Adopt FileLike for more pipeline APIs (#183)

Author: labkey-jeckels

genotyping/src/org/labkey/genotyping/GenotypingController.java

@@ -973,8 +973,8 @@ public boolean handlePost(ImportReadsForm form, BindException errors) throws Exc
         {
             if (null == form.getReadsPath())
             {
-                File readsFile = form.getValidatedSingleFile(getContainer());
-                form.setReadsPath(readsFile.getPath());
+                FileLike readsFile = form.getValidatedSingleFile(getContainer());
+                form.setReadsPath(readsFile.toNioPathForRead().toFile().getPath());
                 return false;
             }
 
@@ -1395,24 +1395,15 @@ public boolean handlePost(PipelinePathForm form, BindException errors) throws IO
         {
             Container container = getContainer();
             // Manual upload of genotyping analysis; pipeline provider posts to this action with matches file.
-            Path singleFile = form.getValidatedSinglePath(container);
+            FileLike singleFile = form.getValidatedSingleFile(container);
+            FileLike analysisDir = singleFile.getParent();
 
-            if (form.getPipeRoot(container).getRootFileLike().isDescendant(singleFile.toUri()))
-            {
-
-                FileLike matches = form.getPipeRoot(container).resolvePathToFileLike(singleFile.toString());
-                FileLike analysisDir = matches.getParent();
+            // Load properties to determine the run.
+            Properties props = GenotypingManager.get().readProperties(analysisDir);
+            int analysisId = Integer.parseInt((String) props.get("analysis"));
+            importAnalysis(analysisId, analysisDir, getUser());
 
-                // Load properties to determine the run.
-                Properties props = GenotypingManager.get().readProperties(analysisDir);
-                int analysisId = Integer.parseInt((String) props.get("analysis"));
-                importAnalysis(analysisId, analysisDir, getUser());
-
-                return true;
-            }
-
-            errors.reject(ERROR_MSG, "File was not found under the pipeline root");
-            return false;
+            return true;
         }
 
         @Override

genotyping/src/org/labkey/genotyping/Import454ReadsJob.java

@@ -17,7 +17,7 @@
 
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.data.Table;
@@ -69,7 +69,7 @@ public Import454ReadsJob(ViewBackgroundInfo info, PipeRoot root, File reads, Gen
         super(Import454ReadsPipelineProvider.NAME, info, root, run);
         FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), reads.getAbsolutePath());
         _reads = FileSystemLike.toFile(verifiedFileLike);
-        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
+        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
     }
 
     @Override
@@ -91,7 +91,7 @@ public void run()
             }
             catch (SQLException se)
             {
-                if (RuntimeSQLException.isConstraintException(se) && StringUtils.containsIgnoreCase(se.getMessage(), "uq_reads_name"))
+                if (RuntimeSQLException.isConstraintException(se) && Strings.CI.contains(se.getMessage(), "uq_reads_name"))
                     throw new RuntimeException("A readname in this file already exists in the database; this run may have been imported previously", se);
                 else
                     throw se;
@@ -126,8 +126,7 @@ private void importReads() throws IOException, SQLException, PipelineJobExceptio
 
         try (TabLoader loader = new TabLoader(_reads, true))
         {
-            List<ColumnDescriptor> columns = new ArrayList<>();
-            columns.addAll(Arrays.asList(loader.getColumns()));
+            List<ColumnDescriptor> columns = new ArrayList<>(Arrays.asList(loader.getColumns()));
 
             for (ColumnDescriptor col : columns)
             {

genotyping/src/org/labkey/genotyping/ImportAnalysisJob.java

@@ -61,7 +61,7 @@ public ImportAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike pipeli
         super("Import Analysis", info, root);
         _dir = pipelineDir;
         _analysis = analysis;
-        setLogFile(_dir.resolveChild(FileUtil.makeFileNameWithTimestamp("import_analysis", "log")).toNioPathForWrite());
+        setLogFile(_dir.resolveChild(FileUtil.makeFileNameWithTimestamp("import_analysis", "log")));
 
         if (!_dir.exists())
             throw new IllegalArgumentException("Pipeline directory does not exist: " + _dir.toNioPathForRead().toAbsolutePath());

genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java

@@ -77,7 +77,7 @@ public ImportIlluminaReadsJob(ViewBackgroundInfo info, PipeRoot root, File sampl
         FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), sampleFile.getAbsolutePath());
         _sampleFile = FileSystemLike.toFile(verifiedFileLike);
         _fastqPrefix = fastqPrefix;
-        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
+        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
     }
 
     @Override

genotyping/src/org/labkey/genotyping/ImportPacBioReadsJob.java

@@ -73,7 +73,7 @@ public ImportPacBioReadsJob(ViewBackgroundInfo info, PipeRoot root, File sampleF
         FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), sampleFile.getAbsolutePath());
         _sampleFile = FileSystemLike.toFile(verifiedFileLike);
         _fastqPrefix = fastqPrefix;
-        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_pacbio_reads", "log")).toNioPathForWrite());
+        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_pacbio_reads", "log")));
     }
 
     @Override

genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java

@@ -110,7 +110,7 @@ public SubmitAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike reads,
             throw new MinorConfigurationException("Can't create analysis directory: " + _analysisDir.getPath());
         }
 
-        setLogFile(_analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("submit_analysis", "log")).toNioPathForWrite());
+        setLogFile(_analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("submit_analysis", "log")));
         info("Creating analysis directory: " + _analysisDir.getName());
         _analysis.setPath(FileUtil.getAbsolutePath(_analysisDir.toNioPathForRead()));
         _analysis.setFileName(_analysisDir.getName());