diff --git a/src/main/java/nl/fairbydesign/backend/data/objects/DiskUsage.java b/src/main/java/nl/fairbydesign/backend/data/objects/DiskUsage.java index fbc1c6b185fb5eebee855f125bd0f4f12a1e85e5..085a732dbfbc454105cb47564b4a66f7e830874f 100644 --- a/src/main/java/nl/fairbydesign/backend/data/objects/DiskUsage.java +++ b/src/main/java/nl/fairbydesign/backend/data/objects/DiskUsage.java @@ -3,7 +3,8 @@ package nl.fairbydesign.backend.data.objects; public class DiskUsage { private String project; private String investigation; - private long size; + private long tapeSize; + private long diskSize; public void setProject(String project) { this.project = project; @@ -13,13 +14,6 @@ public class DiskUsage { return project; } - public void setSize(long size) { - this.size = size; - } - - public long getSize() { - return size; - } public String getInvestigation() { return investigation; @@ -28,4 +22,20 @@ public class DiskUsage { public void setInvestigation(String investigation) { this.investigation = investigation; } + + public void setTapeSize(long tapeSize) { + this.tapeSize = tapeSize; + } + + public long getTapeSize() { + return tapeSize; + } + + public void setDiskSize(long diskSize) { + this.diskSize = diskSize; + } + + public long getDiskSize() { + return diskSize; + } } diff --git a/src/main/java/nl/fairbydesign/backend/irods/Data.java b/src/main/java/nl/fairbydesign/backend/irods/Data.java index bb86996f3f9e4a486f058c3eb8c7c96234077fc5..f5a79c65449431c451ca4e70e553a0b6c47d0be1 100644 --- a/src/main/java/nl/fairbydesign/backend/irods/Data.java +++ b/src/main/java/nl/fairbydesign/backend/irods/Data.java @@ -195,9 +195,10 @@ public class Data { // Obtain all disk usage for each project IRODSGenQueryBuilder queryBuilder = new IRODSGenQueryBuilder(true, null); - queryBuilder.addConditionAsGenQueryField(COL_COLL_NAME, QueryConditionOperators.LIKE, "/" + irodsAccount.getZone() + "/projects/" + process.getProjectIdentifier() + "/" + process.getInvestigationIdentifier() + "%"); + queryBuilder.addConditionAsGenQueryField(COL_COLL_NAME, QueryConditionOperators.LIKE, "/" + irodsAccount.getZone() + "%" + process.getProjectIdentifier() + "/" + process.getInvestigationIdentifier() + "%"); // Column name as default does a distinct? + queryBuilder.addSelectAsGenQueryValue(COL_R_RESC_NAME); queryBuilder.addSelectAsAgregateGenQueryValue(RodsGenQueryEnum.COL_DATA_SIZE, GenQueryField.SelectFieldTypes.SUM); // Set limit? @@ -212,13 +213,15 @@ public class Data { DiskUsage diskUsage = new DiskUsage(); diskUsage.setProject(process.getProjectIdentifier()); diskUsage.setInvestigation(process.getInvestigationIdentifier()); + diskUsage.setTapeSize(0); + diskUsage.setDiskSize(0); for (IRODSQueryResultRow irodsQueryResultRow : irodsQueryResultSetResults) { - String size = irodsQueryResultRow.getColumn(0).trim().strip(); - if (StringUtils.isNumeric(size) && size.length() > 0) { - diskUsage.setSize(Long.parseLong(size) / (1024 * 1024 * 1024)); - } else { - diskUsage.setSize(-1); - } + String resource = irodsQueryResultRow.getColumn(0); + String size = irodsQueryResultRow.getColumn(1).trim().strip(); + if (resource.contains("archiveResc") && StringUtils.isNumeric(size) && size.length() > 0) + diskUsage.setTapeSize(Long.parseLong(size) / (1024 * 1024 * 1024)); + if (resource.contains("dataResc") && StringUtils.isNumeric(size) && size.length() > 0) + diskUsage.setDiskSize(Long.parseLong(size) / (1024 * 1024 * 1024)); } return diskUsage; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/NCBI.java b/src/main/java/nl/fairbydesign/backend/ncbi/NCBI.java index 6b16b3bbe2c5a0ac944af67075701db24e3fb401..a9da98dbd469fb3b73c7fa92ce931e8bc399c7d3 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/NCBI.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/NCBI.java @@ -6,8 +6,6 @@ import com.fasterxml.jackson.databind.MapperFeature; import com.fasterxml.jackson.databind.ObjectMapper; import nl.fairbydesign.backend.ncbi.objects.esearch.Root; import nl.fairbydesign.backend.parsers.ExcelGenerator; -import org.apache.jena.sparql.function.library.print; -import org.apache.poi.ddf.EscherTertiaryOptRecord; import org.jboss.logging.Logger; import org.json.JSONObject; import org.json.XML; @@ -26,7 +24,6 @@ import java.util.HashSet; import java.util.Scanner; import static nl.fairbydesign.backend.ncbi.XLSX.setup; -import static nl.fairbydesign.backend.ncbi.XLSX.studies; public class NCBI { public static final Logger logger = Logger.getLogger(ExcelGenerator.class); diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/BASECALL.