
6e06ee766a96ebe4d6a735e0299bcf657b4058306f5b88dbe250476840525f5b | Java | 992 | 29 | package org.jeecg.modules.system.service;
import com.alibaba.fastjson.JSONObject;
import org.jeecg.modules.system.entity.SysAnnouncement;
import com.baomidou.mybatisplus.extension.plugins.pagination.Page;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* @Description: 系统通告表
* @Author: jeecg-boot
*... |
743d1a2e86e0931b266bfa40dfd37b860d46c976a7ad22ff9fca4700fd46bd55 | Java | 992 | 33 | package org.janelia.colormipsearch.cmd;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.cmd.jacsdata.ColorDepthMIP;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
/**
* This class is used for generating and persisting all corresponding neuron metadata from a color depth MIP.
* Fro... |
a25d1d1b7f134cf951030393f368f36f0b2c4011c886ae7468640fcb56b0fb02 | Java | 1,010 | 26 | package org.janelia.colormipsearch.model.json;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import org.janelia.colormipsearch.model.FileData;
public class FileDataSerialize... |
507d55837c554c107e73e9473ed32399f0d7501bd7224f26a88a5e887771b336 | Java | 1,025 | 37 | package jaolho.data.lma;
/**
* The matrix to be used in LMA.
* Implement this to make LMA operational if you
* don't or can't use jama or flanagan math libraries.
*/
public interface LMAMatrix {
public static class InvertException extends RuntimeException {
public InvertException(String message) {
super(mess... |
5f321686cebfdbca5add6ca1242c9b57205fcc6cbe005be6f16d3466f75ac4a1 | Java | 1,032 | 35 | package org.jeecg.modules.quartz.job;
import lombok.extern.slf4j.Slf4j;
import org.jeecg.common.util.DateUtils;
import org.quartz.*;
/**
* @Description: 同步定时任务测试
*
* 此处的同步是指 当定时任务的执行时间大于任务的时间间隔时
* 会等待第一个任务执行完成才会走第二个任务
*
*
* @author: taoyan
* @date: 2020年06月19日
*/
@PersistJobDataAfterExecution
@DisallowConcur... |
b3da30e0d0980e8152ce8caae46faf5185371e015e0fde7a3399da1fe91e8bd2 | Java | 1,033 | 32 | package org.janelia.colormipsearch.dao.mongo.support;
import java.math.BigInteger;
import org.bson.BsonReader;
import org.bson.BsonWriter;
import org.bson.codecs.Codec;
import org.bson.codecs.DecoderContext;
import org.bson.codecs.EncoderContext;
/**
* BigIntegerCodec implements a Codec for a big integer type. The ... |
f2d718d2a9a80f6814730d03ca43b7f5eb9cc3757a90e89b2ec8ffa0b50faec4 | Java | 1,033 | 39 | package org.janelia.colormipsearch.cmd;
import org.apache.commons.lang3.StringUtils;
import org.janelia.colormipsearch.config.Config;
import org.janelia.colormipsearch.config.ConfigProvider;
import org.janelia.colormipsearch.dao.DaosProvider;
abstract class AbstractCmd {
static final long _1M = 1024 * 1024;
... |
d51aacca53c799b4281ed5374a9a0e9f01064283ac65df572ba71d97bc320f8b | Java | 1,037 | 45 | package org.janelia.colormipsearch.dataio;
import java.util.List;
import java.util.Set;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.ProcessingType;
/**
* Writer for Color Depth MIPs metadata.
