Merge github.com:genenetwork/genenetwork2 into current_production

8 files changed, 21 insertions, 207 deletions

diff --git a/doc/API_readme.md b/doc/API_readme.md
index be6668dc..17d10e44 100644
--- a/doc/API_readme.md
+++ b/doc/API_readme.md
@@ -1,169 +1,3 @@
 # API Query Documentation #
----
-# Fetching Dataset/Trait info/data #
----
-## Fetch Species List ##
 
-To get a list of species with data available in GN (and their associated names and ids):
-```
-curl http://genenetwork.org/api/v_pre1/species
-[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ]
-```
-
-Or to get a single species info:
-```
-curl http://genenetwork.org/api/v_pre1/species/mouse
-``` 
-OR 
-```
-curl http://genenetwork.org/api/v_pre1/species/mouse.json
-```
-
-*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later*
-
-## Fetch Groups/RISets ##
-
-This query can optionally filter by species:
-
-```
-curl http://genenetwork.org/api/v_pre1/groups (for all species)
-```
-OR
-```
-curl http://genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets)
-[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ]
-```
-
-## Fetch Genotypes for Group/RISet ##
-```
-curl http://genenetwork.org/api/v_pre1/genotypes/bimbam/BXD
-curl http://genenetwork.org/api/v_pre1/genotypes/BXD.bimbam
-```
-Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes)
-
-Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example:
-```
-curl http://genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip
-```
-
-## Fetch Datasets ##
-```
-curl http://genenetwork.org/api/v_pre1/datasets/bxd
-```
-OR
-```
-curl http://genenetwork.org/api/v_pre1/datasets/mouse/bxd
-[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ]
-```
-(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
-
-## Fetch Individual Dataset Info ##
-### For mRNA Assay/"ProbeSet" ###
-
-```
-curl http://genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
-```
-OR
-```
-curl http://genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
-{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 }
-```
-(This also has the option to specify group/riset)
-
-### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ###
-For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example:
-```
-curl http://genenetwork.org/api/v_pre1/dataset/bxd/10001
-{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" }
-```
-
-## Fetch Sample Data for Dataset ##
-``` 
-curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
-```
-
-Returns a CSV file with sample/strain names as the columns and trait IDs as rows
-
-## Fetch Sample Data for Single Trait ##
-```
-curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
-[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ]
-```
-
-## Fetch Trait List for Dataset ##
-```
-curl http://genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json
-[ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ]
-```
-
-Both JSON and CSV formats can be specified, with JSON as default. There is also an optional "ids_only" and "names_only" parameter that will only return a list of trait IDs or names, respectively.
-
-## Fetch Trait Info (Name, Description, Location, etc) ##
-### For mRNA Expression/"ProbeSet" ###
-```
-curl http://genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
-{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" }
-```
-
-### For "Phenotypes" ###
-For phenotypes this just gets the  max LRS, its location, and additive effect (as calculated by qtlreaper)
-
-Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input
-```
-curl http://genenetwork.org/api/v_pre1/trait/BXD/10001
-{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
-```
-
----
-
-# Analyses #
----
-## Mapping ##
-Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper
-
-Each method's query takes the following parameters respectively (more will be added):
-### GEMMA ###
-* trait_id (*required*) - ID for trait being mapped
-* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
-* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false)
-* maf - minor allele frequency (default = 0.01)
-
-Example query:
-```
-curl http://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
-```
-
-### R/qtl ###
-(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf)
-* trait_id (*required*) - ID for trait being mapped
-* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
-* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function.
-* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function
-* num_perm - number of permutations; 0 by default
-* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate
-* interval_mapping - Whether to use interval mapping; "false" by default
-* pair_scan - *NYI*
-
-Example query:
-```
-curl http://genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
-```
-
-Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case)
-
-## Calculate Correlation ##
-Currently only Sample and Tissue correlations are implemented
-
-This query currently takes the following parameters (though more will be added):
-* trait_id (*required*) - ID for trait used for correlation
-* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets)
-* target_db (*required*) - Target DB name to be correlated against
-* type - sample (default) | tissue
-* method - pearson (default) | spearman
-* return - Number of results to return (default = 500)
-
-Example query:
-```
-curl http://genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
-[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ]
-```
+This document has moved to [gn-docs](https://github.com/genenetwork/gn-docs/blob/master/api/GN2-REST-API.md)!
diff --git a/doc/README.org b/doc/README.org
index 8839aefc..e1c6b614 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -26,7 +26,7 @@
 
 * Introduction
 
-Large system deployments can get very [[http://biogems.info/contrib/genenetwork/gn2.svg ][complex]]. In this document we
+Large system deployments can get very [[http://genenetwork.org/environments/][complex]]. In this document we
 explain the GeneNetwork version 2 (GN2) reproducible deployment system
 which is based on GNU Guix (see also [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix
 system can be used to install GN with all its files and dependencies.
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 70c58136..768ad49b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -754,8 +754,8 @@ class DataSet:
         # Postgres doesn't have that limit, so we can get rid of this after we transition
         chunk_size = 50
         number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-        cached_results = fetch_cached_results(self.name, self.type)
-        # cached_results =    None
+        # cached_results = fetch_cached_results(self.name, self.type)
+        cached_results =  None
         if cached_results is None:
             trait_sample_data = []
             for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
@@ -800,8 +800,6 @@ class DataSet:
                 results = g.db.execute(query).fetchall()
                 trait_sample_data.append([list(result) for result in results])
 
