Remove auto deploy from ci

.gitlab-ci.yml

@@ -16,8 +16,8 @@ build:
 deploy:
   script:
   - singularity run 'docker://monachus/hugo' hugo
-  - singularity run 'docker://monachus/hugo' hugo deploy aws --maxDeletes -1
-  - aws s3 ls s3://www.strandlab.net/ --recursive | awk '{cmd="aws s3api put-object-acl --acl bucket-owner-full-control --bucket www.strandlab.net --key "$4; system(cmd)}'
+  - ##singularity run 'docker://monachus/hugo' hugo deploy aws --maxDeletes -1
+  - ##aws s3 ls s3://www.strandlab.net/ --recursive | awk '{cmd="aws s3api put-object-acl --acl bucket-owner-full-control --bucket www.strandlab.net --key "$4; system(cmd)}'
   artifacts:
     paths:
     - public

data/repository/filters.json

-[
-    {"id": "disease", "parent": "#", "text": "Disease Phenotype",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
-    {"id": "disease.b", "parent":"disease", "text": "BPH"},
-    {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
-    {"id": "demographics", "parent": "#", "text": "Demographics",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
-    {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
-    {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
-    {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
-    {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
-    {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "age.40", "parent":"age", "text": "<40yo"},
-    {"id": "age.50", "parent":"age", "text": "41-50yo"},
-    {"id": "age.60", "parent":"age", "text": "51-60yo"},
-    {"id": "age.70", "parent":"age", "text": "61-70yo"},
-    {"id": "age.80", "parent":"age", "text": "71-80yo"},
-    {"id": "age.90", "parent":"age", "text": "81-90yo"},
-    {"id": "age.100", "parent":"age", "text": "91+yo"},
-    {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
-    {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
-    {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
-    {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
-    {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
-    {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
-    {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
-    {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
-    {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
-    {"id": "t2d.n", "parent":"t2d", "text": "No"},
-    {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
-    {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
-    {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
-    {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
-    {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
-    {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
-    {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
-    {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
-    {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
-    {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
-    {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
-    {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
-    {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
-    {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
-    {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
-    {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
-    {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
-    {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
-    {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
-    {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
-    {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
-    {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
-    {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
-    {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
-    {"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
-    {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+[
+    {"id": "disease", "parent": "#", "text": "Disease Phenotype",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
+    {"id": "disease.b", "parent":"disease", "text": "BPH"},
+    {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
+    {"id": "demographics", "parent": "#", "text": "Demographics",  "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
+    {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
+    {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
+    {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
+    {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
+    {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "age.40", "parent":"age", "text": "<40yo"},
+    {"id": "age.50", "parent":"age", "text": "41-50yo"},
+    {"id": "age.60", "parent":"age", "text": "51-60yo"},
+    {"id": "age.70", "parent":"age", "text": "61-70yo"},
+    {"id": "age.80", "parent":"age", "text": "71-80yo"},
+    {"id": "age.90", "parent":"age", "text": "81-90yo"},
+    {"id": "age.100", "parent":"age", "text": "91+yo"},
+    {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
+    {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
+    {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
+    {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
+    {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
+    {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
+    {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
+    {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
+    {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
+    {"id": "t2d.n", "parent":"t2d", "text": "No"},
+    {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
+    {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
+    {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
+    {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
+    {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
+    {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
+    {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
+    {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
+    {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
+    {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
+    {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
+    {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
+    {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
+    {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
+    {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
+    {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
+    {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
+    {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+    {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
+    {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
+    {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
+    {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
+    {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
+    {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
+    {"id": "repo.vd", "parent":"repo", "text": "Vas Deference"},
+    {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
 ]
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