*/
public interface CDMIPsWriter {
/**
* Open and prepar... |
262262acc5373572f5a1c4bdf9dfc88e54c20b11a486603bc929c7e805c91236 | Java | 1,039 | 30 | package org.janelia.colormipsearch.dao;
import java.util.LinkedHashMap;
import java.util.Map;
import org.janelia.colormipsearch.model.annotations.PersistenceInfo;
public class EntityUtils {
private static final Map<Class<?>, PersistenceInfo> MONGO_MAPPING_CACHE = new LinkedHashMap<>();
private static Persi... |
031eb9d205b05556904ba8c1c4bd0a62ad1b37637988991d1962f9d691e55e03 | Java | 1,048 | 40 | package org.janelia.colormipsearch.dao;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
/**
* @param <T> field value type
*/
public abstract class AbstractEntityFieldValueHandler<T> implements EntityFieldValueHandler<T> {
private final T fieldValue... |
dca3750bc48a4c8f45a66bb4fe080eeafdc60fb1144f7f6e9b3ebb504476b739 | Java | 1,052 | 51 | package org.jeecg.modules.message.handle.enums;
import org.jeecg.common.util.oConvertUtils;
/**
* 发送消息类型枚举
*/
public enum SendMsgTypeEnum {
//推送方式：1短信 2邮件 3微信
SMS("1", "org.jeecg.modules.message.handle.impl.SmsSendMsgHandle"),
EMAIL("2", "org.jeecg.modules.message.handle.impl.EmailSendMsgHandle"),
WX("3","org.j... |
02e667b1109d98b32844d86e51d074c2580f10415d7aa84f2fca0035f210661f | Java | 1,056 | 42 | package org.janelia.colormipsearch.datarequests;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
public class ScoresFilter {
public static class ScoreField {
private final String fieldName; // score field name
private final Double minScore; // min s... |
76b7f30b5f334c133a9c69891c5318533ee3b8dbe5a51cb5b6af508bbe08103f | Java | 1,062 | 34 | package org.janelia.colormipsearch.api_v2;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.util.List;
import com.fasterxml.jackson.databind.ObjectWriter;
import org.apache.commons.collections4.CollectionUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
... |
6ce89fe4ae86aecc90bd81c60b9ae48fc992d0ae1098ca6a29548b59e6b6eff2 | Java | 1,071 | 38 | package org.jeecg.modules.system.util;
import java.util.Date;
import org.apache.commons.lang3.RandomStringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.redis.core.RedisTemplate;
import org.springframework.stereotype.Component;
/**
* 生成sourceId工具类
*/
@Componen... |
fb82f99f07fd03ac3896217382afe35645776b66d966d5544e41943055c51deb | Java | 1,078 | 38 | package org.jeecg.modules.message.entity;
import org.jeecg.common.system.base.entity.JeecgEntity;
import org.jeecgframework.poi.excel.annotation.Excel;
import com.baomidou.mybatisplus.annotation.TableName;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.experimental.Accessors;
/**
* @Description... |
71658bcba6ecc051a2673e86c05923c44e5fc89c8afc7841ccaf3984358b927f | Java | 1,082 | 33 | package org.jeecg.modules.system.service.impl;
import org.jeecg.modules.system.entity.SysDataLog;
import org.jeecg.modules.system.mapper.SysDataLogMapper;
import org.jeecg.modules.system.service.ISysDataLogService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Ser... |
2fadea8cc98e47fd7c30d6de2f52b30ee2ac33752e670b027a2e0c66e58d60ef | Java | 1,084 | 47 | package org.janelia.colormipsearch.model;
public class TestEMNeuronEntity extends EMNeuronEntity {
private String neuronType;
private String neuronInstance;
private Gender gender;
private String anatomicalArea;
public String getNeuronType() {
return neuronType;
}
public void setNe... |
715c458f2b0cc91754634bfc6d2c582fd012c0f2d1e8459a302d6acf79e09589 | Java | 1,087 | 47 | package org.janelia.colormipsearch.dataio;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.ProcessingType;
/**
* Writer for Color Depth MIPs metadata.
