From 56afa375bf391642f9b0b10503aa7d4b3f85eacf Mon Sep 17 00:00:00 2001 From: Ian Wright Date: Tue, 3 Nov 2020 11:10:33 +0000 Subject: [PATCH 1/3] Add an Int column to indicate if a person is a contact --- create_files.py | 8 +++++++- schema.sql | 19 +++---------------- settings_nosecrets | 4 ++-- 3 files changed, 12 insertions(+), 19 deletions(-) diff --git a/create_files.py b/create_files.py index a9de5fb..50d4c93 100755 --- a/create_files.py +++ b/create_files.py @@ -524,8 +524,14 @@ def getAlfStudyLdapPeople(ldapPeople, alfStudy, panoptesAlfStudyLdapPeopleGroups for p in alfStudyLdapPeople: if p['malariagenUID'] == malariagenUID: p['class'].append(group_type) + if group_type == 'Contact': + p['contact'] = '1' else: person['class'] = [group_type] + if group_type == 'Contact': + person['contact'] = '1' + else: + person['contact'] = '0' study_people[malariagenUID] = person alfStudyLdapPeople.append(person) @@ -568,4 +574,4 @@ def establishGSheetsCredentials(client_secret_path, credentials_path, auth_host_ return credentials -run() \ No newline at end of file +run() diff --git a/schema.sql b/schema.sql index a256211..af97a1f 100755 --- a/schema.sql +++ b/schema.sql @@ -90,6 +90,7 @@ CREATE TABLE "study_ldap_people" ( "study" Text, "twitterURL" Text, "uid" Text, + "contact" Int, PRIMARY KEY("uid", "study") ); @@ -134,6 +135,7 @@ CREATE TABLE "study_publications" ( ); CREATE TABLE "pf_samples" ( + "id" int, "ARTresistant" Text, "ASMQresistant" Text, "CQresistant" Text, @@ -188,6 +190,7 @@ CREATE TABLE "pf_samples" ( ); CREATE TABLE "gene_diff" ( + "id" Int, "gene_id" Text PRIMARY KEY, "gene_name" Text, "chrom" Text, @@ -229,19 +232,3 @@ ALTER TABLE "pf_drug_gene" ADD FOREIGN KEY ("drug_id") REFERENCES "pf_drugs" ("d ALTER TABLE "pf_drug_gene" ADD FOREIGN KEY ("gene_id") REFERENCES "pf_resgenes" ("gene_id"); ALTER TABLE "pf_resgenes" ADD FOREIGN KEY ("gene_id") REFERENCES "gene_diff" ("gene_id"); - -\COPY countries ("country_id", "lat", "lng", "name", "alpha_3_code", "geojson", "num_samples", "CQresistance", "PYRresistance", "SDXresistance", "MQresistance", "ARTresistance", "PPQresistance") FROM 'output/countries/data' DELIMITER E'\t' CSV HEADER; -\COPY gene_diff ("gene_id", "gene_name", "chrom", "start", "end", "global_differentiation_score", "local_differentiation_score", "distance_to_higher_local_diff_score") FROM 'output/gene_diff/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_drugs ("drug_id", "is_combination", "name", "short_description", "description") FROM 'output/pf_drugs/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_features ("feature_id", "name", "category", "description") FROM 'output/pf_features/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_featuretypes ("feature_id", "type_id", "description", "feature") FROM 'output/pf_featuretypes/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_regions ("region_id", "lat", "lng", "name", "description", "num_samples", "web_colour", "CQresistance", "PYRresistance", "SDXresistance", "MQresistance", "ARTresistance", "PPQresistance", "SPIPTpresistance", "ASMQresistance", "DHAPPQresistance", "HRP2deletion", "HRP3deletion", "HRP23deletion", "SPresistance", "geojson") FROM 'output/pf_regions/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_resgenes ("gene_id", "name", "long_name", "short_description", "description", "marker_name") FROM 'output/pf_resgenes/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_sites ("site_id", "lat", "lng", "name", "num_samples", "pf_region_id", "country_id", "CQresistance", "PYRresistance", "SDXresistance", "MQresistance", "ARTresistance", "PPQresistance", "SPIPTpresistance", "ASMQresistance", "DHAPPQresistance", "HRP2deletion", "HRP3deletion", "HRP23deletion", "SPresistance", "AnyHRPdeletion") FROM 