updates for deciphon api surface changes and about page

.gitignore

@@ -27,3 +27,8 @@ yarn-error.log*
 
 cypress/screenshots
 cypress/videos
+
+*.db
+test-results/
+downloads
+databases/

cypress/fixtures/dbs.json

@@ -2,11 +2,15 @@
   {
     "id": 1,
     "xxh64": -2550112168598887000,
-    "filename": "pfam24.dcp"
+    "file": {
+      "name": "pfam24.dcp"
+    }
   },
   {
     "id": 2,
     "xxh64": 7603259662449547000,
-    "filename": "Pfam-A.quarter.dcp"
+    "file": {
+      "name": "Pfam-A.quarter.dcp"
+    }
   }
 ]

cypress/fixtures/job_done.json

@@ -1,10 +1,10 @@
 {
   "id": 99,
-  "type": 0,
+  "type": "scan",
   "state": "done",
   "progress": 100,
   "error": "",
-  "submission": 0,
-  "exec_started": 0,
-  "exec_ended": 0
+  "submission": "2023-12-08T15:59:42.046396",
+  "exec_started": "2023-12-08T15:59:52.046396",
+  "exec_ended": "2023-12-08T15:59:56.046396"
 }

cypress/fixtures/job_pending.json

@@ -1,6 +1,6 @@
 {
   "id": 100,
-  "type": 0,
+  "type": "scan",
   "state": "pend",
   "progress": 0,
   "error": "",

cypress/fixtures/jobs_list.json

@@ -0,0 +1,18 @@
+[
+  {
+    "id": 1,
+    "state": "done"
+  },
+  {
+    "id": 90,
+    "state": "done"
+  },
+  {
+    "id": 90,
+    "state": "pend"
+  },
+  {
+    "id": 100,
+    "state": "pend"
+  }
+]

cypress/fixtures/prod_alignments.txt

@@ -0,0 +1,23 @@
+Alignments for each domain:
+== domain 1  score: 247.9 bits;  conditional E-value: 2.9e-78
+               HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT--GGGSEE--STTS-HH CS
+PF00742.20   3 ISTLKESLIGDRITRIEGILNGTMNYILTEMEEEGASFSEALKEAQQLGYAEADPTDDVEGLDAARKLAILARLAFGLEVELEDVEVEAIEKLTAE 98
+               istlkesl gdritriegilngt+nyiltemeeegasfsealkeaq+lGyaEaDptdDveGlDaarKlailarlafgleveledveve iekltae
+             1 ISTLKESLIGDRITRIEGILNGTMNYILTEMEEEGASFSEALKEAQQLGYAEADPTDDVEGLDAARKLAILARLAFGLEVELEDVEVEAIEKLTAE 96
+   example   1 ATACAGTCAGGCAACAGGATAGCTATACAGAGGGGGTTTGGCAGGCCTGTGGGGCAGGGGGCGGGAACGACGATGTGTGGGTGGGGGGGAGACAGG 284
+               TCCTAACTTGAGTCGTAGTTAGCGAATTCATAAAGCCTCACTAACAATGACACACCAATAGTACCGATCTTCGTCTGTATATAATATACTAATCCA
+               TGGCGGGGATCTTTACAGAACC..TCTCTGGGAGGTACTGGGGGAGAGCCGAGTTGCTGAGATTTAGGATACAGATGAGCGGGCAGGAATAGGTCA
+               ................................................................................................
+               ................................................................................................
+               79********************************************************************************************** PP
+
+               HHHHHHCTTEEEEEEEEECEEEEEEEEEETTSGGGHSSST.EEEEEEESSSEE..EEEEES-SSHHHHHHHH CS
+PF00742.20  99 DIEKIKEEGKVLKLVASAVEARVKPELVPKSHPLASVKGSDNAVAVETERHSVgeLVVQGPGAGEEPTASAV 170
+               die+ keegkvlklvasavearvkpelvpkshplasvkgsdnavaveter++   lvvqGpgaG+epTAsav
+            97 DIEKIKEEGKVLKLVASAVEARVKPELVPKSHPLASVKGSDNAVAVETERHSVGELVVQGPGAGEEPTASAV 168
+   example 287 GAGAAAGGGAGTACGGAGGGGAGACGCGCATCCTGTGAGTGAGGGGGAGCCTGGGCGGCGCGGGGGCAGTGG 501
+               ATAATAAAGATTATTCGCTACGTACATTCACACTCCTAGCAACTCTACAGACGGATTTAGCGCGAACCCCCT
+               TTAAAGAGTATAAAGACCCACGCGTGGATGATAACGAACTCCCGTAAGAATTTCACAGGAAGTCAGACACTA
+               ....................................................A...................
+               ........................................................................
+               *************************************************987667***************** PP

cypress/fixtures/prod_amino.txt

@@ -1,14 +1,4 @@
->1 Homoserine_dh-consensus
-PIISTLKESLTGDRITRIEGILNGTLNYILTEMEEEGASFSEALKEAQELGYAEADPTDD
-VEGLDAARKLAILARLAFGLEVELEDVEVEGIEKLTAEDIEEAKEEGKVLKLVASAVEAR
-VKPELVPKSHPLASVKGSDNAVAVETERVGELVVQGPGAGAEPTASAVLADLL
->2 AA_kinase-consensus
-KRVVVKLGGSSLTDKEEASLRRLAEQIAALKESGNKLVVVHGGGSFTDGLLALKSGLSSG
-ELAAGLRSTLEEAGEVATRDALASLGERLVAALLAAGLPAVGLSAAALDATEAGRDEGSD
-GNVESVDAEAIEELLEAGVVPVLTGFIGLDEEGELGRGSSDTIAALLAEALGADKLIILT
-DVDGVYDADPKKVPDARLLPEISVDEAEESASELATGGMKVKHPAALAAARRGGIPVVIT
-N
->3 23ISL-consensus
-QGLDNANRSLVRATKAESSDIRKEVTNGIAKGLKLDSLETAAESKNCSSAQKGGSLAWAT
-NSQPQPLRESKLEPLEDSPRKALKTPVLQKTSSTITLQAVKVQPEPRAPVSGALSPSGEE
-RKRPAASAPATLPTRQSGLGSQEVVSKVATRKIPMESQREST
+>19
+ISTLKESLIGDRITRIEGILNGTMNYILTEMEEEGASFSEALKEAQQLGYAEADPTDDVE
+GLDAARKLAILARLAFGLEVELEDVEVEAIEKLTAEDIEKIKEEGKVLKLVASAVEARVK
+PELVPKSHPLASVKGSDNAVAVETERHSVGELVVQGPGAGEEPTASAVLA