*/
public interface CDMIPsWriter {
... |
94369aa04970f909c43eeb103bdb9d3f6ebc2e1f1a67dfdfc06205a9d15712eb | Java | 1,094 | 31 | package org.janelia.colormipsearch;
import java.util.function.BiPredicate;
import ij.ImagePlus;
import org.janelia.colormipsearch.imageprocessing.ImageArrayUtils;
import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;
import org.janelia.colormipsearch.imageprocessing.LImage;
public class ImageTestU... |
c4fbf50e3b39c7b847eaaa45ea54a374921a657c63e9fbdff883757592cf83f8 | Java | 1,096 | 49 | package org.janelia.colormipsearch.dto;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class EMNeuronMetadata extends AbstractNeuronMetadata {
/** This will be used to generate the export file name for PPPM */
private String emRefId;
private String neuronType;
private String neuronInstance... |
e3df814cf598d074467da7f820ccad5af0f426a7e7ecd05f5fd53d43565c6ec8 | Java | 1,100 | 31 | package org.janelia.colormipsearch.dao.mongo.support;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ser.impl.SimpleFilterProvider;
import org.bson.codecs.confi... |
887cd164ebc9c97014838973ac961e158c90d16f0a65f7f330ff8eca0b67c88a | Java | 1,105 | 30 | package org.janelia.colormipsearch.api_v2.pppsearch;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
/**
* This is the published PPP match. It is very similar with the source PPP match
* but... |
db09cba8fb2a3390d3840985a81805348afb3eb2a4163784a74a62cdfe09a445 | Java | 1,114 | 26 | package org.janelia.colormipsearch.cmd.dataexport;
import java.util.Map;
import org.janelia.colormipsearch.dto.AbstractNeuronMetadata;
public class ImageStoreMapping {
private final String defaultImageStore;
private final Map<ImageStoreKey, String> imageStoreByMetadataFields;
public ImageStoreMapping(St... |
4c44cb03cfbbd1fd4b276abced5421c7ebcfada577d30329252cd66304339a01 | Java | 1,118 | 59 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.experimental.Accessors;
/**
* <p>
* 用户角色表
* </p>
*
* @Author scott
* @... |
baeed2e6847d6a680af53c737687706ab2d38e5ba5b3ceb2c4ab7d281371cf63 | Java | 1,120 | 51 | package org.janelia.colormipsearch.dto;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class EMNeuronMetadata extends AbstractNeuronMetadata {
/** This will be used to generate the export file name for PPPM */
private String emRefId;
private String neuronType;
priva... |
05de484cf9c8cf75b9ca5ddc55b470c32a6543400a6053502a491f312935060f | Java | 1,126 | 33 | package org.jeecg.config.init;
import org.apache.catalina.Context;
import org.apache.tomcat.util.scan.StandardJarScanner;
import org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
... |
557852d5253e0f3b91ef91309dc28d1889daa5998fa2ca56560f25dd65d10e83 | Java | 1,127 | 26 | package org.janelia.colormipsearch.dao.mongo;
import com.mongodb.client.MongoClient;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Indexes;
import org.janelia.colormipsearch.dao.IdGenerator;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.mode... |
34020be1903a1b2884cb5e490011e9868c1a7ec9e6fb0d8ebf990fc4bde04dc4 | Java | 1,131 | 35 | package org.janelia.colormipsearch.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonTypeInfo;
/**
* This is the base entity persisted in the database.
*/
@JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, property = "class")
public interface BaseEntity {
Number ge... |
5bedc8b05d9bc8c7ea00a76f1e8dd7808650d8a4547514c2b72ec7b8a2231111 | Java | 1,134 | 50 | package org.janelia.colormipsearch.results;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @param <K> key type
* @par... |
ad0489f63588b0ca68fd2c5ee013814b274e0e75aac01b8e58572cd06084f5c5 | Java | 1,139 | 30 | package org.janelia.colormipsearch.cmd.dataexport;
import java.io.IOException;
import java.util.Set;
import javax.validation.ConstraintViolation;
