Put filepaths

src/dissectBCL/drHouse.py

@@ -142,7 +142,11 @@ def initClass(
     muxDF = pd.read_csv(muxPath)
     totalReads = int(muxDF['# Reads'].sum())
     if len(muxDF[muxDF['SampleID'] == 'Undetermined']) == 1:
-        undReads = int(muxDF[muxDF['SampleID'] == 'Undetermined']['# Reads'])
+        undReads = int(
+            muxDF[
+                muxDF['SampleID'] == 'Undetermined'
+            ]['# Reads'].iloc[0]
+        )
     else:
         undDic = dict(
             muxDF[

src/wd40/release.py

@@ -1,45 +1,33 @@
 import os
+import requests
+from subprocess import check_output
 import sys
 import glob
 from pathlib import Path
 from rich import print
 
 
 def fetchLatestSeqDir(pref, PI, postfix):
-    globStr = os.path.join(
-        pref,
-        PI,
-        postfix + '*'
-    )
+    globStr = os.path.join(pref, PI, postfix + "*")
     if len(glob.glob(globStr)) == 1:
         return glob.glob(globStr)[0]
     else:
         maxFolder = 0
-        for seqDir in glob.glob(
-            os.path.join(
-                pref,
-                PI,
-                postfix + '*'
-            )
-        ):
+        for seqDir in glob.glob(os.path.join(pref, PI, postfix + "*")):
             try:
                 seqInt = int(seqDir[-1])
             except ValueError:
                 seqInt = 0
                 continue
             if seqInt > maxFolder:
                 maxFolder = seqInt
-        return (os.path.join(
-            pref,
-            PI,
-            postfix + str(maxFolder)
-        ))
+        return os.path.join(pref, PI, postfix + str(maxFolder))
 
 
 def fetchFolders(flowcellPath, piList, prefix, postfix):
     institute_PIs = piList
     flowcellPath = os.path.abspath(flowcellPath)
-    FID = flowcellPath.split('/')[-1]
+    FID = flowcellPath.split("/")[-1]
     projDic = {}
     try:
         int(FID[:6])
@@ -48,33 +36,26 @@ def fetchFolders(flowcellPath, piList, prefix, postfix):
         sys.exit(
             "First 6 digits of flowcellpath don't convert to an int. Exiting."
         )
-    for projF in glob.glob(
-        os.path.join(
-            flowcellPath,
-            'Project_*'
-        )
-    ):
-        proj = projF.split('/')[-1]
+    for projF in glob.glob(os.path.join(flowcellPath, "Project_*")):
+        proj = projF.split("/")[-1]
         PI = proj.split("_")[-1].lower()
-        if PI == 'cabezas-wallscheid':
-            PI = 'cabezas'
+        if PI == "cabezas-wallscheid":
+            PI = "cabezas"
         if PI in institute_PIs:
             seqFolder = fetchLatestSeqDir(prefix, PI, postfix)
-            if os.path.exists(
-                os.path.join(seqFolder, FID)
-            ):
+            if os.path.exists(os.path.join(seqFolder, FID)):
                 projDic[proj] = [
-                    PI + 'grp',
+                    PI + "grp",
                     [
                         os.path.join(seqFolder, FID),
                         os.path.join(seqFolder, FID, proj),
-                        os.path.join(seqFolder, FID, 'FASTQC_' + proj),
+                        os.path.join(seqFolder, FID, "FASTQC_" + proj),
                         os.path.join(
                             seqFolder,
                             FID,
-                            'Analysis_' + proj.replace('Project_', '')
-                        )
-                    ]
+                            "Analysis_" + proj.replace("Project_", ""),
+                        ),
+                    ],
                 ]
             else:
                 print(
@@ -107,12 +88,8 @@ def release_folder(grp, lis):
     succes_fqc = release_rights(fastqcF, grp)
     if os.path.exists(analysisF):
         succes_analysis = release_rights(analysisF, grp)
-        return (
-            [succes_project, succes_fqc, succes_analysis]
-        )
-    return (
-        [succes_project, succes_fqc]
-    )
+        return [succes_project, succes_fqc, succes_analysis]
+    return [succes_project, succes_fqc]
 
 
 def release_rights(F, grp):
@@ -122,10 +99,7 @@ def release_rights(F, grp):
     for r, dirs, files in os.walk(F):
         for d in dirs:
             try:
-                os.chmod(
-                    os.path.join(r, d),
-                    0o750
-                )
+                os.chmod(os.path.join(r, d), 0o750)
                 changed += 1
             except PermissionError:
                 print("Permission error for {}".format(d))
@@ -136,10 +110,7 @@ def release_rights(F, grp):
                 if grp != Path(fil).group():
                     grouperror = True
                 try:
-                    os.chmod(
-                        fil,
-                        0o750
-                    )
+                    os.chmod(fil, 0o750)
                     changed += 1
                 except PermissionError:
                     print("Permission error for {}".format(f))
@@ -151,37 +122,75 @@ def release_rights(F, grp):
                 F
             )
         )
-    return (successRate)
+    return successRate
 