cypress/fixtures/prod_codon.txt

@@ -1,34 +1,10 @@
->1 Homoserine_dh-consensus
-CCTATCATTTCGACGCTCAAGGAGTCGCTGACAGGTGACCGTATTACTCGAATCGAAGGG
-ATATTAAACGGCACCCTGAATTACATTCTCACTGAGATGGAGGAAGAGGGGGCTTCATTC
-TCTGAGGCGCTGAAGGAGGCACAGGAATTGGGCTACGCGGAAGCGGATCCTACGGACGAT
-GTGGAAGGGCTAGATGCTGCTAGAAAGCTGGCAATTCTAGCCAGATTGGCATTTGGGTTA
-GAGGTCGAGTTGGAGGACGTAGAGGTGGAAGGAATTGAAAAGCTGACTGCCGAAGATATT
-GAAGAAGCGAAGGAAGAGGGTAAAGTTTTAAAACTAGTGGCAAGCGCCGTCGAAGCCAGG
-GTCAAGCCTGAGCTGGTACCTAAGTCACATCCATTAGCCTCGGTAAAAGGCTCTGACAAC
-GCCGTGGCTGTAGAAACGGAACGGGTAGGCGAACTCGTAGTGCAGGGACCAGGGGCTGGC
-GCAGAGCCAACCGCATCCGCTGTACTCGCTGACCTTCTC
->2 AA_kinase-consensus
-AAACGTGTAGTTGTAAAGCTTGGGGGTAGTTCTCTGACAGATAAGGAAGAGGCATCACTC
-AGGCGTTTAGCTGAGCAGATTGCAGCATTAAAAGAGAGTGGCAATAAACTAGTGGTCGTG
-CATGGAGGCGGCAGCTTCACTGATGGTCTGCTGGCATTGAAAAGTGGCCTGAGCTCGGGC
-GAATTAGCTGCGGGGTTGAGGAGCACGTTAGAAGAGGCCGGAGAAGTAGCGACGAGGGAC
-GCCCTAGCTAGCTTAGGGGAACGGCTTGTTGCAGCGCTGCTGGCGGCGGGTCTCCCTGCT
-GTAGGACTCAGCGCCGCTGCGTTAGATGCGACGGAGGCGGGCCGGGATGAAGGCAGCGAC
-GGGAACGTCGAGTCCGTGGACGCAGAAGCAATTGAGGAGTTGCTTGAGGCCGGGGTGGTC
-CCCGTCCTAACAGGATTTATCGGCTTAGACGAAGAAGGGGAACTGGGAAGGGGATCTTCT
-GACACCATCGCTGCGTTACTCGCTGAAGCTTTAGGCGCGGACAAACTCATAATACTGACC
-GACGTAGACGGCGTTTACGATGCCGACCCTAAAAAGGTCCCAGACGCGAGGCTCTTGCCA
-GAGATAAGTGTGGACGAGGCCGAGGAAAGCGCCTCCGAATTAGCGACCGGTGGGATGAAG
-GTCAAACATCCAGCGGCTCTTGCTGCAGCTAGACGGGGGGGTATTCCGGTCGTGATAACG
-AAT
->3 23ISL-consensus
-CAGGGTCTGGATAACGCTAATCGTTCGCTAGTTCGCGCTACAAAAGCAGAAAGTTCAGAT
-ATACGGAAAGAGGTGACTAACGGCATCGCTAAAGGGCTGAAGCTAGACAGTCTGGAAACA
-GCTGCAGAGTCGAAGAACTGCTCAAGCGCACAGAAAGGCGGATCGCTAGCTTGGGCAACC
-AACTCCCAACCACAGCCTCTCCGTGAAAGTAAGCTTGAGCCATTGGAAGACTCCCCACGT
-AAGGCTTTAAAAACACCTGTGTTGCAAAAGACATCCAGTACCATAACTTTACAAGCAGTC
-AAGGTTCAACCTGAACCCCGCGCTCCCGTCTCCGGGGCGCTGTCCCCGAGCGGGGAGGAA
-CGCAAGCGCCCAGCTGCGTCTGCTCCCGCTACCTTACCGACACGACAGAGTGGTCTAGGT
-TCTCAGGAAGTCGTTTCGAAGGTGGCGACTCGCAAAATTCCAATGGAGTCACAACGCGAG
-TCGACT
+>19
+ATTTCGACGCTCAAGGAGTCGCTGATAGGTGACCGTATTACTCGAATCGAAGGGATATTA
+AACGGCACCATGAATTACATTCTCACTGAGATGGAGGAAGAGGGGGCTTCATTCTCTGAG
+GCGCTGAAGGAGGCACAGCAATTGGGCTACGCGGAAGCGGATCCTACGGACGATGTGGAA
+GGGCTAGATGCTGCTAGAAAGCTGGCAATTCTAGCCAGATTGGCATTTGGGTTAGAGGTC
+GAGTTGGAGGACGTAGAGGTGGAAGCAATTGAAAAGCTGACTGCCGAAGATATTGAAAAA
+ATAAAGGAAGAGGGTAAAGTTTTAAAACTAGTGGCAAGCGCCGTCGAAGCCAGGGTCAAG
+CCTGAGCTGGTACCTAAGTCACATCCATTAGCCTCGGTAAAAGGCTCTGACAACGCCGTG
+GCTGTAGAAACGGAACGACATTCTGTAGGCGAACTCGTAGTGCAGGGACCAGGGGCTGGC
+GAAGAGCCAACCGCATCCGCTGTACTCGCT

