AWS Update

cgi-bin/rnaSeqMapCoverage.cgi

@@ -107,15 +107,8 @@ def determineReadMapNumber(filedir, filename, readMappedNumber, remoteDrive, bam
         readsMappedHold = []  # Holds the number
 
         # Clear temporary files and name a new one
-        os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;")
+        os.system("find /var/www/html/eFP-Seq_Browser/temp/* -mtime +1 -exec rm -f {} \\;")
 
-        # Set the environment
-        bai_directory = ("data/" + filedir)
-        if os.path.isdir(bai_directory):
-            os.chdir(bai_directory)
-        else:
-            os.makedirs(bai_directory)
-            os.chdir(bai_directory)
         my_env = os.environ.copy()
         my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/"
 
@@ -126,8 +119,6 @@ def determineReadMapNumber(filedir, filename, readMappedNumber, remoteDrive, bam
         except:
             pass
 
-        os.chdir("../../../")
-
         if flagstat is None:
             return "FAILED: determineReadMapNumber-flagstat NONE"
 
@@ -152,21 +143,10 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode
     x_bp_vals = []  # Holds nucleotide positions...
     y_reads_values = []  # Holds the valid mapped reads for the position...
 
-    if bamType == "Google Drive":
-        # Clear temporary files and name a new one
-        # os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;")
-        tempfile = "../temp/RNASeqGraph.png"
-
     # Call samtools and get mpileup
     region = chromosome + ":" + str(start) + "-" + str(end)
 
     # Set the environment
-    bai_directory = ("data/" + filedir)
-    if os.path.isdir(bai_directory):
-        os.chdir(bai_directory)
-    else:
-        os.makedirs(bai_directory)
-        os.chdir(bai_directory)
     my_env = os.environ.copy()
     my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/"
 
@@ -178,8 +158,6 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode
     except:
         pass
 
-    os.chdir("../../../")
-
     if mpileup is None:
         return "FAILED"
 
@@ -247,9 +225,9 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode
 
     if bamType == "Amazon AWS":
         # Clear temporary files and name a new one
-        os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;")
+        os.system("find /var/www/html/eFP-Seq_Browser/temp/* -mtime +1 -exec rm -f {} \\;")
 
-    tempfile = "../temp/RNASeqGraph.png"
+    tempfile = "/var/www/html/eFP-Seq_Browser/temp/RNASeqGraph.png"
     # Output the GD image to temp PNG file
     f = open(tempfile, "wb")
     rnaseq_graph_image.save(f)
@@ -263,7 +241,7 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode
 
 
 ################################################################################
-# Ouput functions
+# Output functions
 ################################################################################
 # Error function
 def dumpError(result, locus=None, record=None, my_base64img=None, abs_fpkm=None, r=None, totalReadsMapped=None):
@@ -401,63 +379,16 @@ def main():
             expectedGeneLength.append(exonGeneLength)
 
