updated outreach

Author: jeevangelista

script/ingestion/outreach.py

@@ -15,13 +15,24 @@
 for k,v in dccs.iterrows():
 	dcc_mapper[v["short_label"]] = k
 
-outreach_columns = ["title", "short_description", "description", "tags", "agenda", "featured", "active", "start_date", "end_date", "application_start", "application_end", "link", "image", "carousel", "carousel_description", "cfde_specific", "flyer"]
+centers = pd.read_csv('https://cfde-drc.s3.amazonaws.com/database/files/current_centers.tsv', sep="\t", index_col=0, header=0)
+# map dcc names to their respective ids
+center_mapper = {}
+for k,v in centers.iterrows():
+	center_mapper[v["short_label"]] = k
+
+
+outreach_columns = ["title", "short_description", "description", "tags", "agenda", "featured", "active", "start_date", "end_date", "application_start", "application_end", "link", "image", "carousel", "carousel_description", "cfde_specific", "flyer", "recurring", "ical", "schedule"]
 dcc_outreach_columns = ["outreach_id", "dcc_id"]
+center_outreach_columns = ["outreach_id", "center_id"]
 
 outreach_df = pd.DataFrame("-", index=[], columns=outreach_columns)
 outreach_df.index.name = 'id'
 dcc_outreach_df = pd.DataFrame("-", index=[], columns=dcc_outreach_columns)
 ind = 0
+
+center_outreach_df = pd.DataFrame("-", index=[], columns=center_outreach_columns)
+cind = 0
 outreach_df = outreach_df.fillna('')
 
 for filename in glob('../../src/pages/outreach/*.md'):
@@ -51,6 +62,12 @@
 					dcc_id = dcc_mapper[dcc]
 					dcc_outreach_df.loc[ind] = [uid, dcc_mapper[dcc]]
 					ind += 1
+			if val.get('center'):
+				for center in val["center"]:
+					center_id = center_mapper[center]
+					center_outreach_df.loc[cind] = [uid, center_mapper[center]]
+					cind += 1
+
 
 # webinars
 webinars = {}
@@ -79,16 +96,22 @@
 outreach_df['active'] = outreach_df['active'].fillna(0).astype(bool)
 outreach_df['featured'] = outreach_df['featured'].fillna(0).astype(bool)
 outreach_df['carousel'] = outreach_df['carousel'].fillna(0).astype(bool)
+outreach_df['recurring'] = outreach_df['recurring'].fillna(0).astype(bool)
 outreach_df['cfde_specific'] = outreach_df['cfde_specific'].fillna(0).astype(bool)
 backup_file(outreach_df, "outreach", quoting=False)
 backup_file(dcc_outreach_df, "dcc_outreach", False)
+backup_file(center_outreach_df, "center_outreach", False)
 
 cur = connection.cursor()
 
 cur.execute('''
   DELETE FROM dcc_outreach;
 ''')
 
+cur.execute('''
+  DELETE FROM center_outreach;
+''')
+
 cur.execute('''
   DELETE FROM outreach;
 ''') 
@@ -146,6 +169,34 @@
     ;
   ''')
 cur.execute('drop table dcc_outreach_tmp;')
+
+# centers
+
+cur = connection.cursor()
+cur.execute('''
+  create table center_outreach_tmp
+  as table center_outreach
+  with no data;
+''')
+c_buf = io.StringIO()
+center_outreach_df.to_csv(c_buf, header=True, sep="\t", index=None)
+c_buf.seek(0)
+columns = next(c_buf).strip().split('\t')
+cur.copy_from(c_buf, 'center_outreach_tmp',
+	columns=center_outreach_columns,
+	null='',
+	sep='\t',
+)
+
+cur.execute('''
+    insert into center_outreach (outreach_id, center_id)
+      select outreach_id, center_id
+      from center_outreach_tmp
+      on conflict 
+        do nothing
+    ;
+  ''')
+cur.execute('drop table center_outreach_tmp;')
 connection.commit()
 
 print("Ingested outreach and webinars")

src/pages/outreach/Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science 2025-02-01.md