'output/pf_sites/data' DELIMITER E'\t' CSV HEADER; -\COPY studies ("study", "study_number", "webTitle", "description") FROM 'output/studies/data' DELIMITER E'\t' CSV HEADER; -\COPY study_ldap_people ("study", "jobTitle1", "jobTitle2", "jobTitle3", "uid", "researchGateURL", "scholarURL", "twitterURL", "malariagenUID", "oProfile1", "oProfile2", "oProfile3", "ORCID", "sn", "mail", "givenName", "o1", "o2", "o3") FROM 'output/study_ldap_people/data' DELIMITER E'\t' CSV HEADER; -\COPY study_publications ("study", "doi", "name", "title", "citation", "pmid") FROM 'output/study_publications/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_drug_gene ("gene_id", "drug_id") FROM 'output/pf_drug_gene/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_drug_regions ("region_id", "drug_region_id", "text", "resistance", "drug_id") FROM 'output/pf_drug_regions/data' DELIMITER E'\t' CSV HEADER; -\COPY pf_samples ("sample_id", "PYRresistant", "MQresistant", "country_lat", "country_lng", "region_lng", "HRP23deletion", "ARTresistant", "site_id", "site_lng", "year", "country", "CQresistant", "pc_genome_callable", "ASMQresistant", "HRP2deletion", "qc_pass", "site_lat", "region_lat", "DHAPPQresistant", "SPresistant", "SPIPTpresistant", "mean_coverage", "HRP3deletion", "site", "PPQresistant", "region_id", "SDXresistant", "run_accessions", "region", "study_id", "country_id", "crt_76[K]", "crt_72-76[CVMNK]", "dhfr_51[N]", "dhfr_59[C]", "dhfr_108[S]", "dhfr_164[I]", "dhps_437[G]", "dhps_540[K]", "dhps_581[A]", "dhps_613[A]", "k13_class", "k13_alleles", "cn_mdr1", "cn_pm2", "cn_gch1", "breakpoint_mdr1", "breakpoint_pm2", "breakpoint_gch1", "Fws") FROM 'output/pf_samples/data' DELIMITER E'\t' CSV HEADER; - diff --git a/settings_nosecrets b/settings_nosecrets index 9b134e4..2889fd8 100755 --- a/settings_nosecrets +++ b/settings_nosecrets @@ -25,7 +25,7 @@ panoptesAlfStudyPublicationsTable: study_publications ### LDAP server (people) # This setting is changed for tunneling as in the README -ldapServerURL: ldaps://sso1.malariagen.net:7777 +ldapServerURL: ldaps://sso1.malariagen.net ldapUserDN: cn=website,ou=users,ou=system,dc=malariagen,dc=net ldapUserPass: PASS ldapPeopleBaseDN: ou=people,dc=malariagen,dc=net @@ -35,7 +35,7 @@ ldapPeopleFields: ['mail', 'jobTitle1', 'givenName', 'sn', 'jobTitle1', 'o1', 'j ### Cross-server relations panoptesAlfStudyLdapPeopleTable: study_ldap_people panoptesAlfStudyLdapPeopleGroups: ['Contact', 'Public'] -panoptesAlfStudyLdapPeopleFields: ['jobTitle1', 'jobTitle2', 'jobTitle3', 'uid', 'researchGateURL', 'scholarURL', 'twitterURL', 'malariagenUID', 'oProfile1', 'oProfile2', 'oProfile3', 'ORCID', 'sn', 'mail', 'givenName', 'o1', 'o2', 'o3'] +panoptesAlfStudyLdapPeopleFields: ['contact', 'jobTitle1', 'jobTitle2', 'jobTitle3', 'uid', 'researchGateURL', 'scholarURL', 'twitterURL', 'malariagenUID', 'oProfile1', 'oProfile2', 'oProfile3', 'ORCID', 'sn', 'mail', 'givenName', 'o1', 'o2', 'o3'] ### Post-fetch processing panoptesObsRegionsTable: pf_regions From 3f1cc211237a7693d81ccbf21485bc1d3bb1321d Mon Sep 17 00:00:00 2001 From: Ian Wright Date: Tue, 3 Nov 2020 11:11:47 +0000 Subject: [PATCH 2/3] Update README --- README.md | 45 +++++++++++++++++++++------------------------ 1 file changed, 21 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 5835c99..f457eb0 100644 --- a/README.md +++ b/README.md @@ -32,41 +32,27 @@ gsheetsCredentialsPath: PATH_AS_ABOVE_BUT_WITH_credentials.json ```jupyter notebook fetch_and_convert.ipynb``` Run all cells to produce 3 csv files. +(Visual Studio Code works quite nicely for this) +### Backup