full path on submit job for cron

Zooniverse/cron.txt

@@ -0,0 +1,14 @@
+# Cron job for weekly runs on the HiPerGator
+# This is currently running under ethanwhite's account on daemon2
+# To recreate copy, paste, and modify this text into the editor resulting
+# from `crontab -e`
+# WEECOLOGYDEPLOYGITHUBPAT needs to be replaced with the appropriate GITHUB
+# Personal Access Token
+# cron jobs on HiPerGator run from a blank environment so we need to set both
+# basic environmental variables (HOME and PATH) and also the GitHub tokens
+# because they are not loaded into the cronjob environment
+
+HOME=/home/b.weinstein/
+PATH=/opt/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/home/b.weinstein/bin
+[email protected]
+15 15 * * * sbatch ${HOME}/EvergladesWadingBird/Zooniverse/submit_job.sbatch >> ${HOME}/logs/cron.log 2>&1

Zooniverse/manifest.py

@@ -116,7 +116,7 @@ def main(path, everglades_watch, save_dir="/orange/ewhite/everglades/Zooniverse/
             assert os.path.exists(saved_file)
             uploaded = uploaded.path.append(pd.Series({"path":saved_file}),ignore_index=True)
         except Exception as e:
-            print("{} failed with exception".format(path))
+            print("{} failed with exception {e}".format(path, e))
 
     #Overwrite uploaded manifest
     uploaded.to_csv("uploaded.csv")

Zooniverse/submit_job.sbatch

@@ -16,4 +16,4 @@ source activate everglades
 rclone sync everglades:"WadingBird2020Deliverables" /orange/ewhite/everglades/WadingBirds2020/
 
 #Upload
-python manifest.py
+python /home/b.weinstein/EvergladesWadingBird/Zooniverse/manifest.py

Zooniverse/tests/submit_test.sbatch

@@ -0,0 +1,17 @@
+#test connect in sbatch
+#!/bin/bash
+#SBATCH --job-name=Everglades_rclone   # Job name
+#SBATCH --mail-type=END               # Mail events
+#SBATCH [email protected]  # Where to send mail
+#SBATCH --account=ewhite
+#SBATCH --nodes=1                 # Number of MPI ranks
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=10GB
+#SBATCH --time=72:00:00       #Time limit hrs:min:sec
+#SBATCH --output=/home/b.weinstein/logs/rclone_%j.out   # Standard output and error log
+#SBATCH --error=/home/b.weinstein/logs/rclone_%j.err
+
+#comet debug
+
+#Sync data
+python tests/test_connect.py

Zooniverse/zooniverse.wpu

@@ -6,8 +6,8 @@
 [user attributes]
 debug.exceptions-ignored = {loc('../../../miniconda3/envs/crowns/lib/python3.7/site-packages/_pytest/config/__init__.py'): {1130: True}}
 guimgr.overall-gui-state = {'windowing-policy': 'combined-window',
-                            'windows': [{'name': 'P17d1M9PDrDDNBOIKLr7d7agln'\
-        'JSlCRG',
+                            'windows': [{'name': 'LfPD5D2a8ynAK2sybEe3c4A0IQ'\
+        'zTXQPX',
         'size-state': '',
         'type': 'dock',
         'view': {'area': 'tall',
@@ -149,42 +149,22 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window',
                       'wide',
                       1,
                       {})],
-        'primary_view_state': {'editor_states': ({'bookmarks': ([[loc('manifest.py'),
-        {'attrib-starts': [],
-         'first-line': 0L,
-         'folded-linenos': [],
-         'sel-line': 3L,
-         'sel-line-start': 48L,
-         'selection_end': 68L,
-         'selection_start': 48L,
-         'zoom': 0L},
-        1584653319.210618]],
-        1),
-        'current-loc': loc('submit_job.sbatch'),
+        'primary_view_state': {'editor_states': ({'bookmarks': ([],
+        0),
+        'current-loc': loc('manifest.py'),
         'editor-state-list': [(loc('manifest.py'),
                                {'attrib-starts': [],
-                                'first-line': 0L,
+                                'first-line': 113L,
                                 'folded-linenos': [],
-                                'sel-line': 3L,
-                                'sel-line-start': 48L,
-                                'selection_end': 68L,
-                                'selection_start': 48L,
-                                'zoom': 0L}),
-                              (loc('submit_job.sbatch'),
-                               {'attrib-starts': [],
-                                'first-line': 0L,
-                                'folded-linenos': [],
-                                'sel-line': 10L,
-                                'sel-line-start': 451L,
-                                'selection_end': 469L,
-                                'selection_start': 469L,
+                                'sel-line': 121L,
+                                'sel-line-start': 3768L,
+                                'selection_end': 3803L,
+                                'selection_start': 3803L,
                                 'zoom': 0L})],
         'has-focus': True,
         'locked': False},
-        [loc('manifest.py'),
-         loc('submit_job.sbatch')]),
-                               'open_files': [u'manifest.py',
-        u'submit_job.sbatch']},
+        [loc('manifest.py')]),
+                               'open_files': [u'manifest.py']},
         'saved_notebook_display': None,
         'split_percents': {0: 0.5},
         'splits': 2,
@@ -195,12 +175,12 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window',
                  'splits': 2,
                  'tab_location': 'left',
                  'user_data': {}},
-        'window-alloc': (0,
+        'window-alloc': (20,
                          23,
-                         1418,
+                         1414,
                          877)}]}
-guimgr.recent-documents = [loc('submit_job.sbatch'),
-                           loc('manifest.py')]
+guimgr.recent-documents = [loc('manifest.py'),
+                           loc('submit_job.sbatch')]
 guimgr.visual-state = {loc('upload.sh'): {'attrib-starts': [],
         'first-line': 0L,
         'folded-linenos': [],