import javax.validation.Validator;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.data... |
42d1645ae19fcc734e3654e88a899a28111a4c82d6f3f79f3951d7284d0baa94 | Java | 1,154 | 39 | package fiji.plugin.DOM;
public interface DOMConstants {
public static final String DOMversion="1.2.5";
public static final double FITRADIUS=3.0;
//order of results column in the table
public static int Col_X=0;
public static int Col_Y=1;
public static int Col_FrameN=2;
public static int Col_Xnm=3;
publi... |
0eab0830e42ca874a7cdd8832e3b3687b818ab620cc47e5ddd11368dbf307c2e | Java | 1,158 | 35 | package cn.sdaict.fldatauploader.config;
import org.apache.catalina.connector.Connector;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory;
import org.springframework.boot.web.servlet.server.ServletWebServerFactory;
import org.s... |
fcbe996e2ae351bfa188dd13c8da828ff4bea63e9c858667d7d81fa17d5f7bc4 | Java | 1,160 | 38 | package jaolho.data.lma.implementations;
import jaolho.data.lma.LMA;
import jaolho.data.lma.LMAFunction;
/** An example fit which fits a straight line to some data points and prints out the resulting fit parameters. */
public class ExampleFit {
/** An example function with a form of y = a0 * x + a1 */
public stati... |
24907ca6c44357012f5ca20c0c623ce658791f1915c906c75b6a1244ee3b8687 | Java | 1,164 | 36 | package org.janelia.colormipsearch.cmd;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import com.be... |
aade497be5564c007e2a38f03befa400664ac449090b5c1e7a7f7a604a8752f9 | Java | 1,169 | 56 | package org.jeecg.modules.system.service;
import java.util.Date;
import java.util.List;
import java.util.Map;
import org.jeecg.modules.system.entity.SysLog;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* <p>
* 系统日志表 服务类
* </p>
*
* @Author zhangweijian
* @since 2018-12-26
*/
public interfac... |
a0af73856e74d5b557772c71e1d142ae86f018c5d65b48568cee57906d5077d2 | Java | 1,171 | 36 | package org.jeecg.modules.system.rule;
import com.alibaba.fastjson.JSONObject;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.math.RandomUtils;
import org.jeecg.common.handler.IFillRuleHandler;
import java.text.SimpleDateFormat;
import java.util.Date;
/**
* 填值规则Demo：生成订单号
* 【测试示例】
*/
p... |
665b9e4b59c435dd5350b80b0646a74efdb3be12830b8dea5bfc536a1b8dc1a2 | Java | 1,179 | 30 | package org.janelia.colormipsearch.cmd;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import com.google.common.util.concurrent.ThreadFactoryBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class CmdUtils {
private static final Logger LOG = LoggerFactory.get... |
62a866044043e722e6e55474aefa099abc9cd17485c3d0c763d468addb865d20 | Java | 1,186 | 34 | package org.janelia.colormipsearch.cmd_v2;
import java.util.Collections;
import java.util.Set;
import java.util.stream.Collectors;
import com.beust.jcommander.Parameter;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
class CommonArgs {
@Parameter(names = {"-... |
60725f63fbae91d5129191270f62ebf4090a0982decd3ff6a3dde73aaa4a481e | Java | 1,188 | 41 | package org.janelia.colormipsearch.api_v2.cdsearch;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class NegativeColorDepthMatchScore implements ColorDepthMatchScore {
private final long gradientAreaGap;
private final long highExpressionArea;
private final boolean mirrored;
NegativeC... |
8ad6dcbe1175b636ccac353ab558814b75e32e01f5605c3117239a9314830a68 | Java | 1,188 | 56 | package org.janelia.colormipsearch.cmd_v2;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
class CDMIPSample {
@JsonProperty("_id")
String id;
@JsonProperty
String name;
@JsonProperty
String dataSet;
@J... |
d39bc225793efb97cac1ee24fba2a624fd04d4cfcdc98b230f4ad4718a7ec411 | Java | 1,196 | 47 | package org.janelia.colormipsearch.model;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.MapUtils;
import org.apache.commons.lang3.StringUtils;
/**
* This is the representation of a CDS run.