-            cache_dataset_results(
-                self.name, self.type, trait_sample_data)
 
         else:
             trait_sample_data = cached_results
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 42010a1e..55915a74 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -86,30 +86,17 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
     corr_results = correlation_data['correlation_results']
     results_list = []
 
-    file_name = f"{target_dataset['name']}_metadata.json"
-
-    file_path = os.path.join(TMPDIR, file_name)
-    new_traits_metadata = {}
-
-    try:
-        with open(file_path,"r+") as file_handler:
-            dataset_metadata = json.load(file_handler)
-
-    except FileNotFoundError:
-        Path(file_path).touch(exist_ok=True)
-        dataset_metadata = {}
 
     for i, trait_dict in enumerate(corr_results):
         trait_name = list(trait_dict.keys())[0]
         trait = trait_dict[trait_name]
 
-        target_trait = dataset_metadata.get(trait_name)
+        target_trait = None
         if  target_trait is None: 
             target_trait_ob = create_trait(dataset=target_dataset_ob,
                                            name=trait_name,
                                            get_qtl_info=True)
             target_trait = jsonable(target_trait_ob, target_dataset_ob)
-            new_traits_metadata[trait_name] = target_trait
         if target_trait['view'] == False:
             continue
         results_dict = {}
@@ -184,12 +171,6 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
 
         results_list.append(results_dict)
 
-
-    if bool(new_traits_metadata):
-        # that means new traits exists
-        dataset_metadata.update(new_traits_metadata)
-        with open(file_path,"w+") as file_handler:
-            json.dump(dataset_metadata, file_handler)
     return json.dumps(results_list)
 
 
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 2516e4fb..31f3305c 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -82,13 +82,14 @@ class GSearch:
                     this_trait['species'] = line[0]
                     this_trait['group'] = line[1]
                     this_trait['tissue'] = line[2]
-                    this_trait['symbol'] = line[6]
+                    this_trait['symbol'] = "N/A"
+                    if line[6]:
+                        this_trait['symbol'] = line[6]
+                    this_trait['description'] = "N/A"
                     if line[7]:
                         this_trait['description'] = line[7].decode(
                             'utf-8', 'replace')
-                    else:
-                        this_trait['description'] = "N/A"
-                    this_trait['location_repr'] = 'N/A'
+                    this_trait['location_repr'] = "N/A"
                     if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
                         this_trait['location_repr'] = 'Chr%s: %.6f' % (
                             line[8], float(line[9]))
diff --git a/wqflask/wqflask/jupyter_notebooks.py b/wqflask/wqflask/jupyter_notebooks.py
index dbea04dd..7d76828e 100644
--- a/wqflask/wqflask/jupyter_notebooks.py
+++ b/wqflask/wqflask/jupyter_notebooks.py
@@ -6,16 +6,12 @@ jupyter_notebooks = Blueprint('jupyter_notebooks', __name__)
 def launcher():
     links = (
     {
-        "main_url": "http://notebook.genenetwork.org/51091/tree?",
-        "notebook_name": "COVID-19 in mybinder.org federation",
-        "src_link_url": "https://github.com/jgarte/covid19_in_binder"},
+        "main_url": "http://notebook.genenetwork.org/34301/notebooks/genenetwork-api-using-r.ipynb",
+        "notebook_name": "R notebook showing how to query the GeneNetwork API.",
+        "src_link_url": "https://github.com/jgarte/genenetwork-api-r-jupyter-notebook"},
     {
-        "main_url": "http://notebook.genenetwork.org/35639/tree?",
-        "notebook_name": "Simple requirements.txt based example",
-        "src_link_url": "https://github.com/jgarte/requirements"},
-    {
-        "main_url": "http://notebook.genenetwork.org/40733/tree?",
-        "notebook_name": "Guile Jupyter Notebook Querying GeneNetwork API",
-        "src_link_url": "https://github.com/jgarte/guile-notebook-genenetwork-api"})
+        "main_url": "http://notebook.genenetwork.org/57675/notebooks/genenetwork.ipynb",
+        "notebook_name": "Querying the GeneNetwork API declaratively with python.",
+        "src_link_url": "https://github.com/jgarte/genenetwork-jupyter-notebook-example"})
 
     return render_template("jupyter_notebooks.html", links=links)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index a231c48c..e037246a 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -93,7 +93,11 @@
                                   <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
                                   <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
                                   <li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li>
+<<<<<<< HEAD
                                   <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li>
+=======
+                                  <li><a href="{{url_for('jupyter_notebooks.launcher')}}">Jupyter Notebooks</a></li>
+>>>>>>> dea1afa01025026a0754de60615b974a5cb3fd24
                                   <li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li>
                                 </ul>
                         </li>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 6b125221..4e9ea0fb 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -236,7 +236,7 @@
         <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %}
         {% if this_trait.dataset.type == 'Publish' %}
-        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/{{ this_trait.dataset.id }}/traits/{{ this_trait.name }}?resource-id={{ resource_id }}', '_blank')">Edit</button>
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/{{ this_trait.dataset.group.id }}/traits/{{ this_trait.name }}?resource-id={{ resource_id }}', '_blank')">Edit</button>
         {% endif %}
 
         {% if this_trait.dataset.type == 'ProbeSet' %}