chore(metadata): migrate agg MDS configs

preprod.healdata.org/manifest.json

@@ -1,7 +1,7 @@
 {
   "notes": [
     "This is the preprod environment manifest",
-    "That's all I have to say"
+    "That's all I have to say."
   ],
   "jenkins": {
     "autodeploy": "yes"
@@ -33,6 +33,10 @@
   "arborist": {
     "deployment_version": "2"
   },
+  "metadata": {
+    "USE_AGG_MDS": true,
+    "AGG_MDS_NAMESPACE": "healpreprod"
+  },
   "portal": {
     "GEN3_BUNDLE": "heal"
   },

preprod.healdata.org/metadata/aggregate_config.json

@@ -0,0 +1,379 @@
+{
+	"gen3_commons": {
+		"HEAL": {
+			"mds_url": "https://preprod.healdata.org",
+			"commons_url": "preprod.healdata.org"
+
+		},
+		"JCOIN": {
+			"mds_url": "https://jcoin.datacommons.io/",
+			"commons_url" : "jcoin.datacommons.io",
+			"columns_to_fields": {
+				"short_name": "name",
+				"full_name": "full_name",
+				"_subjects_count" : "_subjects_count",
+				"study_id" : "study_id",
+				"_unique_id" : "study_id",
+				"study_description" : "study_description"
+			}
+		}
+	},
+	"adapter_commons": {
+		"ICPSR": {
+			"mds_url": "https://www.icpsr.umich.edu/icpsrweb/neutral/oai/studies",
+			"commons_url": "https://www.icpsr.umich.edu",
+			"adapter": "icpsr",
+			"keep_original_fields": false,
+			"filters": {
+				"study_ids": [4256, 30122, 34945, 35197, 37887, 37833, 37842, 37841, 35197 ]
+			},
+			"field_mappings" : {
+				"tags": [],
+				"authz": "",
+				"sites": "",
+				"summary": {
+					"path":"description",
+					"filters": ["strip_html"]
+				},
+				"study_url" : {
+					"path":"ipcsr_study_id",
+					"filters": ["add_icpsr_source_url"]
+				},
+				"location": "path:coverage[0]",
+				"subjects": "",
+				"__manifest": "",
+				"study_name": "",
+				"study_type": "",
+				"institutions": "path:contributor",
+				"year_awarded": "",
+				"investigators": "path:creator",
+				"project_title": "path:title",
+				"protocol_name": "",
+				"study_summary": "",
+				"_file_manifest": "",
+				"dataset_1_type": "",
+				"dataset_2_type": "",
+				"dataset_3_type": "",
+				"dataset_4_type": "",
+				"dataset_5_type": "",
+				"project_number": "path:identifier",
+				"dataset_1_title": "",
+				"dataset_2_title": "",
+				"dataset_3_title": "",
+				"dataset_4_title": "",
+				"dataset_5_title": "",
+				"administering_ic": "",
+				"advSearchFilters": [],
+				"dataset_category": "path:type",
+				"research_program": "",
+				"research_question": "",
+				"study_description": "",
+				"clinical_trial_link": "",
+				"dataset_description": "",
+				"research_focus_area": "",
+				"dataset_1_description": "",
+				"dataset_2_description": "",
+				"dataset_3_description": "",
+				"dataset_4_description": "",
+				"dataset_5_description": "",
+				"data_availability": "pending"
+			},
+			"per_item_values" : {
+				"10.3886/ICPSR30122.v5": {
+					"__manifest": [
+						{
+							"md5sum": "7cf87ce47b91e3a766753222bc22d098",
+							"file_name": "TEDS-D-2018-DS0001-bndl-data-spss.zip",
+							"file_size": 69297783,
+							"object_id": "dg.XXXX/208f4c52-771e-409a-b810-4bcba3c03c51",
+							"commons_url": "externaldata.healdata.org"
+						}
+					],
+					"data_availability": "available"
+				}
+			}
+		},
+		"clinicaltrials": {
+			"mds_url": "https://clinicaltrials.gov/api/query/full_studies",
+			"commons_url": "http://clinicaltrials.gov",
+			"adapter": "clinicaltrials",
+			"filters": {
+				"term": "OUD",
+				"maxItems": 25
+			},
+			"keep_original_fields": false,
+			"field_mappings": {
+				"tags": [],
+				"authz": "/programs/open",
+				"sites": "",
+				"summary": "path:BriefSummary",
+				"study_url" : {
+					"path":"NCTId",
+					"filters": ["add_clinical_trials_source_url"]
+				},
+				"location": "",
+				"subjects": "path:EnrollmentCount",
+				"__manifest": "",
+				"study_name": "",
+				"study_type": "",
+				"institutions": "path:LeadSponsorName",
+				"year_awarded": "",
+				"investigators": "path:OverallOfficial[0].OverallOfficialName",
+				"project_title": "path:BriefTitle",
+				"protocol_name": "",
+				"study_summary": "",
+				"_file_manifest": "",
+				"dataset_1_type": "",
+				"dataset_2_type": "",
+				"dataset_3_type": "",
+				"dataset_4_type": "",
+				"dataset_5_type": "",
+				"project_number": "path:OrgStudyId",
+				"dataset_1_title": "",
+				"dataset_2_title": "",