*/
... |
13d1985b672bf670757f0309f7fb3142f805be7ef4dc1cf6c992afafa80e10d9 | Java | 1,202 | 40 | package org.janelia.colormipsearch.model;
import javax.annotation.Nullable;
public enum PPPScreenshotType {
RAW(FileType.SignalMip, null),
MASKED_RAW(FileType.SignalMipMasked, null),
SKEL(FileType.SignalMipMaskedSkel, null),
CH(FileType.CDMBest, FileType.CDMBestThumbnail), // for a CH file we generate... |
a48376a952521d3b2eb06dc2c8e37c1bbc2528c1f0e769a17f5ea279a87f8b3e | Java | 1,202 | 83 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.experimental.Accessors;
/**
* <p>
* 菜单权限规则表
* </p>... |
86f59aba6c7b8c3ab3c2fe50b81c64f8eae2a7d4ecca606ecbea010170aab2a7 | Java | 1,208 | 46 | package org.janelia.colormipsearch.cmd;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import com.beust.jcommander.ParametersDelegate;
import org.apache.commons.lang3.StringUtils;
class AbstractCmdArgs {... |
f014378f29d0e88c5a2656f6ea5cb0e1e86b0090a0f39bf16e9432d4fd231fe2 | Java | 1,209 | 36 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.fasterxml.jackson.annotation.JsonFormat;
import ... |
f853a382d10604cc28bdf964f5b4b2494c8499e4828755134414190dc4d82dce | Java | 1,214 | 55 | package org.jeecg.modules.system.model;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
/**
* 登录表单
*
* @Author scott
* @since 2019-01-18
*/
@ApiModel(value="登录对象", description="登录对象")
public class SysLoginModel {
@ApiModelProperty(value = "账号", required = true)
priva... |
10022da3a6fc4c6d69f13ad1b6573f152c15c5f12ec3edf52d889fc8a63f7e0e | Java | 1,223 | 41 | package org.jeecg.config.jimureport;
import org.jeecg.common.system.api.ISysBaseAPI;
import org.jeecg.common.system.util.JwtUtil;
import org.jeecg.common.util.RedisUtil;
import org.jeecg.common.util.TokenUtils;
import org.jeecg.modules.jmreport.api.JmReportTokenServiceI;
import org.springframework.beans.factory.annota... |
09d9cd67487535a3f9253fc0ec8d58913627f32f57a4922bcdecb485720330a1 | Java | 1,256 | 40 | package org.jeecg.modules.quartz.job;
import lombok.extern.slf4j.Slf4j;
import org.jeecg.modules.federalml.entity.TmachineLearningModelInfo;
import org.jeecg.modules.federalml.service.IFlModelInfoService;
import org.jeecg.modules.federalml.service.ItMachineLearningModelInfoService;
import org.quartz.*;
import org.spri... |
c7038cd0f81c450aff190c35c2be1417979b1accb8b32a65d80054b47e90b4e9 | Java | 1,263 | 55 | package org.jeecg.modules.system.service;
import java.util.List;
import org.jeecg.modules.system.entity.SysPermissionDataRule;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* <p>
* 菜单权限规则 服务类
* </p>
*
* @Author huangzhilin
* @since 2019-04-01
*/
public interface ISysPermissionDataRuleServic... |
de4f8f94da46c92ffbb011aa042f21cd334296e7ecef0f474dd1a17c3b27676b | Java | 1,282 | 37 | package org.janelia.colormipsearch.dao;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.TypeVariable;
import org.janelia.colormipsearch.model.BaseEntity;
/**
* Abstract base interface for data access.
