updated tool script

Author: jeevangelista

script/ingestion/s3_update.py

@@ -36,9 +36,9 @@ def backup_file(df, suffix, include_index=True, quoting=True):
 	s_buf = io.StringIO()
 	# df.to_csv(s_buf, header=True, sep="\t")
 	# print(s_buf.read())
-	if include_index:
+	if include_index and quoting:
 		df.to_csv(s_buf, header=True, sep="\t")
-	elif not quoting:
+	elif not quoting and include_index:
 		df.to_csv(s_buf, header=True, sep="\t", quoting=csv.QUOTE_NONE)
 	else:
 		df.to_csv(s_buf, header=True, sep="\t",  index=None)

script/ingestion/tools.py

@@ -7,6 +7,7 @@
 from ingest_common import connection
 import io
 import csv
+import json
 publication_df = pd.read_csv('https://cfde-drc.s3.amazonaws.com/database/files/current_publications.tsv', sep="\t", index_col=0)
 publication_mapper = {}
 for i, row in publication_df.iterrows():
@@ -31,8 +32,11 @@
 						doi = v.replace("https://doi.org/", "")
 						pub_id = publication_mapper[doi]
 						publication_df.at[pub_id, 'tool_id'] = uid
-				elif k not in ["layout", "id"]:
+				elif k not in ["layout", "id", "tutorial"]:
 					val[k] = v
+				elif k == "tutorial":
+					val[k] = json.dumps(v)
+					print(val[k], type(v))
 
 			tools[uid] = val
 

src/pages/tools/GDLPA.md

@@ -6,8 +6,9 @@ label: GDLPA
 layout: '@/layouts/Tools.astro'
 short_description: Query 53 gene-centric, 18 variant-centric, and 19 drug-centric
   repositories
-tutorial: '[  "https://www.youtube.com/watch?v=eO9zsT6Tyzk",  "https://www.youtube.com/watch?v=up8WY7N44ws"
-  ]'
+tutorial: 
+  - https://www.youtube.com/watch?v=eO9zsT6Tyzk
+  - https://www.youtube.com/watch?v=up8WY7N44ws
 url: https://cfde-gene-pages.cloud/
 ---
 Gene and Drug Landing Page Aggregator (GDLPA) has links to 53 gene, 18 variant and 19 drug repositories that provide direct links to gene and drug landing pages. You can search by gene or drug name and then choose the sites that contain knowledge about your gene or drug of interest. Resources supported by the NIH Common Fund are listed first and have the CFDE logo at their top right corner.

src/pages/tools/GeneSetCart.md

@@ -7,7 +7,8 @@ layout: '@/layouts/Tools.astro'
 short_description: GeneSetCart is interactive web-based application that enables users
   to fetch gene sets, augment, perform set operations, visualize, and analyze gene
   sets in a single session.
-tutorial: '[ "https://www.youtube.com/watch?v=yp0pfpJt1_M" ]'
+tutorial:
+  - https://www.youtube.com/watch?v=yp0pfpJt1_M
 url: https://genesetcart.cfde.cloud/
 doi: https://doi.org/10.1093/gigascience/giaf025
 ---

src/pages/tools/Playbook Workflow Builder.md

@@ -5,8 +5,9 @@ image: /img/pwb-screenshot.png
 label: Playbook Workflow Builder
 layout: '@/layouts/Tools.astro'
 short_description: Web-based platform to construct biomedical workflows
-tutorial: '[  "https://www.youtube.com/watch?v=xfnaNJL5-8c",  "https://www.youtube.com/watch?v=k_3wLDWDj8M"
-  ]'
+tutorial:
+  - https://www.youtube.com/watch?v=xfnaNJL5-8c
+  - https://www.youtube.com/watch?v=k_3wLDWDj8M
 url: https://playbook-workflow-builder.cloud/
 doi: https://doi.org/10.1371/journal.pcbi.1012901
 ---

src/pages/tools/ReproTox-KG.md

@@ -6,8 +6,9 @@ image: /img/reprotox-kg-screenshot.png
 label: ReproTox-KG
 layout: '@/layouts/Tools.astro'
 short_description: Toxicology knowledge graph for structural birth defects
-tutorial: '[ "https://www.youtube.com/watch?v=Gt3CCsvTppc", "https://www.youtube.com/watch?v=nqzDOsDFJ7g"
-  ]'
+tutorial: 
+  - https://www.youtube.com/watch?v=Gt3CCsvTppc
+  - https://www.youtube.com/watch?v=nqzDOsDFJ7g
 url: https://maayanlab.cloud/reprotox-kg
 ---
 To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes.