Just added ## to some "processing file" output.

legumeinfo · Oct 5, 2022 · a45e394 · a45e394
1 parent 05c6823
commit a45e394
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Showing 13 changed files with 5 additions and 5 deletions.
diff --git a/lis-annotation/libs/ncgr-datastore.jar b/lis-annotation/libs/ncgr-datastore.jar
diff --git a/lis-expression/libs/ncgr-datastore.jar b/lis-expression/libs/ncgr-datastore.jar
diff --git a/lis-genome/libs/ncgr-datastore.jar b/lis-genome/libs/ncgr-datastore.jar
diff --git a/lis-gwas/libs/ncgr-datastore.jar b/lis-gwas/libs/ncgr-datastore.jar
diff --git a/lis-hsh/src/main/java/org/intermine/bio/dataconversion/HSHFileConverter.java b/lis-hsh/src/main/java/org/intermine/bio/dataconversion/HSHFileConverter.java
@@ -60,6 +60,7 @@ public void process(Reader reader) throws IOException {
         if (getCurrentFile().getName().startsWith("README")) {
             processReadme(reader);
         } else if (getCurrentFile().getName().endsWith(".hsh.tsv")) {
+            System.out.println("## Processing "+getCurrentFile().getName());
             processHSHFile(reader);
 	}
     }
@@ -87,7 +88,6 @@ public void close() throws ObjectStoreException {
      * glysp.mixed.pan2.SoyPan000001   glyma.Lee.gnm1.ann1.GlymaLee.16G153800.1
      */
     void processHSHFile(Reader reader) throws IOException {
-        System.out.println("Processing "+getCurrentFile().getName());
         String[] fileParts = getCurrentFile().getName().split("\\.");
         if (fileParts.length!=6) {
             throw new RuntimeException("HSH file does not have the required 6 dot-separated parts: "+getCurrentFile().getName());

diff --git a/lis-info-annot/src/main/java/org/intermine/bio/dataconversion/InfoAnnotFileConverter.java b/lis-info-annot/src/main/java/org/intermine/bio/dataconversion/InfoAnnotFileConverter.java
@@ -100,6 +100,7 @@ public void process(Reader reader) throws IOException {
                 // README not yet processed, store this reader for processing after README
                 annotFileReader = reader;
             } else {
+                System.out.println("## Processing "+getCurrentFile().getName());
                 processInfoAnnotFile(reader);
             }
 	}
@@ -158,7 +159,6 @@ public void close() throws ObjectStoreException {
      * 37170591 Phvul.001G000400 Phvul.001G000400.1 Phvul.001G000400.1.p PF00504 PTHR21649,PTHR21649:SF24 1.10.3.9 K14172 GO:0016020,GO:0009765 AT1G76570.1 Chlorophyll family protein
      */
     void processInfoAnnotFile(Reader reader) throws IOException {
-        System.out.println("Processing "+getCurrentFile().getName());
         // spin through the file
         BufferedReader br = new BufferedReader(reader);
         String line = null;

diff --git a/lis-ipr-gff/src/main/java/org/intermine/bio/dataconversion/IPRGFFConverter.java b/lis-ipr-gff/src/main/java/org/intermine/bio/dataconversion/IPRGFFConverter.java
@@ -57,6 +57,7 @@ public void process(Reader reader) throws IOException {
             processReadme(reader);
             setStrain();
         } else if (getCurrentFile().getName().endsWith("iprscan.gff3")) {
+            System.out.println("## Processing "+getCurrentFile().getName());
             processGFF(reader);
         }
     }
@@ -88,7 +89,6 @@ public void close() throws ObjectStoreException {
      * medsa.XinJiangDaYe.gnm1.ann1.RKB9.iprscan.gff3
      */
     void processGFF(Reader reader) throws IOException {
-        System.out.println("Processing "+getCurrentFile().getName());
         // spin through the file
         String line = null;
         BufferedReader br = new BufferedReader(reader);

diff --git a/lis-map/libs/ncgr-datastore.jar b/lis-map/libs/ncgr-datastore.jar
diff --git a/lis-map/src/main/java/org/intermine/bio/dataconversion/MapFileConverter.java b/lis-map/src/main/java/org/intermine/bio/dataconversion/MapFileConverter.java
@@ -87,10 +87,10 @@ public void process(Reader reader) throws IOException {
             }
             geneticMap.setAttribute("genotypes", genotypes);
         } else if (getCurrentFile().getName().endsWith("lg.tsv.gz")) {
-            System.out.println("Processing "+getCurrentFile().getName());
+            System.out.println("## Processing "+getCurrentFile().getName());
             processLgFile();
         } else if (getCurrentFile().getName().endsWith("mrk.tsv.gz")) {
-            System.out.println("Processing "+getCurrentFile().getName());
+            System.out.println("## Processing "+getCurrentFile().getName());
             processMrkFile();
         } else {
             System.out.println("## - Skipping "+getCurrentFile().getName());

diff --git a/lis-markers/libs/ncgr-datastore.jar b/lis-markers/libs/ncgr-datastore.jar
diff --git a/lis-mstmap/libs/ncgr-datastore.jar b/lis-mstmap/libs/ncgr-datastore.jar
diff --git a/lis-qtl/libs/ncgr-datastore.jar b/lis-qtl/libs/ncgr-datastore.jar
diff --git a/lis-synteny/libs/ncgr-datastore.jar b/lis-synteny/libs/ncgr-datastore.jar