         # Public datasets and their directories:
+        # There are no public record as of Sep 2025
         publicDatapoints = {
-            'aerial': ['ERR274310', 'SRR547531', 'SRR548277', 'SRR847503', 'SRR847504', 'SRR847505', 'SRR847506'],
-            'carpel': ['SRR1207194', 'SRR1207195'],
-            'dark': ['SRR1019436', 'SRR1019437', 'SRR1049784', 'SRR477075', 'SRR477076', 'SRR493237', 'SRR493238'],
-            'flower': ['SRR314815', 'SRR800753', 'SRR800754'],
-            'Klepikova': ['SRR3581336', 'SRR3581345', 'SRR3581346', 'SRR3581347', 'SRR3581352', 'SRR3581356',
-                          'SRR3581383', 'SRR3581388', 'SRR3581499', 'SRR3581591', 'SRR3581639', 'SRR3581672',
-                          'SRR3581676', 'SRR3581678', 'SRR3581679', 'SRR3581680', 'SRR3581681', 'SRR3581682',
-                          'SRR3581683', 'SRR3581684', 'SRR3581685', 'SRR3581686', 'SRR3581687', 'SRR3581688',
-                          'SRR3581689', 'SRR3581690', 'SRR3581691', 'SRR3581692', 'SRR3581693', 'SRR3581694',
-                          'SRR3581695', 'SRR3581696', 'SRR3581697', 'SRR3581698', 'SRR3581699', 'SRR3581700',
-                          'SRR3581701', 'SRR3581702', 'SRR3581703', 'SRR3581704', 'SRR3581705', 'SRR3581706',
-                          'SRR3581707', 'SRR3581708', 'SRR3581709', 'SRR3581710', 'SRR3581711', 'SRR3581712',
-                          'SRR3581713', 'SRR3581714', 'SRR3581715', 'SRR3581716', 'SRR3581717', 'SRR3581719',
-                          'SRR3581720', 'SRR3581721', 'SRR3581724', 'SRR3581726', 'SRR3581727', 'SRR3581728',
-                          'SRR3581730', 'SRR3581731', 'SRR3581732', 'SRR3581733', 'SRR3581734', 'SRR3581735',
-                          'SRR3581736', 'SRR3581737', 'SRR3581738', 'SRR3581740', 'SRR3581831', 'SRR3581833',
-                          'SRR3581834', 'SRR3581835', 'SRR3581836', 'SRR3581837', 'SRR3581838', 'SRR3581839',
-                          'SRR3581840', 'SRR3581841', 'SRR3581842', 'SRR3581843', 'SRR3581844', 'SRR3581845',
-                          'SRR3581846', 'SRR3581847', 'SRR3581848', 'SRR3581849', 'SRR3581850', 'SRR3581851',
-                          'SRR3581852', 'SRR3581853', 'SRR3581854', 'SRR3581855', 'SRR3581856', 'SRR3581857',
-                          'SRR3581858', 'SRR3581859', 'SRR3581860', 'SRR3581861', 'SRR3581862', 'SRR3581863',
-                          'SRR3581864', 'SRR3581865', 'SRR3581866', 'SRR3581867', 'SRR3581868', 'SRR3581869',
-                          'SRR3581870', 'SRR3581871', 'SRR3581872', 'SRR3581873', 'SRR3581874', 'SRR3581875',
-                          'SRR3581876', 'SRR3581877', 'SRR3581878', 'SRR3581879', 'SRR3581880', 'SRR3581881',
-                          'SRR3581882', 'SRR3581883', 'SRR3581884', 'SRR3581885', 'SRR3581886', 'SRR3581887',
-                          'SRR3581888', 'SRR3581889', 'SRR3581890', 'SRR3581891', 'SRR3581892', 'SRR3581893',
-                          'SRR3581894', 'SRR3581895', 'SRR3581896', 'SRR3581897', 'SRR3581898', 'SRR3581899',
-                          'SRR3724649', 'SRR3724650', 'SRR3724651', 'SRR3724652', 'SRR3724663', 'SRR3724668',
-                          'SRR3724737', 'SRR3724739', 'SRR3724741', 'SRR3724768', 'SRR3724774', 'SRR3724778',
-                          'SRR3724782', 'SRR3724785', 'SRR3724786', 'SRR3724787', 'SRR3724798', 'SRR3724806',
-                          'SRR3724814', 'SRR3725446', 'SRR3725458', 'SRR3725471', 'SRR3725482', 'SRR3725493',
-                          'SRR3725503', 'SRR3725516', 'SRR3725527', 'SRR3725538', 'SRR3725550', 'SRR3725561',
-                          'SRR847501', 'SRR847502'],
-            'leaf': ['SRR1105822', 'SRR1105823', 'SRR1159821', 'SRR1159827', 'SRR1159837', 'SRR314813', 'SRR446027',
-                     'SRR446028', 'SRR446033', 'SRR446034', 'SRR446039', 'SRR446040', 'SRR446484', 'SRR446485',
-                     'SRR446486', 'SRR446487', 'SRR493036', 'SRR493097', 'SRR493098', 'SRR493101', 'SRR764885',
-                     'SRR924656', 'SRR934391', 'SRR942022'],
-            'light': ['SRR070570', 'SRR070571', 'SRR1001909', 'SRR1001910', 'SRR1019221', 'SRR345561', 'SRR345562',
-                      'SRR346552', 'SRR346553', 'SRR394082', 'SRR504179', 'SRR504180', 'SRR504181', 'SRR515073',
-                      'SRR515074', 'SRR527164', 'SRR527165', 'SRR584115', 'SRR584121', 'SRR584129', 'SRR584134',
-                      'SRR653555', 'SRR653556', 'SRR653557', 'SRR653561', 'SRR653562', 'SRR653563', 'SRR653564',
-                      'SRR653565', 'SRR653566', 'SRR653567', 'SRR653568', 'SRR653569', 'SRR653570', 'SRR653571',
-                      'SRR653572', 'SRR653573', 'SRR653574', 'SRR653575', 'SRR653576', 'SRR653577', 'SRR653578',
-                      'SRR797194', 'SRR797230', 'SRR833246'],
-            'pollen': ['SRR847501', 'SRR847502'],
-            'RAM': ['SRR1260032', 'SRR1260033', 'SRR1261509'],
-            'receptacle': ['SRR401413', 'SRR401414', 'SRR401415', 'SRR401416', 'SRR401417', 'SRR401418', 'SRR401419',
-                           'SRR401420', 'SRR401421'],
-            'root': ['ERR274309', 'SRR1046909', 'SRR1046910', 'SRR1524935', 'SRR1524938', 'SRR1524940', 'SRR314814'],
-            'SAM': ['SRR949956', 'SRR949965', 'SRR949988', 'SRR949989']
+
         }
 
