attempt to use dummy files experiment with parameters of partial pipe…

…line; for geneontology/pipeline#382

metadata/datasets/cgd.yaml

@@ -16,10 +16,10 @@ datasets:
    dataset: cgd
    submitter: cgd
    compression: gzip
-   source: http://www.candidagenome.org/download/go/gene_association.cgd.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
-   species_code: 
+   species_code:
    taxa:
     - NCBITaxon:5476
     - NCBITaxon:5478

metadata/datasets/dictybase.yaml

@@ -52,8 +52,7 @@ datasets:
    dataset: dictybase
    submitter: dictyBase
    compression: gzip
-   #source: https://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/dictybase-src.gaf.gz
-   source: https://ftp.ebi.ac.uk/pub/contrib/goa/dictyBase.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Ddis

metadata/datasets/ecocyc.yaml

@@ -14,7 +14,7 @@ datasets:
     type: gaf
     dataset: ecocyc
     submitter: ecocyc
-    source: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa
+    source: http://skyhook.berkeleybop.org/empty.gaf
     entity_type:
     status: active
     species_code: Ecol

metadata/datasets/fb.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: fb
    submitter: fb
    compression: gzip
-   source: ftp://ftp.flybase.net/releases/current/precomputed_files/go/gene_association.fb.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Dmel

metadata/datasets/genedb.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: genedb_lmajor
    submitter: genedb
    compression: gzip
-   source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Lmajor.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Lmaj
@@ -31,12 +31,12 @@ datasets:
    dataset: genedb_tbrucei
    submitter: genedb
    compression: gzip
-   source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Tbruceibrucei927.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    status: active
    species_code: Tbru
    taxa:
     - NCBITaxon:185431
- -  
+ -
    id: genedb_pfalciparum.gaf
    label: "genedb_pfalciparum gaf file"
    description: "gaf file for genedb_pfalciparum from GeneDB"
@@ -45,7 +45,7 @@ datasets:
    dataset: genedb_pfalciparum
    submitter: genedb
    compression: gzip
-   source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Pfalciparum.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Pfal

metadata/datasets/goa.yaml

@@ -744,8 +744,7 @@ datasets:
    dataset: goa_chicken
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_chicken_plus.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/CHICKEN/goa_chicken_plus.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code: Ggal
@@ -765,8 +764,7 @@ datasets:
    dataset: goa_cow
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_cow_plus.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/COW/goa_cow_plus.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code: Btau
@@ -784,8 +782,7 @@ datasets:
    dataset: goa_dog
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_dog_plus.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/DOG/goa_dog_plus.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code: Cfam
@@ -801,8 +798,7 @@ datasets:
    dataset: goa_human
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_human_plus.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human_plus.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code: Hsap
@@ -818,8 +814,7 @@ datasets:
    dataset: goa_pdb
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_pdb.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/goa_pdb.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code:
@@ -835,8 +830,7 @@ datasets:
    dataset: goa_pig
    submitter: goa
    compression: gzip
-   source: https://mirror.geneontology.io/goa_pig_plus.gaf.gz
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/PIG/goa_pig_plus.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: protein
    status: active
    species_code: Sscr
@@ -852,8 +846,7 @@ datasets:
    dataset: goa_uniprot_all
    submitter: goa
    compression: gzip
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz
-   source: https://mirror.geneontology.io/goa_uniprot_all.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: all
    status: active
    aggregates: goa
@@ -903,8 +896,7 @@ datasets:
    dataset: goa_uniprot_gcrp
    submitter: goa
    compression: gzip
-   mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_gcrp.gaf.gz
-   source: https://mirror.geneontology.io/goa_uniprot_gcrp.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: all
    status: active
    aggregates: goa

metadata/datasets/japonicusdb.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: japonicusdb
    submitter: japonicusdb
    compression: gzip
-   source: https://www.japonicusdb.org/data/annotations/Gene_ontology/gene_association.japonicusdb.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Sjap

metadata/datasets/pombase.yaml

@@ -16,8 +16,7 @@ datasets:
    dataset: pombase
    submitter: pombase
    compression: gzip
-   #source: https://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/pombase-src.gaf.gz
-   source: https://www.pombase.org/data/annotations/Gene_ontology/gene_association.pombase.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Spom

metadata/datasets/pseudocap.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: pseudocap
    submitter: pseudocap
    compression: gzip
-   source: https://github.com/brinkmanlab/pseudomonas-genome-database/raw/master/pseudocap-annotation-files/gene_association.pseudocap.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Pseudomonas

metadata/datasets/reactome.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: reactome
    submitter: reactome
    compression: gzip
-   source: https://www.reactome.org/download/current/gene_association.reactome.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: inactive
    species_code:

metadata/datasets/rgd.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: rgd
    submitter: rgd
    compression: gzip
-   source: https://github.com/rat-genome-database/rgd-annotation-files/raw/master/gene_association.rgd.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Rnor

metadata/datasets/sgd.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: sgd
    submitter: sgd
    compression: gzip
-   source: https://sgd-prod-upload.s3.amazonaws.com/latest/gene_association.sgd.gaf.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Scer

metadata/datasets/sgn.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: sgn
    submitter: sgn
    compression: gzip
-   source: https://solgenomics.net/ftp/ontology/GO/gene_association.sgn.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type: gene
    status: active
    species_code: Solanaceae

metadata/datasets/tair.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: tair
    submitter: tair
    compression: gzip
-   source: https://www.arabidopsis.org/api/download-files/download?filePath=GO_and_PO_Annotations/Gene_Ontology_Annotations/gene_association.tair.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Atal

metadata/datasets/wb.yaml

@@ -23,9 +23,7 @@ datasets:
    dataset: wb
    submitter: wb
    compression: gzip
-   source: https://downloads.wormbase.org/species/c_elegans/PRJNA13758/annotation/gene_association/c_elegans.canonical_bioproject.current.gene_association.wb.gz
-   #source: http://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/wb-src.gaf.gz
-   #source: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_association/c_elegans.PRJNA13758.current.gene_association.wb.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Cele

metadata/datasets/xenbase.yaml

@@ -31,7 +31,7 @@ datasets:
     dataset: xenbase
     submitter: xenbase
     compression: gzip
-    source: https://ftp.xenbase.org/pub/DataExchange/GO/xenbase.EBI.only.2.2.gaf.gz
+    source: http://skyhook.berkeleybop.org/empty.gaf.gz
     entity_type:
     status: active
     species_code: Xenopus

metadata/datasets/zfin.yaml

@@ -16,7 +16,7 @@ datasets:
    dataset: zfin
    submitter: zfin
    compression: gzip
-   source: https://zfin.org/downloads/gene_association2.2_automated_only.zfin.gz
+   source: http://skyhook.berkeleybop.org/empty.gaf.gz
    entity_type:
    status: active
    species_code: Drer