cypress/fixtures/prod_gff.txt

@@ -1,7 +1,2 @@
 ##gff-version 3
-##sequence-region Homoserine_dh-consensus 1 519
-Homoserine_dh-consensus	deciphon:0.1.0	CDS	1	519	285.981201171875	.	0	Epsilon=0.01;ID=1;Profile_acc=PF00742.20;Target_alph=dna
-##sequence-region AA_kinase-consensus 1 723
-AA_kinase-consensus	deciphon:0.1.0	CDS	1	723	343.647705078125	.	0	Epsilon=0.01;ID=2;Profile_acc=PF00696.29;Target_alph=dna
-##sequence-region 23ISL-consensus 1 486
-23ISL-consensus	deciphon:0.1.0	CDS	1	486	354.7095947265625	.	0	Epsilon=0.01;ID=3;Profile_acc=PF16620.6;Target_alph=dna
+19	deciphon	CDS	1	509	0	+	0	Profile=PF00742.20;Alphabet=dna;ID=1

cypress/fixtures/prod_hmm.txt

@@ -0,0 +1,11 @@
+>19
+SBM3M4M5M6M7M8M9M10M11M12M13M14M15M16M17M18M19M20M21M22M23M2
+4M25M26M27M28M29M30M31M32M33M34M35M36M37M38M39M40M41M42M43M4
+4M45M46M47M48M49M50M51M52M53M54M55M56M57M58M59M60M61M62M63M6
+4M65M66M67M68M69M70M71M72M73M74M75M76M77M78M79M80M81M82M83M8
+4M85M86M87M88M89M90M91M92M93M94M95M96M97M98M99M100M101M102M1
+03M104M105M106M107M108M109M110M111M112M113M114M115M116M117M1
+18M119M120M121M122M123M124M125M126M127M128M129M130M131M132M1
+33M134M135M136M137M138M139M140M141M142M143M144M145M146M147M1
+48M149M150M151I151I151M152M153M154M155M156M157M158M159M160M1
+61M162M163M164M165M166M167M168M169M170ET

cypress/fixtures/prod_queries.txt

@@ -0,0 +1,10 @@
+>19
+ATTTCGACGCTCAAGGAGTCGCTGATAGGTGACCGTATTACTCGAATCGAAGGGATATTA
+AACGGCCCTGAATTACATTCTCACTGAGATGGAGGAAGAGGGGGCTTCATTCTCTGAGGC
+GCTGAAGGAGGCACAGCAATTGGGCTACGCGGAAGCGGATCCTACGGACGATGTGGAAGG
+GCTAGATGCTGCTAGAAAGCTGGCAATTCTAGCCAGATTGGCATTTGGGTTAGAGGTCGA
+GTTGGAGGACGTAGAGGTGGAAGCAATTGAAAAGCTGACTGCCGAAGATATTGAAAAAAT
+AAAGGAAGAGGGTAAAGTTTTAAAACTAGTGGCAAGCGCCGTCGAAGCCAGGGTCAAGCC
+TGAGCTGGTACCTAAGTCACATCCATTAGCCTCGGTAAAAGGCTCTGACAACGCCGTGGC
+TGTAGAAACGGAACGACATTCTGGTAGGCGAACTCGTAGTGCAGGGACCAGGGGCTGGCG
+AAGAGCCAACCGCATCCGCTGTACTCGCT

cypress/fixtures/scan_done.json

@@ -1 +1 @@
-{"id":9,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":99}
+[{"id":9,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":99}]

cypress/fixtures/scan_failed.json

@@ -1 +1 @@
-{"id":13,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":103}
+[{"id":13,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":103}]

cypress/fixtures/scan_new.json

@@ -1,11 +1,13 @@
 {
   "id": 100,
-  "db_id": 0,
   "multi_hits": false,
   "hmmer3_compat": false,
-  "state": "done",
-  "error": "",
-  "submission": 0,
-  "exec_started": 0,
-  "exec_ended": 0
+  "job": {
+    "state": "done",
+    "error": "",
+    "submission": 0,
+    "exec_started": 0,
+    "exec_ended": 0,
+    "id": 100
+  }
 }

cypress/fixtures/scan_pending.json

@@ -1 +1 @@
-{"id":10,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":100}
+[{"id":10,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":100}]

cypress/fixtures/scan_running.json

@@ -1 +1 @@
-{"id":11,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":101}
+[{"id":11,"db_id":1,"multi_hits":true,"hmmer3_compat":false,"job_id":101}]