 
-def rel(flowcellPath, piList, prefix, postfix):
-    projDic = fetchFolders(
-        flowcellPath,
-        piList,
-        prefix,
-        postfix
-    )
+def rel(
+    flowcellPath,
+    piList,
+    prefix,
+    postfix,
+    parkourURL,
+    parkourAuth,
+    parkourCert,
+    fexBool,
+    fromAddress,
+):
+    projDic = fetchFolders(flowcellPath, piList, prefix, postfix)
     print("Print number of changed/(changed+unchanged)!")
     for proj in projDic:
-        '''
+        """
         every projDic[proj] is a nested list of:
         [grp, [flowcell, project, fastqc]]
-        '''
+        """
         successes = release_folder(projDic[proj][0], projDic[proj][1])
         if len(successes) == 2:
             print(
                 "[green]Project[/green] {},{} proj,{} fqc".format(
-                    proj,
-                    successes[0],
-                    successes[1]
+                    proj, successes[0], successes[1]
                 )
             )
         else:
             print(
                 "[green]Project[/green] {},{} proj,{} fqc,{} analysis".format(
-                    proj,
-                    successes[0],
-                    successes[1],
-                    successes[2]
+                    proj, successes[0], successes[1], successes[2]
                 )
             )
+        projectPath = projDic[proj][1][1].split("/")[-1]
+        PI = (
+            projectPath.split("_")[-1]
+            .lower()
+            .replace("cabezas-wallscheid", "cabezas")
+        )
+        d = None
+        if PI in piList:
+            d = {
+                "data": projDic[proj][1][1],
+                "metadata": projDic[proj][1][1] + "/multiqc_report.html",
+            }
+        elif fexBool:
+            fexList = (
+                check_output(["fexsend", "-l", fromAddress])
+                .decode("utf-8")
+                .replace("\n", " ")
+                .split(" ")
+            )
+            tar_lane, tar_proj = projDic[proj][1][1].split("/")[-2:]
+            tarBall = tar_lane + "_" + tar_proj + ".tar"
+            if tarBall in fexList:
+                d = {"data": tarBall, "metadata": None}
+            else:
+                print("fexLink: ", tarBall, " not found!")
+        if d:
+            print(
+                "Adding filepaths to Parkour2:",
+                requests.post(
+                    parkourURL
+                    + "/api/requests/"
+                    + proj.split("_")[1]
+                    + "/put_filepaths/",
+                    auth=parkourAuth,
+                    data=d,
+                    verify=parkourCert,
+                ),
+            )  # print the returned answer from the API

src/wd40/wd40.py

@@ -73,6 +73,14 @@ def cli(ctx, configpath, debug):
     ctx.obj['postfixDir'] = cnf['Internals']['seqDir']
     ctx.obj['fastqDir'] = cnf['Dirs']['outputDir']
     ctx.obj['solDir'] = cnf['Dirs']['baseDir']
+    ctx.obj['parkourURL'] = cnf['parkour']['URL']
+    ctx.obj['parkourAuth'] = (
+                            cnf['parkour']['user'],
+                            cnf['parkour']['password']
+                            )
+    ctx.obj['parkourCert'] = cnf['parkour']['cert']
+    ctx.obj['fexBool'] = cnf['Internals'].getboolean('fex')
+    ctx.obj['fromAddress'] = cnf['communication']['fromAddress']
 
 
 @cli.command()
@@ -88,7 +96,12 @@ def rel(ctx, flowcell):
         flowcell,
         ctx.obj['piList'],
         ctx.obj['prefixDir'],
-        ctx.obj['postfixDir']
+        ctx.obj['postfixDir'],
+        ctx.obj['parkourURL'],
+        ctx.obj['parkourAuth'],
+        ctx.obj['parkourCert'],
+        ctx.obj['fexBool'],
+        ctx.obj['fromAddress']
     )