+				"dataset_3_title": "",
+				"dataset_4_title": "",
+				"dataset_5_title": "",
+				"administering_ic": "",
+				"advSearchFilters": [],
+				"dataset_category": "",
+				"research_program": "",
+				"research_question": "",
+				"study_description": "",
+				"clinical_trial_link": "",
+				"dataset_description": "",
+				"research_focus_area": "",
+				"dataset_1_description": "",
+				"dataset_2_description": "",
+				"dataset_3_description": "",
+				"dataset_4_description": "",
+				"dataset_5_description": "",
+				"data_availability": "pending"
+			},
+			"per_item_values" : {
+			    "STU-2019-0743": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04059016?titles=Innovatively+Increasing+PCP+Prescribing+of+Buprenorphine%3A+Measurement+Based+Care+and+Integrated+Electronic+Solution&draw=2&rank=1"
+			    },
+				"1903499841": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03950492?titles=Feasibility+of+Deep+Brain+Stimulation+as+a+Novel+Treatment+for+Refractory+Opioid+Use+Disorder&draw=2&rank=1"
+				},
+				"2018-1-100-OUD": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03633929?titles=mHealth+for+Patient+Self-Management+of+Opioid+Use+Disorder&draw=2&rank=1"
+				},
+				"MHBB-010-17F": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03605342?titles=Optimal+Treatment+of+Veterans+With+PTSD+and+Comorbid+OUD&draw=2&rank=1"
+				},
+				"999920014": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04316559?titles=Biased+Opioid+Agonists+for+Treatment+of+Opioid+Withdrawal+in+OUD&draw=2&rank=1"
+				},
+				"2000026223": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04180020?titles=Coordinating+Opioid+Use+Treatment+Through+Medical+Management+With+Infection+Treatment+%28Project+COMMIT%29&draw=2&rank=1"
+				},
+				"2019-131-DCYF": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04901312?titles=Preventing+OUD+in+Justice-Involved+Youth&draw=2&rank=1"
+				},
+				"842717": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04401917?titles=FNOS+in+HIV+Subjects&draw=2&rank=1"
+				},
+				"HIC 2000023783": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03658642?titles=Clinical+Decision+Support+to+Implement+ED-initiated+Buprenorphine+for+OUD&draw=2&rank=1"
+				},
+				"MS057": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04027166?titles=Cognitive+Function+and+Pain+Threshold+in+People+Who+Are+Methadone+Maintained&draw=2&rank=1"
+				},
+				"2000028548(2000027149)": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04253782?titles=SafetyNet+Program+for+Opioid+Use+Disorder+%28OUD%29&draw=2&rank=1"
+				},
+				"CBOTDA049616": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04850664?titles=Computerized+Chemosensory-Based+Orbitofrontal+Cortex+%28CBOT%29+for+Opioid+Use+Disorder&draw=2&rank=1"
+				},
+				"CTN - 0095": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04198428?titles=Clinical+Decision+Support+for+Opioid+Use+Disorders+in+Medical+Settings+%28COMPUTE+2.0%29&draw=2&rank=1"
+				},
+				"2020P002928": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04759703?titles=Treatment+of+Restless+Legs+Symptoms+With+Pramipexole+to+Improve+the+Outcomes+of+Protracted+Opioid+Withdrawal+in+OUD&draw=2&rank=1"
+				},
+				"NIDA CTN 0098A": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04345718?titles=EXHIT+ENTRE+Comparative+Effectiveness+Trial&draw=2&rank=1"
+				},
+				"STUDY20060069": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04888962?titles=Quantitative+Sensory+Psychophysical+Correlates+of+Pain+in+Pregnant+Women+With+OUD&draw=2&rank=1"
+				},
+				"UF1MH121944": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04245423?titles=The+Whole+Health+Study%3A+Collaborative+Care+for+OUD+and+Mental+Health+Conditions&draw=1&rank=1"
+				},
+				"0076-ot": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03559179?titles=Clinical+Decision+Support+for+Opioid+Use+Disorders+in+Medical+Settings%3A+Usability+Testing+in+an+EMR&draw=2&rank=1"
+				},
+				"1906002463": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04240093?titles=CoMBAT+Opioid+Use+Disorder&draw=2&rank=1"
+				},
+				"2000030168": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04982627?titles=A+Brief+Negotiation+Interview+Chatbot+to+Improve+Buprenorphine+Engagement+Among+Justice-Involved+Individuals&draw=2&rank=1"
+				},