*
* @param <T> entity type
*/
public abstract class AbstractDao<T extends BaseEntity> imple... |
18423952cf48fefa0aa53c3e408e9862a689bbc603d77641e6f5b7005e49f9ff | Java | 1,298 | 39 | package org.jeecg.modules.system.service.impl;
import java.util.List;
import javax.annotation.Resource;
import org.jeecg.modules.system.entity.SysAnnouncementSend;
import org.jeecg.modules.system.mapper.SysAnnouncementSendMapper;
import org.jeecg.modules.system.model.AnnouncementSendModel;
import org.jeecg.modules.s... |
167da04142fdedce8a90f851cfa4b6f848f90e18b5c77b0905f266d39c30c073 | Java | 1,301 | 59 | package org.janelia.colormipsearch.model;
import javax.annotation.Nonnull;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonInclude;
import org.apache.commons.lang3.builder.ToStringBuilder;
@JsonInclude(JsonInclude.Include.NON_NULL)
public class PPPSkeletonMatch {
... |
951a074dd67437f5f9caf58fab056596c0e5ad0c96e119643d9b39df4149a1c9 | Java | 1,314 | 37 | package org.janelia.colormipsearch.dao.mongo.support;
import java.io.IOException;
import java.util.Date;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonNode;
... |
ac1b24e8206fa23ae6fca0787856bef2479db40006a78ea069ea016c8d7e10f9 | Java | 1,315 | 59 | package org.janelia.colormipsearch.api_v2.pppsearch;
import javax.annotation.Nonnull;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonInclude;
import org.apache.commons.lang3.builder.ToStringBuilder;
@JsonInclude(JsonInclude.Include.NON_NULL)
public class SourceSkelet... |
9706d1ee0971836c8d130d2cf0f4e29739c8eefafdf6124c716eb702ca8b45ed | Java | 1,324 | 72 | package org.jeecg.modules.system.model;
import lombok.Data;
import java.io.Serializable;
/**
* 第三方登录 信息存储
*/
@Data
public class ThirdLoginModel implements Serializable {
private static final long serialVersionUID = 4098628709290780891L;
/**
* 第三方登录 来源
*/
private String source;
/**
... |
825e913cba479e05b538a1389009180fe14de359a5a12bf03be193f3cb912b4e | Java | 1,328 | 35 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import org.janelia.colormipsearch.dao.NeuronMatchesDao;
import org.janelia.colormipsearch.dataio.NeuronMatchesRemover;
import org.janelia.colormipsearch.model.AbstractMatchEntity;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import ... |
90b15a28beaf3fab545dc153175d8f67096b26c5d114fa31770caf250907c46c | Java | 1,341 | 42 | package jaolho.data.lma.implementations;
import jaolho.data.lma.LMA;
import jaolho.data.lma.LMAFunction;
import java.util.Arrays;
public class TestFunctions {
public static LMAFunction sin = new LMAFunction() {
public double getY(double x, double[] a) {
return a[0] * Math.sin(x / a[1]);
}
public double g... |
7b20e6bd996df550d039917c0f5146e27ad4e7145793b735efe3f6886868f35a | Java | 1,350 | 38 | package org.janelia.colormipsearch.imageprocessing;
public class ColorImageArray extends ImageArray<byte[]> {
private static byte[] createPixelsArray(int w, int h, int[] pxs) {
int npixels = w * h;
byte[] bytePixels = new byte[npixels * 3];
for (int i = 0; i < npixels; i++) {
... |
d88da38461af801d220df0ddd01eea0ed09892592b8a6f669a7823650bfc4b7b | Java | 1,351 | 57 | package org.jeecg.modules.system.mapper;
import java.util.Date;
import java.util.List;
import java.util.Map;
import org.apache.ibatis.annotations.Param;
import org.jeecg.modules.system.entity.SysLog;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
/**
* <p>
* 系统日志表 Mapper 接口
* </p>
*
* @Author zhangwei... |
5acbf4252678e5d1efecf6dd23cff59499a8db638984e8c04925d1fb0dd0f53d | Java | 1,355 | 37 | package org.janelia.colormipsearch.dao.mongo;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Indexes;
import org.janelia.colormipsearch.dao.IdGenerator;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.PPPMatchEntity;
public class PPPMatc... |
f7d8bd93d07b74e33e9c98f526e4c02b9d04f58cfefb2ef881d84dd547fd5676 | Java | 1,359 | 41 | package org.jeecg.config.init;
import lombok.extern.slf4j.Slf4j;
import org.jeecg.common.constant.CacheConstant;
import org.jeecg.config.JeecgCloudCondition;
import org.jeecg.modules.system.service.ISysGatewayRouteService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.c... |
2e0b1cf0570e55f18c504447744b8f4b267ca39eef2453b92319964fc3fa3204 | Java | 1,374 | 33 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dao.NeuronSelector;
import org.janelia.colormipsearch.dataio.CDMIPsReader;
import org.janelia.colormipsearch.dataio.DataSourceParam;
import org.janelia.colorm... |
c4f54d1c550e0c6015b92d8683f1bafb7dad19697d81299ebb057bab8c933e21 | Java | 1,383 | 42 | package org.janelia.colormipsearch.model;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.janelia.colormipsearch.model.annot... |
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