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/BASECALL.java deleted file mode 100644 index f8b81b736f83754e7ae56934abd47798d0ddb5b4..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/BASECALL.java +++ /dev/null @@ -1,18 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class BASECALL { - @JsonProperty("match_edge") - public String getMatch_edge() { - return this.match_edge; } - public void setMatch_edge(String match_edge) { - this.match_edge = match_edge; } - String match_edge; - @JsonProperty("content") - public String getContent() { - return this.content; } - public void setContent(String content) { - this.content = content; } - String content; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPECTEDBASECALLTABLE.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPECTEDBASECALLTABLE.java deleted file mode 100644 index 8f633f870ae3318cb9b2c30756135fdfd832f869..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPECTEDBASECALLTABLE.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class EXPECTEDBASECALLTABLE { - @JsonProperty("BASECALL") - public BASECALL getBASECALL() { - return this.bASECALL; } - public void setBASECALL(BASECALL bASECALL) { - this.bASECALL = bASECALL; } - BASECALL bASECALL; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENT.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENT.java index 37a77551810fd95f81bbe4f35e0a2049344cc541..5e9c645ed44ac128028ad142447506213afc61c3 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENT.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENT.java @@ -21,15 +21,12 @@ public class EXPERIMENT{ public void setCenter_name(String center_name) { this.center_name = center_name; } String center_name; - - //String or Object needed - @JsonProperty("PROCESSING") - public Object getPROCESSING() { - return this.pROCESSING; } - public void setPROCESSING(Object pROCESSING) { - this.pROCESSING = pROCESSING; } - Object pROCESSING; - + @JsonProperty("PROCESSING") + public String getPROCESSING() { + return this.pROCESSING; } + public void setPROCESSING(String pROCESSING) { + this.pROCESSING = pROCESSING; } + String pROCESSING; @JsonProperty("alias") public String getAlias() { return this.alias; } @@ -60,10 +57,4 @@ public class EXPERIMENT{ public void setSTUDY_REF(STUDYREF sTUDY_REF) { this.sTUDY_REF = sTUDY_REF; } STUDYREF sTUDY_REF; - @JsonProperty("EXPERIMENT_LINKS") - public EXPERIMENTLINKS getEXPERIMENT_LINKS() { - return this.eXPERIMENT_LINKS; } - public void setEXPERIMENT_LINKS(EXPERIMENTLINKS eXPERIMENT_LINKS) { - this.eXPERIMENT_LINKS = eXPERIMENT_LINKS; } - EXPERIMENTLINKS eXPERIMENT_LINKS; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINK.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINK.java deleted file mode 100644 index e7aeda5cd56367f1f89bc736cdda87b8a8b21d0a..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINK.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class EXPERIMENTLINK { - @JsonProperty("URL_LINK") - public URLLINK getURL_LINK() { - return this.uRL_LINK; } - public void setURL_LINK(URLLINK uRL_LINK) { - this.uRL_LINK = uRL_LINK; } - URLLINK uRL_LINK; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINKS.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINKS.java deleted file mode 100644 index 7cf9ce942f2175a00069143fc19aefa29e489929..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINKS.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class EXPERIMENTLINKS { - @JsonProperty("EXPERIMENT_LINK") - public EXPERIMENTLINK getEXPERIMENT_LINK() { - return this.eXPERIMENT_LINK; } - public void setEXPERIMENT_LINK(EXPERIMENTLINK eXPERIMENT_LINK) { - this.eXPERIMENT_LINK = eXPERIMENT_LINK; } - EXPERIMENTLINK eXPERIMENT_LINK; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPELINE.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPELINE.java deleted file mode 100644 index 8c0a608d57d487cf7f7814bf1b57ff921c369cb6..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPELINE.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class PIPELINE { - @JsonProperty("PIPE_SECTION") - public PIPESECTION getPIPE_SECTION() { - return this.pIPE_SECTION; } - public void setPIPE_SECTION(PIPESECTION pIPE_SECTION) { - this.pIPE_SECTION = pIPE_SECTION; } - PIPESECTION pIPE_SECTION; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPESECTION.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPESECTION.java deleted file mode 100644 index 1e844c0c100436aed16e508a1a08b2568c161f6c..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPESECTION.java +++ /dev/null @@ -1,30 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class PIPESECTION { - @JsonProperty("STEP_INDEX") - public int getSTEP_INDEX() { - return this.sTEP_INDEX; } - public void setSTEP_INDEX(int sTEP_INDEX) { - this.sTEP_INDEX = sTEP_INDEX; } - int sTEP_INDEX; - @JsonProperty("VERSION") - public String getVERSION() { - return this.vERSION; } - public void setVERSION(String vERSION) { - this.vERSION = vERSION; } - String vERSION; - @JsonProperty("PREV_STEP_INDEX") - public String getPREV_STEP_INDEX() { - return this.pREV_STEP_INDEX; } - public void setPREV_STEP_INDEX(String pREV_STEP_INDEX) { - this.pREV_STEP_INDEX = pREV_STEP_INDEX; } - String pREV_STEP_INDEX; - @JsonProperty("PROGRAM") - public String getPROGRAM() { - return this.pROGRAM; } - public void setPROGRAM(String pROGRAM) { - this.pROGRAM = pROGRAM; } - String pROGRAM; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PROCESSING.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PROCESSING.java deleted file mode 100644 index 0ba4582c7761def4f7b1e6b6977730d3e7585881..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PROCESSING.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class PROCESSING { - @JsonProperty("PIPELINE") - public PIPELINE getPIPELINE() { - return this.pIPELINE; } - public void setPIPELINE(PIPELINE pIPELINE) { - this.pIPELINE = pIPELINE; } - PIPELINE pIPELINE; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/READSPEC.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/READSPEC.java index bbe88dcd4a4a10507372fd0da58905a3291d65b8..8d81f98c971c827ace11a408c55273784c78396d 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/READSPEC.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/READSPEC.java @@ -27,16 +27,4 @@ public class READSPEC{ public void setREAD_TYPE(String rEAD_TYPE) { this.rEAD_TYPE = rEAD_TYPE; } String rEAD_TYPE; - @JsonProperty("EXPECTED_BASECALL_TABLE") - public EXPECTEDBASECALLTABLE getEXPECTED_BASECALL_TABLE() { - return this.eXPECTED_BASECALL_TABLE; } - public void setEXPECTED_BASECALL_TABLE(EXPECTEDBASECALLTABLE eXPECTED_BASECALL_TABLE) { - this.eXPECTED_BASECALL_TABLE = eXPECTED_BASECALL_TABLE; } - EXPECTEDBASECALLTABLE eXPECTED_BASECALL_TABLE; - @JsonProperty("RELATIVE_ORDER") - public RELATIVEORDER getRELATIVE_ORDER() { - return this.rELATIVE_ORDER; } - public void setRELATIVE_ORDER(RELATIVEORDER rELATIVE_ORDER) { - this.rELATIVE_ORDER = rELATIVE_ORDER; } - RELATIVEORDER rELATIVE_ORDER; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RELATIVEORDER.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RELATIVEORDER.java deleted file mode 100644 index 073ba48deb054cac375bec2307f23623a34878c5..0000000000000000000000000000000000000000 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RELATIVEORDER.java +++ /dev/null @@ -1,12 +0,0 @@ -package nl.fairbydesign.backend.ncbi.objects.esample; - -import com.fasterxml.jackson.annotation.JsonProperty; - -public class RELATIVEORDER { - @JsonProperty("follows_read_index") - public int getFollows_read_index() { - return this.follows_read_index; } - public void setFollows_read_index(int follows_read_index) { - this.follows_read_index = follows_read_index; } - int follows_read_index; -} diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUN.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUN.java index dad3ca03dc1e8b55864d70201bb5de084995f5aa..d84e2bf7f647e9bf080f66418b96b6d51f9d6bb7 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUN.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUN.java @@ -137,13 +137,6 @@ public class RUN { Bases bases; - @JsonProperty("xmlns") - public String getXmlns() { - return this.xmlns; } - public void setXmlns(String xmlns) { - this.xmlns = xmlns; } - String xmlns; - @JsonProperty("center_name") public String getCenter_name() { return this.center_name; diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNATTRIBUTE.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNATTRIBUTE.java index 817282ed368974559bbf20eb93609ffbb4c8a992..751e5d804e80a50e8192348398d63eda0ebbcce9 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNATTRIBUTE.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNATTRIBUTE.java @@ -15,10 +15,4 @@ public class RUNATTRIBUTE{ public void setVALUE(String vALUE) { this.vALUE = vALUE; } String vALUE; - @JsonProperty("UNITS") - public String getUNITS() { - return this.uNITS; } - public void setUNITS(String uNITS) { - this.uNITS = uNITS; } - String uNITS; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java index bfb7574c459533fce9d3e29cffb1bc3c86c554b5..1c81ff7ef3003f12612f2f6c9ee730c410daef45 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java @@ -12,4 +12,14 @@ public class RUNSET{ public void setRUN(ArrayList<RUN> rUN) { this.rUN = rUN; } ArrayList<RUN> rUN = new ArrayList<>(); - } \ No newline at end of file + } +======= +public class RUNSET{ + @JsonProperty("RUN") + public RUN getRUN() { + return this.rUN; } + public void setRUN(RUN rUN) { + this.rUN = rUN; } + RUN rUN; +} +>>>>>>> 3d2e7bc368880c32d40198f9fb320f8e742a6eea diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLE.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLE.java index f17ff87892a8cfc9684588b371cb1deb61036498..f5cc275aa8f0290d452aaed4d9fd511112192f5b 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLE.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLE.java @@ -3,66 +3,91 @@ package nl.fairbydesign.backend.ncbi.objects.esample; import com.fasterxml.jackson.annotation.JsonProperty; public class SAMPLE { - @JsonProperty("center_name") - public String getCenter_name() { - return this.center_name; } - public void setCenter_name(String center_name) { - this.center_name = center_name; } - String center_name; - @JsonProperty("SAMPLE_NAME") public SAMPLENAME getSAMPLE_NAME() { - return this.sAMPLE_NAME; } + return this.sAMPLE_NAME; + } + public void setSAMPLE_NAME(SAMPLENAME sAMPLE_NAME) { - this.sAMPLE_NAME = sAMPLE_NAME; } + this.sAMPLE_NAME = sAMPLE_NAME; + } + SAMPLENAME sAMPLE_NAME; @JsonProperty("alias") public String getAlias() { - return this.alias; } + return this.alias; + } + public void setAlias(String alias) { - this.alias = alias; } + this.alias = alias; + } + String alias; @JsonProperty("IDENTIFIERS") public IDENTIFIERS getIDENTIFIERS() { - return this.iDENTIFIERS; } + return this.iDENTIFIERS; + } + public void setIDENTIFIERS(IDENTIFIERS iDENTIFIERS) { - this.iDENTIFIERS = iDENTIFIERS; } + this.iDENTIFIERS = iDENTIFIERS; + } + IDENTIFIERS iDENTIFIERS; @JsonProperty("accession") public String getAccession() { - return this.accession; } + return this.accession; + } + public void setAccession(String accession) { - this.accession = accession; } + this.accession = accession; + } + String accession; @JsonProperty("SAMPLE_ATTRIBUTES") public SAMPLEATTRIBUTES getSAMPLE_ATTRIBUTES() { - return this.sAMPLE_ATTRIBUTES; } + return this.sAMPLE_ATTRIBUTES; + } + public void setSAMPLE_ATTRIBUTES(SAMPLEATTRIBUTES sAMPLE_ATTRIBUTES) { - this.sAMPLE_ATTRIBUTES = sAMPLE_ATTRIBUTES; } + this.sAMPLE_ATTRIBUTES = sAMPLE_ATTRIBUTES; + } + SAMPLEATTRIBUTES sAMPLE_ATTRIBUTES; @JsonProperty("SAMPLE_LINKS") public SAMPLELINKS getSAMPLE_LINKS() { - return this.sAMPLE_LINKS; } + return this.sAMPLE_LINKS; + } + public void setSAMPLE_LINKS(SAMPLELINKS sAMPLE_LINKS) { - this.sAMPLE_LINKS = sAMPLE_LINKS; } + this.sAMPLE_LINKS = sAMPLE_LINKS; + } + SAMPLELINKS sAMPLE_LINKS; @JsonProperty("TITLE") public String getTITLE() { - return this.tITLE; } + return this.tITLE; + } + public void setTITLE(String tITLE) { - this.tITLE = tITLE; } + this.tITLE = tITLE; + } + String tITLE; @JsonProperty("DESCRIPTION") public String getDESCRIPTION() { - return this.dESCRIPTION; } + return this.dESCRIPTION; + } + public void setDESCRIPTION(String dESCRIPTION) { - this.dESCRIPTION = dESCRIPTION; } + this.dESCRIPTION = dESCRIPTION; + } + String dESCRIPTION; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLELINK.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLELINK.java index 797970a42ee37d8268d6398ad7c4798ff6efbac4..8b11cae375779bdbf68c277695791b15c5ce4a44 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLELINK.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLELINK.java @@ -9,10 +9,4 @@ public class SAMPLELINK{ public void setXREF_LINK(XREFLINK xREF_LINK) { this.xREF_LINK = xREF_LINK; } XREFLINK xREF_LINK; - @JsonProperty("URL_LINK") - public URLLINK getURL_LINK() { - return this.uRL_LINK; } - public void setURL_LINK(URLLINK uRL_LINK) { - this.uRL_LINK = uRL_LINK; } - URLLINK uRL_LINK; } diff --git a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SUBMISSION.java b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SUBMISSION.java index 3f703e92e0e8b333196fd99986e26af1a0e47629..7aa113db566f705e3ead0b1ea36b28d8a69d0422 100644 --- a/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SUBMISSION.java +++ b/src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SUBMISSION.java @@ -2,27 +2,13 @@ package nl.fairbydesign.backend.ncbi.objects.esample; import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.Date; - public class SUBMISSION{ - @JsonProperty("submission_date") - public Date getSubmission_date() { - return this.submission_date; } - public void setSubmission_date(Date submission_date) { - this.submission_date = submission_date; } - Date submission_date; @JsonProperty("center_name") public String getCenter_name() { return this.center_name; } public void setCenter_name(String center_name) { this.center_name = center_name; } String center_name; - @JsonProperty("broker_name") - public String getBroker_name() { - return this.broker_name; } - public void setBroker_name(String broker_name) { - this.broker_name = broker_name; } - String broker_name; @JsonProperty("alias") public String getAlias() { return this.alias; } diff --git a/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java b/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java index af01311ecb91ec6e45cc2181f5097fcc0e915356..a1a388a1416555569e367effa0aeb0c955a55fc1 100644 --- a/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java +++ b/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java @@ -60,7 +60,7 @@ public class ExcelValidator { public static final String FORWARD_FILENAME = "Forward filename"; public static final String OBSERVATION_UNIT_IDENTIFIER = "Observation unit identifier"; public static final String SAMPLE_IDENTIFIER = "Sample identifier"; - public static final String FILE_NAME = "FileName"; + public static final String FILE_NAME = "Filename"; public static final String ASSAY_IDENTIFIER = "Assay identifier"; public static final String SAME_AS = "Same as"; public static final String LIBRARY_NAME = "Library name"; @@ -756,17 +756,17 @@ public class ExcelValidator { AssayType assayType; if (sheet.getSheetName().endsWith("AmpliconAssay")) { assayType = AssayType.Amplicon; - } else if (sheet.getSheetName().endsWith("AmpliconLibraryAssay")) { + } else if (sheet.getSheetName().endsWith("AmpliconLibrary")) { assayType = AssayType.AmpliconLibrary; - } else if (sheet.getSheetName().endsWith("RNAseqAssay")) { + } else if (sheet.getSheetName().endsWith("RNA")) { assayType = AssayType.Transcriptomics; } else if (sheet.getSheetName().toLowerCase().endsWith("illumina")) { assayType = AssayType.Genomics; } else if (sheet.getSheetName().toLowerCase().endsWith("nanopore")) { assayType = AssayType.Genomics; - } else if (sheet.getSheetName().endsWith("ProteomicsAssay")) { + } else if (sheet.getSheetName().endsWith("Proteomics")) { assayType = AssayType.Proteomics; - } else if (sheet.getSheetName().endsWith("MetabolomicsAssay")) { + } else if (sheet.getSheetName().endsWith("Metabolomics")) { assayType = AssayType.Metabolomics; } else { throw new Exception("The sheet " + sheet.getSheetName() + " is of an unsupported assay type"); @@ -923,7 +923,7 @@ public class ExcelValidator { // parsedHeaders.addAll(Arrays.asList(ASSAY_DESCRIPTION, ASSAY_TITLE, ASSAY_IDENTIFIER, PLATFORM)); if (fileCell.getCellType().equals(CellType.BLANK)) { - logging("No file found for " + assay.getIdentifier()); +// logging("No file found for " + assay.getResource().getURI()); } else { String fileName = getStringValueCell(fileCell); // Check the FileNameForwardPath and FileNameReversePath first diff --git a/src/main/resources/metadata.xlsx b/src/main/resources/metadata.xlsx index d119b32ead6d978ee061af5236d0144cfb6bb78e..7be20a8e6170931223e7eb96dd2146bd26e89476 100755 Binary files a/src/main/resources/metadata.xlsx and b/src/main/resources/metadata.xlsx differ