+				"CTN-0074": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT03407638?titles=PRimary+Care+Opioid+Use+Disorders+Treatment+%28PROUD%29+Trial&draw=2&rank=1"
+				},
+				"OUD001": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04197921?titles=Exablate+for+LIFU+Neuromodulation+in+Patients+With+Opioid+Use+Disorder+%28OUD%29&draw=2&rank=1"
+				},
+				"2000027031": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04240392?titles=Treatment+of+Pregnant+Women+With+OUD&draw=2&rank=1"
+				},
+				"A20-042": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04939727?titles=Suicide+Prediction+and+Prevention+for+People+at+Risk+for+Opioid+Use+Disorder%3A+Supplement+to+COMPUTE+2.0&draw=2&rank=1"
+				},
+				"2019B0287": {
+					"data_availability": "pending",
+					"authz": "/programs/open",
+					"source_url": "https://clinicaltrials.gov/ct2/show/NCT04135703?titles=Prevention+of+OUD%3A+The+HOME+Project+%28Housing%2C+Opportunities%2C+Motivation+and+Engagement%29&draw=2&rank=1"
+				}
+			}
+
+		},
+		"PDAPS": {
+			"mds_url": "https://api.monqcle.com/",
+			"commons_url": "https://externaldata.healprod.org",
+			"adapter": "pdaps",
+			"filters": {
+				"datasets": [
+					"laws-regulating-administration-of-naloxone",
+					"drug-induced-homicide",
+					"civil-commitment-for-substance-users",
+					"medicaid-funded-mat-for-justice-involved-persons",
+					"medication-assisted-treatment-in-correctional-facilities",
+					"direct-dispensing-of-controlled-substances-laws",
+					"opioid-prescribing-guidelines-for-acute-and-emergency-care",
+					"pain-management-clinic-laws",
+					"medication-assisted-treatment-licensure-and-operations"
+				]
+			},
+			"keep_original_fields": false,
+			"field_mappings": {
+				"tags": [],
+				"authz": "",
+				"sites": "",
+				"summary": {
+					"path":" preview[0].description",
+					"filters": ["strip_html"]
+				},
+				"location": "United States",
+				"subjects": "",
+				"__manifest": "",
+				"study_name": "",
+				"study_type": "",
+				"institutions": "Temple University",
+				"year_awarded": "",
+				"investigators": "path:preview[0].created_by",
+				"project_title": "path:preview[0].title",
+				"protocol_name": "",
+				"study_summary": { "path":" preview[0].description", "filters": ["strip_html"] },
+				"_file_manifest": "",
+				"dataset_1_type": "Data",
+				"dataset_2_type": "Codebook",
+				"dataset_3_type": "Protocol",
+				"dataset_4_type": "Final report",
+				"dataset_5_type": "",
+				"project_number": "path:display_id",
+				"dataset_1_title": "path:preview[0].data_data",
+				"dataset_2_title": "path:preview[0].data_codebook",
+				"dataset_3_title": "path:preview[0].data_protocol",
+				"dataset_4_title": "path:preview[0].final_report",
+				"dataset_5_title": "",
+				"administering_ic": "NIDA",
+				"advSearchFilters": [],
+				"dataset_category": "",
+				"research_program": "",
+				"research_question": "",
+				"study_description": "",
+				"clinical_trial_link": "",
+				"dataset_description": "",
+				"research_focus_area": "",
+				"dataset_1_description": "",
+				"dataset_2_description": "",
+				"dataset_3_description": "",
+				"dataset_4_description": "",
+				"dataset_5_description": "",
+				"data_availability": "pending"
+			},
+			"per_item_values": {
+				"57b45d83d6c9e7e8693ccdfd": {
+					"__manifest": [
+						{
+							"md5sum": "40dcac42435d323ebdb92d615f42d0c3",
+							"file_name": "Naloxone_Data_09112020.xlsx",
+							"file_size": 88921,
+							"object_id": "dg.XXXX/77045ea3-595b-4846-9ad0-6d48fe476925",
+							"commons_url": "externaldata.healdata.org"
+						},
+						{
+							"md5sum": "93b6b346a400978cde37ab8d778d6412",
+							"file_name": "20180810_Good_Samaritan_Law_Stat_Data.xlsx",
+							"file_size": 24100,
+							"object_id": "dg.XXXX/065cf957-505e-4bf4-929e-c2327742bae1",
+							"commons_url": "externaldata.healdata.org"
+						},
+						{
+							"md5sum": "19ed44f408f221a7af860821c796972a",
+							"file_name": "20170216-RM-Stat-Data.xlsx",
+							"file_size": 36710,
+							"object_id": "dg.XXXX/c3489b65-e8b7-42ac-9a74-2b19e034ce5a",
+							"commons_url": "externaldata.healdata.org"
+						}
+					],
+					"data_availability": "available",
+					"authz": "/programs/open",
+					"study_url": "https://pdaps.org/datasets/laws-regulating-administration-of-naloxone-1501695139"
+				}
+			}
+		}
+	}
+}