@@ -5,7 +5,6 @@ carousel: true
 cfde_specific: true
 dcc:
 - LINCS
-end_date: '2025-02-01T17:00:00-04:00'
 featured: true
 image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/Maayan_program.png
 layout: '@/layouts/Outreach.astro'
@@ -17,7 +16,7 @@ short_description: "The LINCS DCC Summer Research Training Program in Biomedical
   \ in the areas: data harmonization, machine learning, cloud computing, and dynamic\
   \ data visualization. <br/><br /> Application Deadline: February 1, 2025 <br />Program\
   \ Dates: June 2, 2025 \u2013 August 8, 2025 "
-start_date: '2024-10-01T12:00:00-05:00'
+application_start: '2024-10-01T12:00:00-05:00'
 tags: '["training program", "application deadline"]'
 title: Accepting Application for the 2025 Summer Research Training Program in Biomedical
   Big Data Science

src/pages/outreach/CFDE Centers 2025-12-31.md

@@ -14,5 +14,7 @@ short_description: 'In this course the LINCS DCC covers computational methods in
 tags: '["course"]'
 title: 'Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and
   Integration Center'
+recurring: true
+start_date: '2025-04-30T00:00:00-04:00'
 ---
 In this course the LINCS DCC introduces the data generation centers that collected data for the LINCS program. Then, the course covers metadata and how metadata is linked to ontologies. The course then introduces data processing methods used to clean and harmonize the LINCS data. This is followed by discussions about how data is served as RESTful APIs. Most importantly, the course covers computational methods including: clustering, gene-set enrichment analysis, interactive data visualization, and supervised learning.

src/pages/outreach/CFDE Webinar Series 2025-01-23.md

@@ -11,6 +11,8 @@ link: https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc
 short_description: This 10h course introduces the HuBMAP project which aims to create
   an open, global reference atlas of the human body at the cellular level.
 tags: '["course"]'
+recurring: true
+start_date: '2020-08-04T00:00:00-04:00'
 title: HuBMAP Visible Human MOOC (VHMOOC)
 ---
 This 10h course introduces the HuBMAP project which aims to create an open, global reference atlas of the human body at the cellular level. Among others, the course describes the compilation and coverage of HuBMAP data, demonstrates new single-cell analysis and mapping techniques, and introduces major features of the HuBMAP portal.

src/pages/outreach/Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center.md

@@ -5,14 +5,16 @@ cfde_specific: false
 dcc:
 - MoTrPAC
 featured: false
-image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/MoTrPAC.png
+image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/motrpac-office-hours.png
 layout: '@/layouts/Outreach.astro'
 link: https://motrpac-data.org/
 short_description: The MoTrPAC Bioinformatics Center (BIC) hosts monthly open office
   hours to support the scientific community. Each session is hosted by one member
   from our infrastructure team and one from our bioinformatics team with a focus on
   the discussions of MoTrPAC data.
 tags: '["office hours"]'
+start_date: '2025-05-08T00:00:00-07:00'
 title: MoTrPAC Office Hours
+recurring: true
 ---
 The MoTrPAC Bioinformatics Center (BIC) hosts monthly open office hours to support the scientific community. Each session is hosted by one member from our infrastructure team and one from our bioinformatics team with a focus on the discussions of MoTrPAC data.

src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md

@@ -16,7 +16,9 @@ short_description: The webinar featured ARCHS, a resource that provides access
   to gene and transcript counts uniformly processed from all the human and mouse RNA-seq
   experiments deposited by the community in the NCBI Gene Expression Omnibus (GEO).
 start_date: '2025-02-27T14:00:00-05:00'
-tags: '["workshop"]'
+tags: '["webinar"]'
+center:
+- DRC
 title: 'Omics Tools Webinar Series: ARCHS4'
 ---
 The webinar featured [ARCHS4](https://maayanlab.cloud/archs4/), a resource that provides access to gene and transcript counts uniformly processed from all the human and mouse RNA-seq experiments deposited by the community in the NCBI Gene Expression Omnibus (GEO). Watch recording [here](https://www.youtube.com/watch?v=BSz4XWFmfkg).

src/pages/outreach/MoTrPAC Office Hours.md

@@ -10,7 +10,9 @@ image: /img/genesetcart_webinar.png
 layout: '@/layouts/Outreach.astro'
 link: https://mountsinai.zoom.us/webinar/register/WN_ZXBJyN0SRuCj5LaYoGeXuw#/registration
 short_description: In this lecture, Giacomo Marino, a Bioinformatics Software Engineer in the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai, describes a new platform for assembling, augmenting, combining, visualizing, and analyzing gene sets. The platform utilizes LLMs to form hypotheses from datasets produced by NIH Common Fund programs.
-tags: '["workshop"]'
+tags: '["webinar"]'
+center:
+- DRC
 title: 'Omics Tools Webinar Series: GeneSetCart
 '
 ---