existing DB -### Upload to postgres -https://35.185.117.147/phppgadmin/redirect.php (Lee has login) - -Click servers -> PostgreSQL -> login -> observatory_outlandish -> observatory -> samples -> empty - -Then "import", choose `samples.csv` and "Empty string/field" as the only checked options +``` pg_dump -h localhost -p 9999 -U outlandish observatory_outlandish -n observatory --no-owner --no-privileges > obs_dump``` -Back to the list of tables and then do the same for `sampletypes` and `sampletypes1/2.csv`, but importing twice as there are two files -(one is too big for the import process) +### Upload to postgres +```load_files.sh``` ### Tunnel LDAP and postgres 35.185.117.147 is the postgres server -35.189.232.128 is the analytics staging server we use to tunnel - -gcloud.pub is your google ssl key that you add to the analystaging instance (see https://cloud.google.com/compute/docs/instances/adding-removing-ssh-keys) ``` -ssh -N -i ~/.ssh/gcloud.pub -L 127.0.0.1:9999:35.185.117.147:5432 ben_jeffery_well@35.189.232.128 +gcloud beta compute ssh --zone "us-east1-c" --project "ssdtest-141111" observatory-db -- -N -L 9999:localhost:5432 ``` -Tunnel to LDAP: +Connection to LDAP: -``` -ssh -N -i ~/.ssh/gcloud.pub -L 127.0.0.1:7777:sso1.malariagen.net:636 ben_jeffery_well@35.189.232.128 -``` - -LDAP checks the host matches what it expects, so we need to fake it by editing /etc/hosts: - -``` -127.0.0.1 sso1.malariagen.net -``` +Make a temporary hole to allow connection to sso1 on 636 - ask a sysadmin ### Create CSV files: @@ -75,10 +61,21 @@ python create_files.py ``` ### Create postgres DB from the CSVs for export to outlandish -```psql -d pf6 < schema.sql -psql -d pf6 < table-command.sh +```psql -v ON_ERROR_STOP=1 -d pf6 < schema.sql +``` +``` +./table-command.sh +``` +Compare the output of print-tables.sh with load_files.psql to see if any +changes need to be made +``` +psql -v ON_ERROR_STOP=1 -d pf6 < load_files.psql ``` +Remove extra columns introduced as necessary for the loading process +``` +psql -v ON_ERROR_STOP=1 -d pf6 < tidy_up.psql +``` ### Dump out the resulting DB for sending ``` From a56114d64ad69a8d2fd07e28e5e714f59621c23c Mon Sep 17 00:00:00 2001 From: Ian Wright Date: Thu, 8 Apr 2021 08:35:01 +0100 Subject: [PATCH 3/3] Add .gitignore --- .gitignore | 4 ++++ output/pf_regions/data | 9 --------- 2 files changed, 4 insertions(+), 9 deletions(-) create mode 100644 .gitignore delete mode 100644 output/pf_regions/data diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..92e9377 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +env +*.csv +output/** +output/pf_regions/data diff --git a/output/pf_regions/data b/output/pf_regions/data deleted file mode 100644 index 78239d3..0000000 --- a/output/pf_regions/data +++ /dev/null @@ -1,9 +0,0 @@ -region_id lat lng name description num_samples web_colour CQresistance PYRresistance SDXresistance MQresistance ARTresistance PPQresistance SPIPTpresistance ASMQresistance DHAPPQresistance HRP2deletion HRP3deletion HRP23deletion SPresistance geojson -WAF 10.4084977142214 -4.26007159609683 West Africa 2611 #e31a1c 49.5737999102737 86.4064602960969 78.9143113503813 0 0.0906618313689937 0 0 0 0 0 0.358905338716913 0 75.8354755784062 {"geometry": {"coordinates": [[[-17.05687650517658, 20.766923592998385], [-17.10464433499973, 20.862494208009476], [-17.013743325344162, 21.419971097581964], [-14.749973510999641, 21.50008412700026], [-14.22018672700019, 22.309647114999603], [-13.890129354000328, 23.69049306299955], [-13.310009724998318, 23.980552877000697], [-12.990184285998716, 24.469799500001606], [-12.430140949998325, 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