         ### Generate BAM directory link
         bam_dir = ''  # Reset bam_dir value
         # Check if data is public or private dataset
         if cachedDatapoints:
+            # This won't work after Sep 2025
             for x in publicDatapoints:  # If public, find tissue (x) to create bam_dir
                 if record in publicDatapoints[x]:
                     bam_dir = x + '/' + record
@@ -472,80 +403,25 @@ def main():
             else:
                 bam_dir = "uploads" + "/unknownRecord_" + start_time
 
+        # Google Drive and Amazon AWS not longer works!
         bam_file = ''  # Reset bam_file value
-        if bamType == "Google Drive":
-            # Create a Google Drive mount point and muont the bam file.
-            uniqId = str(random.randint(1, 1000000))
-            try:
-                pid = subprocess.Popen(["perl", "gDriveMountFast.pl", remoteDrive, uniqId, bamfilename])
-            except:
-                sys.exit(1)
-
-            # Make S3FS filename here
-            bam_file = "/mnt/gDrive/" + remoteDrive + "_" + uniqId + "/" + bamfilename
-
-            # Wait unilt the file is ready, without locking up the system forever, locking system for five minutes
-            startTime = time.time()
-            while not (os.path.isfile(bam_file)):
-                # pass
-                currentTime = time.time()
-                if currentTime > (startTime + 300):
-                    subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-                    subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-                    dumpError("Mounting timed out", locus, record, base64img, abs_fpkm, r, totalReadsMapped)
-
-            # Now make a image using samtools
-            base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode,
-                                  remoteDrive, bamType)
-
-            if base64img == "FAILED":
-                base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode,
-                                      remoteDrive, bamType)
-                region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end)
-
-            if base64img == "FAILED":
-                base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive,
-                                      bamType)
-
-            if base64img == "FAILED":
-                subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-                subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-                dumpError("Failed to get data.", locus, record, base64img, abs_fpkm, r, totalReadsMapped)
-
-        elif bamType == "Amazon AWS":
-            # Make S3FS filename here
-            bam_file = "s3://" + remoteDrive
 
-            # Now make a image using samtools
-            base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode,
-                                  remoteDrive, bamType)
 
-            if base64img == "FAILED":
-                base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode,
-                                      remoteDrive, bamType)
-                region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end)
+        # Local
+        bam_file = remoteDrive
 
-            if base64img == "FAILED":
-                region = str(chromosome) + ":" + str(start) + "-" + str(end)
-                base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive,
-                                      bamType)
+        # Now make an image using samtools
+        base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode,
+                              remoteDrive, bamType)
 
-        else:
-            # Local
-            bam_file = remoteDrive
-
-            # Now make an image using samtools
-            base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode,
+        if base64img == "FAILED":
+            base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode,
                                   remoteDrive, bamType)
+            region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end)
 
-            if base64img == "FAILED":
-                base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode,
-                                      remoteDrive, bamType)
-                region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end)
-
-            if base64img == "FAILED":
-                region = str(chromosome) + ":" + str(start) + "-" + str(end)
-                base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive,
+        if base64img == "FAILED":
+            region = str(chromosome) + ":" + str(start) + "-" + str(end)
+            base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive,
                                       bamType)
 
         # Correct total reads mapped:
@@ -607,12 +483,6 @@ def main():
         # the same info would be there. So just pass that along instead of
         # making this call .. to speed things up
         # Set the environment
-        bai_directory = ("data/" + bam_dir)
-        if os.path.isdir(bai_directory):
-            os.chdir(bai_directory)
-        else:
-            os.makedirs(bai_directory)
-            os.chdir(bai_directory)
         my_env = os.environ
         my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/"
 
@@ -623,12 +493,11 @@ def main():
         except:
             dumpError("Unable to retrieve BAM data", locus, record, base64img, abs_fpkm, r, totalReadsMapped)
 
-        os.chdir("../../../")
 
         # Change this if FPKM is wrong for local data
-        if bamType == "local":
-            mapped_reads = lines.lower().count("\t" + chromosome + "\t")
-        else:
+        # Sep 2025
+        mapped_reads = lines.lower().count("\t" + chromosome + "\t")
+        if mapped_reads == 0:
             mapped_reads = lines.lower().count('chr')
 
         abs_fpkm = []
@@ -647,16 +516,6 @@ def main():
                 r_val = float(sp / (math.sqrt(ss_x[i] * ss_y)))
                 r.append(round(r_val, PRECISION))
 
-        if bamType == "Google Drive":
-            try:
-                subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-            except:
-                sys.stderr.write("Failed to unmount FUSE file system.")
-
-            try:
-                subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId])
-            except:
-                sys.stderr.write("Failed to delete FUSE mount point.")
 
         RNASeq_ReadsPerNucleotide = base64img[1]